Predicting protein aggregation during storage in lyophilized solids using solid state amide hydrogen/deuterium exchange with mass spectrometric analysis (ssHDX-MS).

PubMed

Moorthy, Balakrishnan S; Schultz, Steven G; Kim, Sherry G; Topp, Elizabeth M

2014-06-02

Solid state amide hydrogen/deuterium exchange with mass spectrometric analysis (ssHDX-MS) was used to assess the conformation of myoglobin (Mb) in lyophilized formulations, and the results correlated with the extent of aggregation during storage. Mb was colyophilized with sucrose (1:1 or 1:8 w/w), mannitol (1:1 w/w), or NaCl (1:1 w/w) or in the absence of excipients. Immediately after lyophilization, samples of each formulation were analyzed by ssHDX-MS and Fourier transform infrared spectroscopy (FTIR) to assess Mb conformation, and by dynamic light scattering (DLS) and size exclusion chromatography (SEC) to determine the extent of aggregation. The remaining samples were then placed on stability at 25 °C and 60% RH or 40 °C and 75% RH for up to 1 year, withdrawn at intervals, and analyzed for aggregate content by SEC and DLS. In ssHDX-MS of samples immediately after lyophilization (t = 0), Mb was less deuterated in solids containing sucrose (1:1 and 1:8 w/w) than in those containing mannitol (1:1 w/w), NaCl (1:1 w/w), or Mb alone. Deuterium uptake kinetics and peptide mass envelopes also indicated greater Mb structural perturbation in mannitol, NaCl, or Mb-alone samples at t = 0. The extent of deuterium incorporation and kinetic parameters related to rapidly and slowly exchanging amide pools (Nfast, Nslow), measured at t = 0, were highly correlated with the extent of aggregation on storage as measured by SEC. In contrast, the extent of aggregation was weakly correlated with FTIR band intensity and peak position measured at t = 0. The results support the use of ssHDX-MS as a formulation screening tool in developing lyophilized protein drug products.

Down Syndrome and Short-Term Memory Impairment: A Storage or Retrieval Deficit?

ERIC Educational Resources Information Center

Adler, Sol; McDade, Hiram L.

1980-01-01

Three groups of eight Ss (Down's syndrome, CA control, and MA control) received a battery of tests to assess recall and recognition memory using either auditory or visual input with verbal and nonverbal responses. Results indicated that the Down's syndrome group possessed deficits in both storage and retrieval abilities, with storage of visually…

ENT COBRA (Consortium for Brachytherapy Data Analysis): interdisciplinary standardized data collection system for head and neck patients treated with interventional radiotherapy (brachytherapy).

PubMed

Tagliaferri, Luca; Kovács, György; Autorino, Rosa; Budrukkar, Ashwini; Guinot, Jose Luis; Hildebrand, Guido; Johansson, Bengt; Monge, Rafael Martìnez; Meyer, Jens E; Niehoff, Peter; Rovirosa, Angeles; Takàcsi-Nagy, Zoltàn; Dinapoli, Nicola; Lanzotti, Vito; Damiani, Andrea; Soror, Tamer; Valentini, Vincenzo

2016-08-01

Aim of the COBRA (Consortium for Brachytherapy Data Analysis) project is to create a multicenter group (consortium) and a web-based system for standardized data collection. GEC-ESTRO (Groupe Européen de Curiethérapie - European Society for Radiotherapy & Oncology) Head and Neck (H&N) Working Group participated in the project and in the implementation of the consortium agreement, the ontology (data-set) and the necessary COBRA software services as well as the peer reviewing of the general anatomic site-specific COBRA protocol. The ontology was defined by a multicenter task-group. Eleven centers from 6 countries signed an agreement and the consortium approved the ontology. We identified 3 tiers for the data set: Registry (epidemiology analysis), Procedures (prediction models and DSS), and Research (radiomics). The COBRA-Storage System (C-SS) is not time-consuming as, thanks to the use of "brokers", data can be extracted directly from the single center's storage systems through a connection with "structured query language database" (SQL-DB), Microsoft Access(®), FileMaker Pro(®), or Microsoft Excel(®). The system is also structured to perform automatic archiving directly from the treatment planning system or afterloading machine. The architecture is based on the concept of "on-purpose data projection". The C-SS architecture is privacy protecting because it will never make visible data that could identify an individual patient. This C-SS can also benefit from the so called "distributed learning" approaches, in which data never leave the collecting institution, while learning algorithms and proposed predictive models are commonly shared. Setting up a consortium is a feasible and practicable tool in the creation of an international and multi-system data sharing system. COBRA C-SS seems to be well accepted by all involved parties, primarily because it does not influence the center's own data storing technologies, procedures, and habits. Furthermore, the method preserves the privacy of all patients.

Evolutionary space station fluids management strategies

NASA Technical Reports Server (NTRS)

1989-01-01

Results are summarized for an 11-month study to define fluid storage and handling strategies and requirements for various specific mission case studies and their associated design impacts on the Space Station. There are a variety of fluid users which require a variety of fluids and use rates. Also, the cryogenic propellants required for NASA's STV, Planetary, and Code Z missions are enormous. The storage methods must accommodate fluids ranging from a high pressure gas or supercritical state fluid to a sub-cooled liquid (and superfluid helium). These requirements begin in the year 1994, reach a maximum of nearly 1800 metric tons in the year 2004, and trail off to the year 2018, as currently planned. It is conceivable that the cryogenic propellant needs for the STV and/or Lunar mission models will be met by LTCSF LH2/LO2 tanksets attached to the SS truss structure. Concepts and corresponding transfer and delivery operations have been presented for STV propellant provisioning from the SS. A growth orbit maneuvering vehicle (OMV) and associated servicing capability will be required to move tanksets from delivery launch vehicles to the SS or co-orbiting platforms. Also, appropriate changes to the software used for OMV operation are necessary to allow for the combined operation of the growth OMV. To support fluid management activities at the Space Station for the experimental payloads and propellant provisioning, there must be truss structure space allocated for fluid carriers and propellant tanksets, and substantial beam strengthening may be required. The Station must have two Mobile Remote Manipulator Systems (MRMS) and the growth OMV propellant handling operations for the STV at the SS. Propellant needs for the Planetary Initiatives and Code Z mission models will most likely be provided by co-orbiting propellant platform(s). Space Station impacts for Code Z mission fluid management activities will be minimal.

Overlapping functions of the starch synthases SSII and SSIII in amylopectin biosynthesis in Arabidopsis

PubMed Central

Zhang, Xiaoli; Szydlowski, Nicolas; Delvallé, David; D'Hulst, Christophe; James, Martha G; Myers, Alan M

2008-01-01

Background The biochemical mechanisms that determine the molecular architecture of amylopectin are central in plant biology because they allow long-term storage of reduced carbon. Amylopectin structure imparts the ability to form semi-crystalline starch granules, which in turn provides its glucose storage function. The enzymatic steps of amylopectin biosynthesis resemble those of the soluble polymer glycogen, however, the reasons for amylopectin's architectural distinctions are not clearly understood. The multiplicity of starch biosynthetic enzymes conserved in plants likely is involved. For example, amylopectin chain elongation in plants involves five conserved classes of starch synthase (SS), whereas glycogen biosynthesis typically requires only one class of glycogen synthase. Results Null mutations were characterized in AtSS2, which codes for SSII, and mutant lines were compared to lines lacking SSIII and to an Atss2, Atss3 double mutant. Loss of SSII did not affect growth rate or starch quantity, but caused increased amylose/amylopectin ratio, increased total amylose, and deficiency in amylopectin chains with degree of polymerization (DP) 12 to DP28. In contrast, loss of both SSII and SSIII caused slower plant growth and dramatically reduced starch content. Extreme deficiency in DP12 to DP28 chains occurred in the double mutant, far more severe than the summed changes in SSII- or SSIII-deficient plants lacking only one of the two enzymes. Conclusion SSII and SSIII have partially redundant functions in determination of amylopectin structure, and these roles cannot be substituted by any other conserved SS, specifically SSI, GBSSI, or SSIV. Even though SSIII is not required for the normal abundance of glucan chains of DP12 to DP18, the enzyme clearly is capable of functioning in production such chains. The role of SSIII in producing these chains cannot be detected simply by analysis of an individual mutation. Competition between different SSs for binding to substrate could in part explain the specific distribution of glucan chains within amylopectin. PMID:18811962

Microfluidic Arrayed Lab-On-A-Chip for Electrochemical Capacitive Detection of DNA Hybridization Events.

PubMed

Ben-Yoav, Hadar; Dykstra, Peter H; Bentley, William E; Ghodssi, Reza

2017-01-01

A microfluidic electrochemical lab-on-a-chip (LOC) device for DNA hybridization detection has been developed. The device comprises a 3 × 3 array of microelectrodes integrated with a dual layer microfluidic valved manipulation system that provides controlled and automated capabilities for high throughput analysis of microliter volume samples. The surface of the microelectrodes is functionalized with single-stranded DNA (ssDNA) probes which enable specific detection of complementary ssDNA targets. These targets are detected by a capacitive technique which measures dielectric variation at the microelectrode-electrolyte interface due to DNA hybridization events. A quantitative analysis of the hybridization events is carried out based on a sensing modeling that includes detailed analysis of energy storage and dissipation components. By calculating these components during hybridization events the device is able to demonstrate specific and dose response sensing characteristics. The developed microfluidic LOC for DNA hybridization detection offers a technology for real-time and label-free assessment of genetic markers outside of laboratory settings, such as at the point-of-care or in-field environmental monitoring.

Soluble Starch Synthase III-1 in Amylopectin Metabolism of Banana Fruit: Characterization, Expression, Enzyme Activity, and Functional Analyses

PubMed Central

Miao, Hongxia; Sun, Peiguang; Liu, Qing; Jia, Caihong; Liu, Juhua; Hu, Wei; Jin, Zhiqiang; Xu, Biyu

2017-01-01

Soluble starch synthase (SS) is one of the key enzymes involved in amylopectin biosynthesis in plants. However, no information is currently available about this gene family in the important fruit crop banana. Herein, we characterized the function of MaSSIII-1 in amylopectin metabolism of banana fruit and described the putative role of the other MaSS family members. Firstly, starch granules, starch and amylopectin content were found to increase during banana fruit development, but decline during storage. The SS activity started to increase later than amylopectin and starch content. Secondly, four putative SS genes were cloned and characterized from banana fruit. Among them, MaSSIII-1 showed the highest expression in banana pulp during fruit development at transcriptional levels. Further Western blot analysis suggested that the protein was gradually increased during banana fruit development, but drastically reduced during storage. This expression pattern was highly consistent with changes in starch granules, amylopectin content, and SS activity at the late phase of banana fruit development. Lastly, overexpression of MaSSIII-1 in tomato plants distinctly changed the morphology of starch granules and significantly increased the total starch accumulation, amylopectin content, and SS activity at mature-green stage in comparison to wild-type. The findings demonstrated that MaSSIII-1 is a key gene expressed in banana fruit and responsible for the active amylopectin biosynthesis, this is the first report in a fresh fruit species. Such a finding may enable the development of molecular markers for banana breeding and genetic improvement of nutritional value and functional properties of banana fruit. PMID:28424724

Corrosion Testing of 304L SS 3013 Inner Container and Teardrop Samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tokash, Justin Charles; Hill, Mary Ann; Lillard, Scott

The Department of Energy (DOE) 3013 Standard specifies a minimum of two containers to be used for the storage of plutonium-bearing materials containing at least 30 wt.% plutonium and uranium. Three nested containers are typically used, the outer, inner, and convenience containers, shown in Figure 1. Both the outer and inner containers are sealed with a weld while the innermost convenience container must not be sealed. Lifetime of the containers is expected to be fifty years. The containers are fabricated of austenitic stainless steels (SS) due to their high corrosion resistance. Potential failure mechanisms of the storage containers have beenmore » examined by Kolman and Lillard et al.« less

Emissions due to the natural gas storage well-casing blowout at Aliso Canyon/SS-25

NASA Astrophysics Data System (ADS)

Herndon, Scott; Daube, Conner; Jervis, Dylan; Yacovitch, Tara; Roscioli, Joseph; Curry, Jason; Nelson, David; Knighton, Berk

2017-04-01

The pronounced increase in unconventional gas production in North America over the last fifteen years has intensified interest in understanding emissions and leaks in the supply chain from well pad to end use. Los Angeles, California is home 19 million consumers of natural gas in both industry and domestic end use. The well blowout at Aliso Canyon Natural Gas Storage Facility in the greater Los Angeles area was quantified using the tracer flux ratio method (TFR). Over 400 tracer plume transects were collected, each lasting 15-300 seconds, using instrumentation aboard a mobile platform on 25 days between December 21, 2015 and March 9, 2016. The leak rate from October 23rd to February 11th has been estimated here using a combination of this work (TFR) and the flight mass balance (FMB) data [Conley et al., 2016]. This estimate relies on the TFR data as the most specific SS-25 emission dataset. Scaling the FMB dataset, the leak rate is projected from Oct 23rd to December 21th. Adding up the emissions inferred and measured suggests a total leak burden of 86,022 ± 8,393 metric tons of methane. This work quantified the emissions during the "bottom kill" procedure which halted the primary emission leak. The ethane to methane enhancement ratio observed downwind of the leak site is consistent with the content of ethane in the natural gas at this site and provides definitive evidence that the methane emission rate quantified via tracer flux ratio is not due to a nearby landfill or other potential biogenic sources. Additionally, the TFR approach employed here is assessing only the leaks due to the SS-25 well blowout and excludes other possible emissions at the facility.

Predicting Protein Aggregation during Storage in Lyophilized Solids Using Solid State Amide Hydrogen/Deuterium Exchange with Mass Spectrometric Analysis (ssHDX-MS)

PubMed Central

2015-01-01

Solid state amide hydrogen/deuterium exchange with mass spectrometric analysis (ssHDX-MS) was used to assess the conformation of myoglobin (Mb) in lyophilized formulations, and the results correlated with the extent of aggregation during storage. Mb was colyophilized with sucrose (1:1 or 1:8 w/w), mannitol (1:1 w/w), or NaCl (1:1 w/w) or in the absence of excipients. Immediately after lyophilization, samples of each formulation were analyzed by ssHDX-MS and Fourier transform infrared spectroscopy (FTIR) to assess Mb conformation, and by dynamic light scattering (DLS) and size exclusion chromatography (SEC) to determine the extent of aggregation. The remaining samples were then placed on stability at 25 °C and 60% RH or 40 °C and 75% RH for up to 1 year, withdrawn at intervals, and analyzed for aggregate content by SEC and DLS. In ssHDX-MS of samples immediately after lyophilization (t = 0), Mb was less deuterated in solids containing sucrose (1:1 and 1:8 w/w) than in those containing mannitol (1:1 w/w), NaCl (1:1 w/w), or Mb alone. Deuterium uptake kinetics and peptide mass envelopes also indicated greater Mb structural perturbation in mannitol, NaCl, or Mb-alone samples at t = 0. The extent of deuterium incorporation and kinetic parameters related to rapidly and slowly exchanging amide pools (Nfast, Nslow), measured at t = 0, were highly correlated with the extent of aggregation on storage as measured by SEC. In contrast, the extent of aggregation was weakly correlated with FTIR band intensity and peak position measured at t = 0. The results support the use of ssHDX-MS as a formulation screening tool in developing lyophilized protein drug products. PMID:24816133

A new standardized data collection system for interdisciplinary thyroid cancer management: Thyroid COBRA.

PubMed

Tagliaferri, Luca; Gobitti, Carlo; Colloca, Giuseppe Ferdinando; Boldrini, Luca; Farina, Eleonora; Furlan, Carlo; Paiar, Fabiola; Vianello, Federica; Basso, Michela; Cerizza, Lorenzo; Monari, Fabio; Simontacchi, Gabriele; Gambacorta, Maria Antonietta; Lenkowicz, Jacopo; Dinapoli, Nicola; Lanzotti, Vito; Mazzarotto, Renzo; Russi, Elvio; Mangoni, Monica

2018-07-01

The big data approach offers a powerful alternative to Evidence-based medicine. This approach could guide cancer management thanks to machine learning application to large-scale data. Aim of the Thyroid CoBRA (Consortium for Brachytherapy Data Analysis) project is to develop a standardized web data collection system, focused on thyroid cancer. The Metabolic Radiotherapy Working Group of Italian Association of Radiation Oncology (AIRO) endorsed the implementation of a consortium directed to thyroid cancer management and data collection. The agreement conditions, the ontology of the collected data and the related software services were defined by a multicentre ad hoc working-group (WG). Six Italian cancer centres were firstly started the project, defined and signed the Thyroid COBRA consortium agreement. Three data set tiers were identified: Registry, Procedures and Research. The COBRA-Storage System (C-SS) appeared to be not time-consuming and to be privacy respecting, as data can be extracted directly from the single centre's storage platforms through a secured connection that ensures reliable encryption of sensible data. Automatic data archiving could be directly performed from Image Hospital Storage System or the Radiotherapy Treatment Planning Systems. The C-SS architecture will allow "Cloud storage way" or "distributed learning" approaches for predictive model definition and further clinical decision support tools development. The development of the Thyroid COBRA data Storage System C-SS through a multicentre consortium approach appeared to be a feasible tool in the setup of complex and privacy saving data sharing system oriented to the management of thyroid cancer and in the near future every cancer type. Copyright © 2018 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

Identification of a novel autoantibody against self-vimentin specific in secondary Sjögren's syndrome.

PubMed

Li, Yu-Hui; Gao, Ya-Ping; Dong, Jie; Shi, Lian-Jie; Sun, Xiao-Lin; Li, Ru; Zhang, Xue-Wu; Liu, Yu; Long, Li; He, Jing; Zhong, Qun-Jie; Morand, Eric; Yang, Guang; Li, Zhan-Guo

2018-02-12

Sjögren's syndrome (SS) is a primary autoimmune disease (pSS) or secondarily associated with other autoimmune diseases (sSS). The mechanisms underlying immune dysregulation in this syndrome remain unknown, and clinically it is difficult to diagnose owing to a lack of specific biomarkers. We extracted immunoglobulins (Igs) from the sera of patients with sSS associated with rheumatoid arthritis (RA) and used them to screen a phage display library of peptides with random sequences. Our results show that an sSS-specific peptide, designated 3S-P, was recognized by sera of 68.2% (60 of 88) patients with sSS, 66.2% of patients with RA-sSS, and 76.5% of patients with systemic lupus erythematosus (SLE)-sSS. The anti-3S-P antibody was scarcely found in patients with pSS (1.8%), RA (1.3%), SLE (4.2%), ankylosing spondylitis (0%), and gout (3.3%), as well as in healthy donors (2%). The 3S-P-binding Igs (antibodies) were used to identify antigens from salivary glands and synovial tissues from patients with sSS. A putative target autoantigen expressed in the synovium and salivary gland recognized by anti-3S-P antibody was identified as self-vimentin. This novel autoantibody is highly specific in the diagnosis of sSS, and the underlying molecular mechanism of the disease might be epitope spreading involved with vimentin.

Positive current collector for Li||Sb-Pb liquid metal battery

NASA Astrophysics Data System (ADS)

Ouchi, Takanari; Sadoway, Donald R.

2017-07-01

Corrosion in grid-scale energy storage devices adversely affects service lifetime and thus has a significant economic impact on their deployment. In this work, we investigate the corrosion of steel and stainless steels (SSs) as positive current collectors in the Li||Sb-Pb liquid metal battery. The erosion and formation of new phases on low-carbon steel, SS301, and SS430 were evaluated both in static conditions and under cell operating conditions. The cell performance is not adversely affected by the dissolution of iron or chromium but rather nickel. Furthermore, the in situ formation of a Fe-Cr-Sb layer helps mitigate the recession of SS430.

3-D transient hydraulic tomography in unconfined aquifers with fast drainage response

NASA Astrophysics Data System (ADS)

Cardiff, M.; Barrash, W.

2011-12-01

We investigate, through numerical experiments, the viability of three-dimensional transient hydraulic tomography (3DTHT) for identifying the spatial distribution of groundwater flow parameters (primarily, hydraulic conductivity K) in permeable, unconfined aquifers. To invert the large amount of transient data collected from 3DTHT surveys, we utilize an iterative geostatistical inversion strategy in which outer iterations progressively increase the number of data points fitted and inner iterations solve the quasi-linear geostatistical formulas of Kitanidis. In order to base our numerical experiments around realistic scenarios, we utilize pumping rates, geometries, and test lengths similar to those attainable during 3DTHT field campaigns performed at the Boise Hydrogeophysical Research Site (BHRS). We also utilize hydrologic parameters that are similar to those observed at the BHRS and in other unconsolidated, unconfined fluvial aquifers. In addition to estimating K, we test the ability of 3DTHT to estimate both average storage values (specific storage Ss and specific yield Sy) as well as spatial variability in storage coefficients. The effects of model conceptualization errors during unconfined 3DTHT are investigated including: (1) assuming constant storage coefficients during inversion and (2) assuming stationary geostatistical parameter variability. Overall, our findings indicate that estimation of K is slightly degraded if storage parameters must be jointly estimated, but that this effect is quite small compared with the degradation of estimates due to violation of "structural" geostatistical assumptions. Practically, we find for our scenarios that assuming constant storage values during inversion does not appear to have a significant effect on K estimates or uncertainty bounds.

A global analysis of the concentration and dynamics of non-structural carbohydrates in plants: does it matter under global change? (Invited)

NASA Astrophysics Data System (ADS)

Sala, A.; Martínez-Vilalta, J.; Asencio, M.; Lloret, F.; Palacio, S.; Galiano, L.; Hoch, G.; Piper, F.

2013-12-01

Forests store significant amounts of C globally and recent reports of forest mortality world-wide have generated strong concern. Evidence suggests that increasing drought associated with climate change is a primary cause of tree stress and subsequent mortality. This has generated an urgent need to predict how forests will cope with increasing stress. Storage of non-structural C compounds (NSC, compounds not permanently invested in structural biomass that can later be used to support diverse plant functions) is critical for survival during periods when C assimilation does not meet demand. However, remarkable knowledge gaps exist to accurately predict plant growth and survival under climate change. Although trees accumulate relatively large pools of NSC, there is a strong debate on how these pools build up over time. On the one hand, it is frequently assumed that the build- up of NSC in trees occurs when supply via photosynthesis exceeds overall demands. If so, the abundant NSC pools in trees reflect an overabundance of C in the long term. An alternative explanation is that trees regulate NSC storage to maintain sufficient pools to cope with asynchronies between demand and supply and with stresses that long lived plants inevitably experience during their life time. However, our understanding of whether and how trees regulate storage in the long term is minimal. Here, we assembled a new global database to examine broad patterns of seasonal NSC variation across organs, life forms and biomes, and the degree to which NSC storage is depleted in plants under a wide range of natural conditions. We compiled seasonal data (at least three measurements over a minimum of four months) for ca. 200 wild species under natural conditions. On average, NSC account for ca. 8-10% of dry plant biomass. NSC and starch concentrations do not vary significantly with biome, but soluble sugars (SS) in plants from Mediterranean biomes are higher than in temperate or tropical biomes. On average, seasonal NSC minimums are between 50 and 60% of the average, indicating that plants rarely deplete NSC. NSC, starch and SS vary strongly seasonally, with a strong depletion of SS during the growing season and a general increase during winter months, particularly in boreal and temperate biomes. In Mediterranean biomes, there is a second SS peak during the dry period. Importantly, with the exception of tropical biomes, the decrease of SS during the growing season is generally accompanied with increases in starch (especially in stems and leaves) despite constant or even decreasing NSC concentrations. These results suggest that during the growing season plants maintain or accumulate reserve compounds, even under high growth demand. Our results tentatively suggest that, on a seasonal basis, plants put aside storage C compounds during periods of maximum growth. Our results are also consistent with an important role of carbon storage in osmotic regulation to cope with winter cold and summer drought.

Particle engineering using sonocrystallization: salbutamol sulphate for pulmonary delivery.

PubMed

Dhumal, Ravindra S; Biradar, Shailesh V; Paradkar, Anant R; York, Peter

2009-02-23

The aim of present work was to produce fine elongated crystals of salbutamol sulphate (SS) by sonocrystallization for pulmonary delivery and compare with micronized and spray dried SS (SDSS) for in vitro aerosolization behavior. Application of ultrasound during anti-solvent crystallization resulted in fine elongated crystals (sonocrystallized SS; SCSS) compared to aggregates of large irregular crystals obtained without sonication. Higher sonication amplitude, time, concentration and lower processing temperatures favored formation of smaller crystals with narrow particle size distribution (PSD). SCSS was separated from dispersion by spray drying in the form of loose aggregates (SD-SCSS). The fine particle fraction (FPF) of formulations with coarse lactose carrier in cascade impactor increased from 16.66% for micronized SS to 31.12% for SDSS (obtained by spray drying aqueous SS solution) and 44.21% for SD-SCSS, due to reduced cohesive/adhesive forces and aerodynamic size by virtue of elongated shape of crystals. SD-SCSS was stable without any change in crystallinity and aerodynamic behavior for 3 months at 40 degrees C/75% RH, but amorphous SDSS showed recrystallization with poor aerosolization performance on storage. Sonocrystallization, a rapid and simple technique is reported for production of SS crystals suitable for inhalation delivery.

78 FR 25739 - Combined Notice of Filings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-02

...: Transcontinental Gas Pipe Line Company. Description: Annual Adjustment to Rate Schedule SS-2 Storage Gas Balances.... Description: Removal of Non Conforming and Neg Rate TSAs and Points of Contact Update Filing to be effective 5...

Field determination of the three-dimensional hydraulic conductivity tensor of anisotropic media: 2. Methodology and application to fractured rocks

USGS Publications Warehouse

Hsieh, Paul A.; Neuman, Shlomo P.; Stiles, Gary K.; Simpson, Eugene S.

1985-01-01

The analytical solutions developed in the first paper can be used to interpret the results of cross-hole tests conducted in anisotropic porous or fractured media. In the particular case where the injection and monitoring intervals are short relative to the distance between them, the test results can be analyzed graphically. From the transient variation of hydraulic head in a given monitoring interval, one can determine the directional hydraulic diffusivity, Kd(e)/Ss, and the quantity D/Ss, by curve matching. (Here Kd(e) is directional hydraulic conductivity parallel to the unit vector, e, pointing from the injection to the monitoring interval, Ss is specific storage, and D is the determinant of the hydraulic conductivity tensor, K.) The principal values and directions of K, together with Ss, can then be evaluated by fitting an ellipsoid to the square roots of the directional diffusivities. Ideally, six directional measurements are required. In practice, a larger number of measurements is often necessary to enable fitting an ellipsoid to the data by least squares. If the computed [Kd(e)/ss]½ values fluctuate so severely that a meaningful least squares fit is not possible, one has a direct indication that the subsurface does not behave as a uniform anisotropic medium on the scale of the test. Test results from a granitic rock near Oracle in southern Arizona are presented to illustrate how the method works for fractured rocks. At the site, the Oracle granite is shown to respond as a near-uniform, anisotropic medium, the hydraulic conductivity of which is strongly controlled by the orientations of major fracture sets. The cross-hole test results are shown to be consistent with the results of more than 100 single-hole packer tests conducted at the site.

VgrG and PAAR Proteins Define Distinct Versions of a Functional Type VI Secretion System

PubMed Central

Cianfanelli, Francesca R.; Alcoforado Diniz, Juliana; Guo, Manman; De Cesare, Virginia; Trost, Matthias; Coulthurst, Sarah J.

2016-01-01

The Type VI secretion system (T6SS) is widespread among bacterial pathogens and acts as an effective weapon against competitor bacteria and eukaryotic hosts by delivering toxic effector proteins directly into target cells. The T6SS utilises a bacteriophage-like contractile machinery to expel a puncturing device based on a tube of Hcp topped with a VgrG spike, which can be extended by a final tip from a PAAR domain-containing protein. Effector proteins are believed to be delivered by specifically associating with particular Hcp, VgrG or PAAR proteins, either covalently (‘specialised’) or non-covalently (‘cargo’ effectors). Here we used the T6SS of the opportunistic pathogen Serratia marcescens, together with integratecd genetic, proteomic and biochemical approaches, to elucidate the role of specific VgrG and PAAR homologues in T6SS function and effector specificity, revealing new aspects and unexpected subtleties in effector delivery by the T6SS. We identified effectors, both cargo and specialised, absolutely dependent on a particular VgrG for delivery to target cells, and discovered that other cargo effectors can show a preference for a particular VgrG. The presence of at least one PAAR protein was found to be essential for T6SS function, consistent with designation as a ‘core’ T6SS component. We showed that specific VgrG-PAAR combinations are required to assemble a functional T6SS and that the three distinct VgrG-PAAR assemblies in S. marcescens exhibit distinct effector specificity and efficiency. Unexpectedly, we discovered that two different PAAR-containing Rhs proteins can functionally pair with the same VgrG protein. Showing that accessory EagR proteins are involved in these interactions, native VgrG-Rhs-EagR complexes were isolated and specific interactions between EagR and cognate Rhs proteins identified. This study defines an essential yet flexible role for PAAR proteins in the T6SS and highlights the existence of distinct versions of the machinery with differential effector specificity and efficiency of target cell delivery. PMID:27352036

Discrimination against RNA Backbones by a ssDNA Binding Protein.

PubMed

Lloyd, Neil R; Wuttke, Deborah S

2018-05-01

Pot1 is the shelterin component responsible for the protection of the single-stranded DNA (ssDNA) overhang at telomeres in nearly all eukaryotic organisms. The C-terminal domain of the DNA-binding domain, Pot1pC, exhibits non-specific ssDNA recognition, achieved through thermodynamically equivalent alternative binding conformations. Given this flexibility, it is unclear how specificity for ssDNA over RNA, an activity required for biological function, is achieved. Examination of the ribose-position specificity of Pot1pC shows that ssDNA specificity is additive but not uniformly distributed across the ligand. High-resolution structures of several Pot1pC complexes with RNA-DNA chimeric ligands reveal Pot1pC discriminates against RNA by utilizing non-compensatory binding modes that feature significant rearrangement of the binding interface. These alternative conformations, accessed through both ligand and protein flexibility, recover much, but not all, of the binding energy, leading to the observed reduction in affinities. These findings suggest that intermolecular interfaces are remarkably sophisticated in their tuning of specificity toward flexible ligands. Copyright © 2018 Elsevier Ltd. All rights reserved.

Application of Framework for Integrating Safety, Security and Safeguards (3Ss) into the Design Of Used Nuclear Fuel Storage Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Badwan, Faris M.; Demuth, Scott F

Department of Energy’s Office of Nuclear Energy, Fuel Cycle Research and Development develops options to the current commercial fuel cycle management strategy to enable the safe, secure, economic, and sustainable expansion of nuclear energy while minimizing proliferation risks by conducting research and development focused on used nuclear fuel recycling and waste management to meet U.S. needs. Used nuclear fuel is currently stored onsite in either wet pools or in dry storage systems, with disposal envisioned in interim storage facility and, ultimately, in a deep-mined geologic repository. The safe management and disposition of used nuclear fuel and/or nuclear waste is amore » fundamental aspect of any nuclear fuel cycle. Integrating safety, security, and safeguards (3Ss) fully in the early stages of the design process for a new nuclear facility has the potential to effectively minimize safety, proliferation, and security risks. The 3Ss integration framework could become the new national and international norm and the standard process for designing future nuclear facilities. The purpose of this report is to develop a framework for integrating the safety, security and safeguards concept into the design of Used Nuclear Fuel Storage Facility (UNFSF). The primary focus is on integration of safeguards and security into the UNFSF based on the existing Nuclear Regulatory Commission (NRC) approach to addressing the safety/security interface (10 CFR 73.58 and Regulatory Guide 5.73) for nuclear power plants. The methodology used for adaptation of the NRC safety/security interface will be used as the basis for development of the safeguards /security interface and later will be used as the basis for development of safety and safeguards interface. Then this will complete the integration cycle of safety, security, and safeguards. The overall methodology for integration of 3Ss will be proposed, but only the integration of safeguards and security will be applied to the design of the UNFSF. The framework for integration of safeguards and security into the UNFSF will include 1) identification of applicable regulatory requirements, 2) selection of a common system that share dual safeguard and security functions, 3) development of functional design criteria and design requirements for the selected system, 4) identification and integration of the dual safeguards and security design requirements, and 5) assessment of the integration and potential benefit.« less

Strand-Specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast.

PubMed

Yu, Chuanhe; Gan, Haiyun; Zhang, Zhiguo

2018-01-01

DNA replication initiates at DNA replication origins after unwinding of double-strand DNA(dsDNA) by replicative helicase to generate single-stranded DNA (ssDNA) templates for the continuous synthesis of leading-strand and the discontinuous synthesis of lagging-strand. Therefore, methods capable of detecting strand-specific information will likely yield insight into the association of proteins at leading and lagging strand of DNA replication forks and the regulation of leading and lagging strand synthesis during DNA replication. The enrichment and Sequencing of Protein-Associated Nascent DNA (eSPAN), which measure the relative amounts of proteins at nascent leading and lagging strands of DNA replication forks, is a step-wise procedure involving the chromatin immunoprecipitation (ChIP) of a protein of interest followed by the enrichment of protein-associated nascent DNA through BrdU immunoprecipitation. The isolated ssDNA is then subjected to strand-specific sequencing. This method can detect whether a protein is enriched at leading or lagging strand of DNA replication forks. In addition to eSPAN, two other strand-specific methods, (ChIP-ssSeq), which detects potential protein-ssDNA binding and BrdU-IP-ssSeq, which can measure synthesis of both leading and lagging strand, were developed along the way. These methods can provide strand-specific and complementary information about the association of the target protein with DNA replication forks as well as synthesis of leading and lagging strands genome wide. Below, we describe the detailed eSPAN, ChIP-ssSeq, and BrdU-IP-ssSeq protocols.

Robo2 determines subtype-specific axonal projections of trigeminal sensory neurons

PubMed Central

Pan, Y. Albert; Choy, Margaret; Prober, David A.; Schier, Alexander F.

2012-01-01

How neurons connect to form functional circuits is central to the understanding of the development and function of the nervous system. In the somatosensory system, perception of sensory stimuli to the head requires specific connections between trigeminal sensory neurons and their many target areas in the central nervous system. Different trigeminal subtypes have specialized functions and downstream circuits, but it has remained unclear how subtype-specific axonal projection patterns are formed. Using zebrafish as a model system, we followed the development of two trigeminal sensory neuron subtypes: one that expresses trpa1b, a nociceptive channel important for sensing environmental chemicals; and a distinct subtype labeled by an islet1 reporter (Isl1SS). We found that Trpa1b and Isl1SS neurons have overall similar axon trajectories but different branching morphologies and distributions of presynaptic sites. Compared with Trpa1b neurons, Isl1SS neurons display reduced branch growth and synaptogenesis at the hindbrain-spinal cord junction. The subtype-specific morphogenesis of Isl1SS neurons depends on the guidance receptor Robo2. robo2 is preferentially expressed in the Isl1SS subset and inhibits branch growth and synaptogenesis. In the absence of Robo2, Isl1SS afferents acquire many of the characteristics of Trpa1b afferents. These results reveal that subtype-specific activity of Robo2 regulates subcircuit morphogenesis in the trigeminal sensory system. PMID:22190641

Lineage-Specific Evolutionary Histories and Regulation of Major Starch Metabolism Genes during Banana Ripening

PubMed Central

Jourda, Cyril; Cardi, Céline; Gibert, Olivier; Giraldo Toro, Andrès; Ricci, Julien; Mbéguié-A-Mbéguié, Didier; Yahiaoui, Nabila

2016-01-01

Starch is the most widespread and abundant storage carbohydrate in plants. It is also a major feature of cultivated bananas as it accumulates to large amounts during banana fruit development before almost complete conversion to soluble sugars during ripening. Little is known about the structure of major gene families involved in banana starch metabolism and their evolution compared to other species. To identify genes involved in banana starch metabolism and investigate their evolutionary history, we analyzed six gene families playing a crucial role in plant starch biosynthesis and degradation: the ADP-glucose pyrophosphorylases (AGPases), starch synthases (SS), starch branching enzymes (SBE), debranching enzymes (DBE), α-amylases (AMY) and β-amylases (BAM). Using comparative genomics and phylogenetic approaches, these genes were classified into families and sub-families and orthology relationships with functional genes in Eudicots and in grasses were identified. In addition to known ancestral duplications shaping starch metabolism gene families, independent evolution in banana and grasses also occurred through lineage-specific whole genome duplications for specific sub-families of AGPase, SS, SBE, and BAM genes; and through gene-scale duplications for AMY genes. In particular, banana lineage duplications yielded a set of AGPase, SBE and BAM genes that were highly or specifically expressed in banana fruits. Gene expression analysis highlighted a complex transcriptional reprogramming of starch metabolism genes during ripening of banana fruits. A differential regulation of expression between banana gene duplicates was identified for SBE and BAM genes, suggesting that part of starch metabolism regulation in the fruit evolved in the banana lineage. PMID:27994606

Impact of the biorefinery size on the logistics of corn stover supply – A scenario analysis

DOE PAGES

Wang, Yu; Ebadian, Mahmood; Sokhansanj, Shahab; ...

2017-03-23

In this study, three scenarios are considered to quantify the impact of the biorefinery size on the required biomass logistical resources. The biorefinery scenarios include small scale (175 dt/day)-SS, medium scale (520 dt/day)-MS and large scale (860 dt/day)-LS. These scenarios are compared against the following logistical resources (1) harvest area and contracted fields, (2) logistics equipment fleet and the workforce to run this fleet and (3) intermediate storage sites and their biomass inventory levels. To this end, the IBSAL-MC simulation model is applied to a corn stover logistics system in Southwestern Ontario. The obtained results show (1) the harvest areamore » and the number of contracted fields increase by 65% and 78% from the SS scenario to the MS and LS scenarios, respectively, (2) the average biomass delivered costs are estimated to be $82.09, $87.49 and $93.75/dry tonne in the SS, MS and LS scenarios. The increase in the capital costs to develop a dedicated logistics equipment fleet are estimated to be far greater than the increase in the delivered costs as the size of the biorefinery increases. The upfront capital costs are estimated to be 6.72 dollars, 21.83 and 35.51 million in these scenarios. To run the logistics equipment fleet efficiently, 37, 136 and 235 well-trained operators are required in the SS, MS ad LS scenarios, respectively, and (3) the inventory level and the land requirement for storage in the MS and LS scenarios are estimated to be 225% and 425% greater than those of the SS scenario. The sensitivity analysis indicates that the logistical resources are highly sensitive to corn yield and farm participation rate. Overall, this study shows the importance of considering the size of the required logistical resources and the associated level of logistical complexity in evaluating the economic viability of a biorefinery project.« less

Impact of the biorefinery size on the logistics of corn stover supply – A scenario analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yu; Ebadian, Mahmood; Sokhansanj, Shahab

In this study, three scenarios are considered to quantify the impact of the biorefinery size on the required biomass logistical resources. The biorefinery scenarios include small scale (175 dt/day)-SS, medium scale (520 dt/day)-MS and large scale (860 dt/day)-LS. These scenarios are compared against the following logistical resources (1) harvest area and contracted fields, (2) logistics equipment fleet and the workforce to run this fleet and (3) intermediate storage sites and their biomass inventory levels. To this end, the IBSAL-MC simulation model is applied to a corn stover logistics system in Southwestern Ontario. The obtained results show (1) the harvest areamore » and the number of contracted fields increase by 65% and 78% from the SS scenario to the MS and LS scenarios, respectively, (2) the average biomass delivered costs are estimated to be $82.09, $87.49 and $93.75/dry tonne in the SS, MS and LS scenarios. The increase in the capital costs to develop a dedicated logistics equipment fleet are estimated to be far greater than the increase in the delivered costs as the size of the biorefinery increases. The upfront capital costs are estimated to be 6.72 dollars, 21.83 and 35.51 million in these scenarios. To run the logistics equipment fleet efficiently, 37, 136 and 235 well-trained operators are required in the SS, MS ad LS scenarios, respectively, and (3) the inventory level and the land requirement for storage in the MS and LS scenarios are estimated to be 225% and 425% greater than those of the SS scenario. The sensitivity analysis indicates that the logistical resources are highly sensitive to corn yield and farm participation rate. Overall, this study shows the importance of considering the size of the required logistical resources and the associated level of logistical complexity in evaluating the economic viability of a biorefinery project.« less

Characterizations of pumping-induced land subsidence in coastal aquifers - model development and field-scale implementations

NASA Astrophysics Data System (ADS)

Ni, C.; Huang, Y.; Lu, C.

2012-12-01

The pumping-induced land subsidence events are typically founded in coastal aquifers in Taiwan especially in the areas of lower alluvial fans. Previous investigations have recognized the irreversible situation for an aquifer deformation even if the pumped water is significantly reduced or stopped. Long-term monitoring projects on land subsidence in Choshui alluvial fan in central Taiwan have improved the understanding of the deformations in the aquifer system. To characterization the detailed land subsidence mechanism, this study develops an inverse numerical model to estimate the deformation parameters such as the specific storage (Ss) and vertical hydraulic conductivity (Kv) for interbeds. Similar to the concept of Hydraulic tomography survey (HTS), the developed model employs the iterative cokriging estimator to improve the accuracy of estimating deformation parameters. A one-dimensional numerical example is employed to assess the accuracy of the developed inverse model. The developed model is then applied to field-scale data from compaction monitoring wells (CMW) installed in the lower Choshui River fan. Results of the synthetic example show that the developed inverse model can reproduce well the predefined geologic features of the synthetic aquifer. The model provides better estimations of Kv patterns and magnitudes. Slightly less detail of the Ss was obtained due to the insensitivity of transient stresses for specified sampling times. Without prior information from field measurements, the developed model associated with deformation measurements form CMW can estimate Kv and Ss fields with great spatial resolution.

[111In-DOTA]LTT-SS28, a first pansomatostatin radioligand for in vivo targeting of somatostatin receptor-positive tumors.

PubMed

Maina, Theodosia; Cescato, Renzo; Waser, Beatrice; Tatsi, Aikaterini; Kaloudi, Aikaterini; Krenning, Eric P; de Jong, Marion; Nock, Berthold A; Reubi, Jean Claude

2014-08-14

Radiolabeled pansomatostatin-like analogues are expected to enhance the diagnostic sensitivity and to expand the clinical indications of currently applied sst2-specific radioligands. In this study, we present the somatostatin mimic [DOTA]LTT-SS28 {[(DOTA)Ser1,Leu8,D-Trp22,Tyr25]SS28} and its 111In radioligand. [DOTA]LTT-SS28 exhibited a pansomatostatin-like profile binding with high affinity to all five hsst1-hsst5 subtypes (IC50 values in the lower nanomolar range). Furthermore, [DOTA]LTT-SS28 behaved as an agonist at hsst2, hsst3, and hsst5, efficiently stimulating internalization of the three receptor subtypes. Radioligand [111In-DOTA]LTT-SS28 showed good stability in the mouse bloodstream. It displayed strong and specific uptake in AR42J tumors 4 h postinjection (9.3±1.6% ID/g vs 0.3±0.0% ID/g during sst2 blockade) in mice. Significant and specific uptake was also observed in HEK293-hsst2-, HEK293-hsst3-, and HEK293-hsst5-expressing tumors (4.43±1.5, 4.88±1.1, and <3% ID/g, respectively, with values of <0.5% ID/g during receptor blockade). In conclusion, the somatostatin mimic [111In-DOTA]LTT-SS28 specifically localizes in sst2-, sst3-, and sst5-expressing xenografts in mice showing promise for multi-sst1-sst5 targeted tumor imaging.

Comparative study of transient hydraulic tomography with varying parameterizations and zonations: Laboratory sandbox investigation

NASA Astrophysics Data System (ADS)

Luo, Ning; Zhao, Zhanfeng; Illman, Walter A.; Berg, Steven J.

2017-11-01

Transient hydraulic tomography (THT) is a robust method of aquifer characterization to estimate the spatial distributions (or tomograms) of both hydraulic conductivity (K) and specific storage (Ss). However, the highly-parameterized nature of the geostatistical inversion approach renders it computationally intensive for large-scale investigations. In addition, geostatistics-based THT may produce overly smooth tomograms when head data used to constrain the inversion is limited. Therefore, alternative model conceptualizations for THT need to be examined. To investigate this, we simultaneously calibrated different groundwater models with varying parameterizations and zonations using two cases of different pumping and monitoring data densities from a laboratory sandbox. Specifically, one effective parameter model, four geology-based zonation models with varying accuracy and resolution, and five geostatistical models with different prior information are calibrated. Model performance is quantitatively assessed by examining the calibration and validation results. Our study reveals that highly parameterized geostatistical models perform the best among the models compared, while the zonation model with excellent knowledge of stratigraphy also yields comparable results. When few pumping tests with sparse monitoring intervals are available, the incorporation of accurate or simplified geological information into geostatistical models reveals more details in heterogeneity and yields more robust validation results. However, results deteriorate when inaccurate geological information are incorporated. Finally, our study reveals that transient inversions are necessary to obtain reliable K and Ss estimates for making accurate predictions of transient drawdown events.

Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaohan; Jawdy, Sara; Tschaplinski, Timothy J

2009-01-01

Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine, Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression, protein motif and intron number were examined. 192, 641 and 109 SS genes were identified in Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers, roots, xylem and cambium or up-regulated by stress. Six conserved motifsmore » in Arabidopsis and Oryza SS proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes. The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nielsen, Yousef W., E-mail: yujwni01@heh.regionh.d; Eiberg, Jonas P.; Logager, Vibeke B.

The purpose of this investigation was to determine if addition of infragenicular steady-state (SS) magnetic resonance angiography (MRA) to first-pass imaging improves diagnostic performance compared with first-pass imaging alone in patients with peripheral arterial disease (PAD) undergoing whole-body (WB) MRA. Twenty consecutive patients with PAD referred to digital-subtraction angiography (DSA) underwent WB-MRA. Using a bolus-chase technique, first-pass WB-MRA was performed from the supra-aortic vessels to the ankles. The blood-pool contrast agent gadofosveset trisodium was used at a dose of 0.03 mmol/kg body weight. Ten minutes after injection of the contrast agent, high-resolution (0.7-mm isotropic voxels) SS-MRA of the infragenicular arteriesmore » was performed. Using DSA as the 'gold standard,' sensitivities and specificities for detecting significant arterial stenoses ({>=}50% luminal narrowing) with first-pass WB-MRA, SS-MRA, and combined first-pass and SS-MRA were calculated. Kappa statistics were used to determine intermodality agreement between MRA and DSA. Overall sensitivity and specificity for detecting significant arterial stenoses with first-pass WB-MRA was 0.70 (95% confidence interval 0.61 to 0.78) and 0.97 (0.94 to 0.99), respectively. In first-pass WB-MRA, the lowest sensitivity was in the infragenicular region, with a value of 0.42 (0.23 to 0.63). Combined analysis of first-pass WB-MRA and SS-MRA increased sensitivity to 0.81 (0.60 to 0.93) in the infragenicular region, with specificity of 0.94 (0.88 to 0.97). Sensitivity and specificity for detecting significant arterial stenoses with isolated infragenicular SS-MRA was 0.47 (0.27 to 0.69) and 0.86 (0.78 to 0.91), respectively. Intermodality agreement between MRA and DSA in the infragenicular region was moderate for first-pass WB-MRA ({kappa} = 0.49), fair for SS-MRA ({kappa} = 0.31), and good for combined first-pass/SS-MRA ({kappa} = 0.71). Addition of infragenicular SS-MRA to first-pass WB MRA improves diagnostic performance.« less

[Validation of the American College of Rheumatology classification criteria for primary Sjogren's syndrome in Chinese patients].

PubMed

Wei, Pan; Lu, Song-he; Fu, Jing-ya; Yan, Zhi-min; Hua, Hong

2014-04-18

To validate the American College of Rheumatology Classification (ACR) Criteria (2012) for the diagnosis of primary Sjogren's syndrome in Chinese patients. All patients involved in this study came from the Department of Oral Medicine Peking University Stomatology Hospital. They were devided into two groups of pSS and non-pSS according to the diagnoses made by two experts. Both groups of the patients had completed medical records kept in the hospital. A total of 239 pSS patients (160 with labial salivary gland biopsy, and 79 without biopsy) and 52 age-matched non-pSS patients [(55.17±14.295),and (55.90±13.38) years old, P>0.05] (9 with biopsy, and 43 without biopsy) were involved in this study. The sensitivity and specificity of ACR criteria in diagnosing pSS were 90.37 % and 88.46 % respectively. The positive and negative likelihood ratios were 7.83 and 0.109, respectively. The sensitivities of ACR criteria in diagnosing pSS patients with and without labial biopsy were 88.75% and 93.67 %, respectively, with specificities of 88.89% and 88.37%, respectively. The most sensitive item adopted in ACR criteria was the ocular staining score with a sensitivity of 85.77%, and the most specific item was the labial salivary gland biopsy, with a specificity of 88.89%. The sensitivity and specificity of ACR criteria in diagnosing Chinese pSS patients were relatively high, and may serve as the diagnosis criteria in research and clinical practice. However, the ACR criteria need to be validated and further revised in the future .

Could the negative effects of static stretching in warm-up be restored by sport specific exercise?

PubMed

Bengtsson, Victor; Yu, Ji-Guo; Gilenstam, Kajsa

2017-04-13

Static stretching (SS) is widely used in warm-up as it is generally believed to increase mobility and reduce the risk of injury; however, SS has been shown to induce transient negative effects on subsequent muscle performance. Interestingly, recent studies have shown that sport specific exercise could restore SS-induced negative effects on certain sports, especially of explosive muscular performance. Whether sport specific exercise could restore SS-induced negative effects on isokinetic muscle performance remains unclear. The present study conducted two different warm-ups: 2-component warm-up and 3-component warm-up on 15 university students. Both protocols contained low intensity aerobic exercise and sport specific exercise, whereas the 3-component warm-up also contained SS which has been previously proven to induce negative effects on subsequent muscle performance. After the warm-ups, the subjects performed an isokinetic test on a Biodex. To make the sport specific exercise mimic the subsequent test, both included concentric isokinetic knee extension. During the tests, muscle performance of peak torque, mean power, and total work was recorded. Comparison of the measurements on each parameter between the two warm-ups was performed using paired t test. The comparisons did not reveal any significant difference in the measurement of any parameter between the two different warm-up protocols, and calculation of Cohen's revealed small effect sizes on all of the three variables. On basis of the present results and that the SS could induce transient negative effects on subsequent muscle performance, we concluded that the negative effects of the SS on the variables were restored by the isokinetic contractions.

Distribution and diversity of bacterial secretion systems across metagenomic datasets.

PubMed

Barret, Matthieu; Egan, Frank; O'Gara, Fergal

2013-02-01

Bacteria can manipulate their surrounding environment through the secretion of proteins into other living organisms and into the extracellular milieu. In Gram stain negative bacteria this process is mediated by different types of secretion systems from type I through type VI secretion system (T1SS-T6SS). In this study the prevalence of these secretion systems in 312 publicly available microbiomes derived from a wide range of ecosystems was investigated by a gene-centric approach. Our analysis demonstrates that some secretion systems are over-represented in some specific samples. In addition, some T3SS and T6SS phylogenetic clusters were specifically enriched in particular ecological niches, which could indicate specific bacterial adaptation to these environments. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Comparative analysis of the 2016 ACR-EULAR and the 2002 AECG classification criteria for Sjögren's syndrome: Findings from the NIH cohort.

PubMed

Billings, M; Amin Hadavand, M; Alevizos, I

2018-03-01

The introduction of new classification criteria for Sjögren's syndrome, known as the 2016 American College of Rheumatology/European League against Rheumatism Classification Criteria (ACR-EULAR), created a need for the evaluation of its performance in an external cohort. The purpose of this study was to compare the performance of the 2016 ACR-EULAR classification set with the widely used American-European Consensus Group Classification criteria (AECG) in the cohort at the National Institutes of Health, USA, and to compare the performance of the sets in classifying both primary and secondary Sjögren's syndrome (pSS and sSS). The study cohort at the NIH (N = 1,303) was enrolled for clinical suspicion of SS. Participants were classified as SS, pSS, and sSS according to both classification sets. Performance of 2016 ACR-EULAR and AECG sets was compared holding each as gold standard to the other. Statistical analysis of test diagnostics and agreement between the two sets were undertaken. By the AECG set, 701 were classified as having SS (627 pSS, 74 sSS) and 714 were classified with SS (647 pSS, 67 sSS) by the 2016 ACR-EULAR set. Sensitivity and specificity of the two sets were comparable in classifying SS, pSS, and sSS. There was high agreement between the two sets for classifying SS (κ = 0.79), pSS (κ = 0.81), and sSS (κ = 0.87). The specificity of the 2016 ACR-EULAR set was significantly higher for classifying sSS than pSS, while the sensitivity was similar for the two disease groups. However, this pattern was also exhibited by the AECG set. There was high agreement between the two classification sets with comparable performance diagnostics. There was no evidence of superior performance value by the new 2016 ACR-EULAR set over the AECG set, and the two sets were found to be equivalent. Findings from our cohort indicate that 2016 ACR-EULAR classification could be extended to classification of sSS. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Ultrasonography of major salivary glands: a highly specific tool for distinguishing primary Sjögren's syndrome from undifferentiated connective tissue diseases.

PubMed

Luciano, Nicoletta; Baldini, Chiara; Tarantini, Gaia; Ferro, Ferro; Sernissi, Francesca; Varanini, Valentina; Donati, Valentina; Martini, Daniela; Mosca, Marta; Caramella, Davide; Bombardieri, Stefano

2015-12-01

Recently, convincing data have been published on the value of salivary gland ultrasonography (SGUS) in differentiating primary SS from non-immune-mediated sicca syndrome. Limited data are available regarding the diagnostic accuracy of SGUS in distinguishing SS from other rheumatic diseases. The purpose of this study was to assess the usefulness of SGUS in distinguishing patients with SS from those with xerostomia and/or xerophthalmia and a diagnosis of stable UCTD. This cross-sectional study consecutively enrolled 150 patients either diagnosed with SS (as established by the American-European Consensus Group criteria) or affected by UCTD but not SS. Parotid and submandibular glands on both sides were assessed for size, parenchymal echogenicity and inhomogeneity by means of SGUS, which was performed by a radiologist blinded to the diagnosis. Echostructural alterations of the salivary glands were graded from 0 to 3 (cut-off >2). This study included 109 patients: 55 with SS and 54 with UCTD. Patients with SS showed a higher SGUS score in comparison with those with UCTD [mean 2.2 (s.d. 1.8) vs 0.2 (s.d. 0.5), P < 0.0001]. The SGUS cut-off >2 showed a sensitivity of 65%, a specificity of 96%, a positive predictive value of 95% and a negative predictive value of 73% for SS diagnosis. A significant correlation was also found between the SGUS score and the minor salivary gland biopsy/focus score (r = 0.484, P < 0.0001). This study confirmed the good sensitivity and the high specificity of SGUS in differentiating SS from other CTDs. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Sjögren's syndrome-associated myositis with germinal centre-like structures.

PubMed

Espitia-Thibault, Alexandra; Masseau, Agathe; Néel, Antoine; Espitia, Olivier; Toquet, Claire; Mussini, Jean-Marie; Hamidou, Mohamed

2017-02-01

Muscular impairment is a rare systemic manifestation of SS that is rarely described in the literature and classically non-specific, both clinically and histologically. We reviewed the cases of 4 patients with primary SS presenting with myositis and a common histologic pattern on muscular biopsy with germinal centre-like structures resembling that which occurs in salivary glands. We analysed the data files of patients with SS who had muscular manifestations and underwent a muscular biopsy. Among 23 patients with SS who had muscle biopsies, 13 had non-specific myositis and 10 (4 primary and 6 secondary SS) had a common histologic pattern consisting of germinal centre-like structures. We analysed the data files of the 4 patients with primary SS presenting with myositis with muscular germinal-centre like structures. The 4 patients had an unspecific clinical presentation, with myalgias, muscular weakness and normal or elevated values of CPK. In the four patients, SS-associated myositis had common histologic characteristics, with endomysial and perimysial inflammatory infiltrate. The cellular infiltrate was composed predominantly of CD4+ T lymphocytes and B lymphocytes. The B and T CD4+ cells infiltrates may gather into masses, even forming lymphoid follicles. Three patients were treated with corticosteroids and/or hydroxychloroquine with improvement of myositis and 1 patient was lost to follow-up. We describe four patients with a common histologic appearance of myositis with lymphoid follicles associated with primary SS. The clinical presentation was non-specific and non-severe, with favorable outcome with corticosteroids and/or hydroxycholoroquine. The discovery of this particular histologic appearance in a muscle biopsy independent of the final diagnosis should indicate the possibility of SS. Copyright © 2016 Elsevier B.V. All rights reserved.

Non-Watson–Crick interactions between PNA and DNA inhibit the ATPase activity of bacteriophage T4 Dda helicase

PubMed Central

Tackett, Alan J.; Corey, David R.; Raney, Kevin D.

2002-01-01

Peptide nucleic acid (PNA) is a DNA mimic in which the nucleobases are linked by an N-(2-aminoethyl) glycine backbone. Here we report that PNA can interact with single-stranded DNA (ssDNA) in a non-sequence-specific fashion. We observed that a 15mer PNA inhibited the ssDNA-stimulated ATPase activity of a bacteriophage T4 helicase, Dda. Surprisingly, when a fluorescein-labeled 15mer PNA was used in binding studies no interaction was observed between PNA and Dda. However, fluorescence polarization did reveal non-sequence-specific interactions between PNA and ssDNA. Thus, the inhibition of ATPase activity of Dda appears to result from depletion of the available ssDNA due to non-Watson–Crick binding of PNA to ssDNA. Inhibition of the ssDNA-stimulated ATPase activity was observed for several PNAs of varying length and sequence. To study the basis for this phenomenon, we examined self-aggregation by PNAs. The 15mer PNA readily self-aggregates to the point of precipitation. Since PNAs are hydrophobic, they aggregate more than DNA or RNA, making the study of this phenomenon essential for understanding the properties of PNA. Non-sequence-specific interactions between PNA and ssDNA were observed at moderate concentrations of PNA, suggesting that such interactions should be considered for antisense and antigene applications. PMID:11842106

Cross-Cultural Adaptation and Initial Validation of the Stroke-Specific Quality of Life Scale into the Yoruba Language

ERIC Educational Resources Information Center

Akinpelu, Aderonke O.; Odetunde, Marufat O.; Odole, Adesola C.

2012-01-01

Stroke-Specific Quality of Life 2.0 (SS-QoL 2.0) scale is used widely and has been cross-culturally adapted to many languages. This study aimed at the cross-cultural adaptation of SS-QoL 2.0 to Yoruba, the indigenous language of south-western Nigeria, and to carry out an initial investigation on its validity. English SS-QoL 2.0 was first adapted…

ARC Researchers at IEEE 2015 Vehicle Power and Propulsion Conference

Science.gov Websites

Sustainability of the Energy Storage Systems Thursday, October 22, 2015 14:00 PM - 16:00 PM Des Pins Room SS5-1 Influence of Battery Downsizing and SOC Operating Window on Battery Pack Performance in a Hybrid Electric

RPA homologs and ssDNA processing during meiotic recombination.

PubMed

Ribeiro, Jonathan; Abby, Emilie; Livera, Gabriel; Martini, Emmanuelle

2016-06-01

Meiotic homologous recombination is a specialized process that involves homologous chromosome pairing and strand exchange to guarantee proper chromosome segregation and genetic diversity. The formation and repair of DNA double-strand breaks (DSBs) during meiotic recombination differs from those during mitotic recombination in that the homologous chromosome rather than the sister chromatid is the preferred repair template. The processing of single-stranded DNA (ssDNA) formed on intermediate recombination structures is central to driving the specific outcomes of DSB repair during meiosis. Replication protein A (RPA) is the main ssDNA-binding protein complex involved in DNA metabolism. However, the existence of RPA orthologs in plants and the recent discovery of meiosis specific with OB domains (MEIOB), a widely conserved meiosis-specific RPA1 paralog, strongly suggest that multiple RPA complexes evolved and specialized to subdivide their roles during DNA metabolism. Here we review ssDNA formation and maturation during mitotic and meiotic recombination underlying the meiotic specific features. We describe and discuss the existence and properties of MEIOB and multiple RPA subunits in plants and highlight how they can provide meiosis-specific fates to ssDNA processing during homologous recombination. Understanding the functions of these RPA homologs and how they interact with the canonical RPA subunits is of major interest in the fields of meiosis and DNA repair.

Global Soil and Sediment transfer during the Anthropocene

NASA Astrophysics Data System (ADS)

Hoffmann, Thomas; Vanacker, Veerle; Stinchcombe, Gary; Penny, Dan; Xixi, Lu

2016-04-01

The vulnerability of soils to human-induced erosion and its downstream effects on fluvial and deltaic ecosystems is highly variable in space and time; dependent on climate, geology, the nature and duration of land use, and topography. Despite our knowledge of the mechanistic relationships between erosion, sediment storage, land-use and climate change, the global patterns of soil erosion, fluvial sediment flux and storage throughout the Holocene remain poorly understood. The newly launched PAGES working group GloSS aims to determine the sensitivity of soil resources and sediment routing systems to varying land use types during the period of agriculture, under contrasting climate regimes and socio-ecological settings. Successfully addressing these questions in relation to the sustainable use of soils, sediments and river systems requires an understanding of past human-landscape interactions. GloSS, therefore, aims to: Develop proxies for, or indices of, human impact on rates of soil erosion and fluvial sediment transfer that are applicable on a global scale and throughout the Holocene; Create a global database of long-term (102-104 years) human-accelerated soil erosion and sediment flux records; Identify hot spots of soil erosion and sediment deposition during the Anthropocene, and Locate data-poor regions where particular socio-ecological systems are not well understood, as strategic foci for future work. This paper will present the latest progress of the PAGES GloSS working group.

Toward a General Approach for RNA-Templated Hierarchical Assembly of Split-Proteins

PubMed Central

Furman, Jennifer L.; Badran, Ahmed H.; Ajulo, Oluyomi; Porter, Jason R.; Stains, Cliff I.; Segal, David J.; Ghosh, Indraneel

2010-01-01

The ability to conditionally turn on a signal or induce a function in the presence of a user-defined RNA target has potential applications in medicine and synthetic biology. Although sequence-specific pumilio repeat proteins can target a limited set of ssRNA sequences, there are no general methods for targeting ssRNA with designed proteins. As a first step toward RNA recognition, we utilized the RNA binding domain of argonaute, implicated in RNA interference, for specifically targeting generic 2-nucleotide, 3' overhangs of any dsRNA. We tested the reassembly of a split-luciferase enzyme guided by argonaute-mediated recognition of newly generated nucleotide overhangs when ssRNA is targeted by a designed complementary guide sequence. This approach was successful when argonaute was utilized in conjunction with a pumilio repeat and expanded the scope of potential ssRNA targets. However, targeting any desired ssRNA remained elusive as two argonaute domains provided minimal reassembled split-luciferase. We next designed and tested a second hierarchical assembly, wherein ssDNA guides are appended to DNA hairpins that serve as a scaffold for high affinity zinc fingers attached to split-luciferase. In the presence of a ssRNA target containing adjacent sequences complementary to the guides, the hairpins are brought into proximity, allowing for zinc finger binding and concomitant reassembly of the fragmented luciferase. The scope of this new approach was validated by specifically targeting RNA encoding VEGF, hDM2, and HER2. These approaches provide potentially general design paradigms for the conditional reassembly of fragmented proteins in the presence of any desired ssRNA target. PMID:20681585

Redox-sensitive micelles composed of disulfide-linked Pluronic-linoleic acid for enhanced anticancer efficiency of brusatol

PubMed Central

Chan, Hon Fai; Lin, Zhixiu; Wang, Yitao

2018-01-01

Brusatol (Bru) exhibits promising anticancer effects, with both proliferation inhibition and chemoresistance amelioration activity. However, the poor solubility and insufficient intracellular delivery of Bru greatly restrict its application. Herein, to simultaneously utilize the advantages of Pluronics as drug carriers and tumor microenvironment-responsive drug release profiles, a flexible amphiphilic copolymer with a polymer skeleton, that is, Pluronic® F68 grafting with linoleic acid moieties by redox-reducible disulfide bonds (F68-SS-LA), was synthesized. After characterization by 1H-nuclear magnetic resonance and Fourier transform infrared spectroscopy, the redox-sensitive F68-SS-LA micelles were self-assembled in a much lower critical micelle concentration than that of the unmodified F68 copolymer. Bru was loaded in micelles (Bru/SS-M) with high loading efficiency, narrow size distribution, and excellent storage stability. The redox-sensitive Bru/SS-M exhibited rapid particle dissociation and drug release in response to a redox environment. Based on the enhanced cellular internalization, Bru/SS-M achieved higher cytotoxicity in both Bel-7402 and MCF-7 cells compared with free Bru and nonreducible micelles. The improved anticancer effect was attributed to the remarkably decreased mitochondrial membrane potential and increased reactive oxygen species level as well as apoptotic rate. These results demonstrated that F68-SS-LA micelles possess great potential as an efficient delivery vehicle for Bru to promote its anticancer efficiency via an oxidation pathway. PMID:29491708

Sjogren's syndrome from the perspective of ophthalmology.

PubMed

Kuklinski, Eric; Asbell, Penny A

2017-09-01

Sjogren's syndrome (SS) is an autoimmune disease affecting the lacrimal glands resulting in dry eye disease (DED). Ophthalmologists may be the first line of detection of Sjogren's syndrome given the frequency of DED in SS and that dry eye is often the presenting symptom. Numerous symptom questionnaires and tests have been developed to help diagnose DED, but as of yet, there is no "gold standard." Minimally invasive objective metrics are needed for a reliable diagnosis of DED. Currently there is no single test to diagnose SS-associated DED. Although there are several approaches to treatment, none are specific for DED in SS, and, generally, several methods need to be tried to find what works best for a specific patient. Treatment for DED continues to be an unmet medical need, especially given that DED in SS is typically on the severe end of the spectrum. Copyright © 2017 Elsevier Inc. All rights reserved.

Association between memory B-cells and clinical and immunological features of primary Sjögren's syndrome and Sicca patients.

PubMed

Barcelos, Filipe; Martins, Catarina; Papoila, Ana; Geraldes, Carlos; Cardigos, Joana; Nunes, Glória; Lopes, Teresa; Alves, Nuno; Vaz-Patto, José; Branco, Jaime; Borrego, Luís-Miguel

2018-06-01

B-cells play a pivotal role in primary Sjögren's syndrome (pSS) pathogenesis. We aim to (1) evaluate the distribution of B-lymphocyte subpopulations in pSS and Sicca patients, (2) establish cut-off points that discriminate pSS from controls, (3) evaluate the association between memory B-cells and phenotypic features in pSS. We included 57 pSS patients, 68 Sicca and 24 healthy controls. Circulating B-cells were characterized by flow cytometry as naïve and memory subsets and classified from Bm1 to Bm5. Compared to controls, pSS patients had lower percentages (29.5 vs 44.4%) and absolute numbers (47 vs 106 cells/µl) of memory B-cells. Through ROC curves, a cut-off of ≤ 58 total memory B-cells/µl yielded a specificity of 0.88 and a sensitivity of 0.60 for pSS, and was met by 59.6% of pSS patients, 38.8% of Sicca and 12.5% of controls. A cut-off of < 23.5 Switched-memory B-cells/µl yielded a specificity of 0.88 and a sensitivity of 0.54 and was met by 54.4% of pSS patients, 37.3% of Sicca and 12.5% of controls. In pSS, lower total memory B-cells count was associated with longer disease duration (14.3 vs 8.1 years, p = 0.006) and more active disease profile, as evaluated by the European League Against Rheumatism (EULAR) Sjögren's Syndrome Disease Activity Index (ESSDAI) (3.1 vs 1.4, p = 0.043). Decreased numbers of memory B-cells clearly discriminated pSS from controls and can also have prognostic value. It remains to be clarified whether Sicca patients with decreased memory B-cells represent pSS and if B-cell profiling could help in the diagnosis of pSS.

Diagnosing environmental allergies: Comparison of skin-prick, intradermal, and serum specific immunoglobulin E testing

PubMed Central

Shtessel, Maria; Lobell, Elizabeth; Hudes, Golda; Rosenstreich, David; de Vos, Gabriele

2017-01-01

Background: Allergists commonly perform intradermal skin testing (IDST) after negative skin-prick testing (SPT) to comprehensively diagnose environmental allergic sensitization. However, with the availability of modern methods to detect serum-specific immunoglobulin E (ssIgE), it is unclear if ssIgE testing could substitute for IDST. Objective: To determine the efficacy of ssIgE testing and IDST when added to SPT in diagnosing environmental allergic sensitizations. Methods: SPT, IDST, and ssIgE testing to nine common environmental allergens were analyzed in 75 patients with oculonasal symptoms who presented to our allergy clinics in the Bronx, New York, between January 2014 and May 2015. Results: A total of 651 SPT and 499 ssIgE tests were independently performed and revealed 162 (25%) and 127 (25%) sensitizations, respectively. When SPT results were negative, IDST results revealed 108 of 452 additional sensitizations (24%). In contrast, when SPT results were negative, ssIgE test results only revealed 9% additional sensitizations. When both SPT and IDST results were negative, ssIgE testing only detected 3% of additional sensitizations, and ssIgE levels were typically low in these cases (median, 1.25 kU/L; range, 0.357–4.47 kU/L). When both SPT and ssIgE test results were negative, IDST results detected 15% additional sensitizations. Conclusion: IDST detected more additional environmental sensitizations compared with ssIgE testing. IDST, therefore, may be useful when the SPT and/or ssIgE testing results were negative, but the exposure history indicated relevant allergic sensitization. Serology added only a little more information if both SPT and IDST results were negative but may be useful in combination with SPT if IDST cannot be performed. PMID:28583228

Diagnosing environmental allergies: Comparison of skin-prick, intradermal, and serum specific immunoglobulin E testing.

PubMed

Ferastraoaru, Denisa; Shtessel, Maria; Lobell, Elizabeth; Hudes, Golda; Rosenstreich, David; de Vos, Gabriele

2017-06-01

Allergists commonly perform intradermal skin testing (IDST) after negative skin-prick testing (SPT) to comprehensively diagnose environmental allergic sensitization. However, with the availability of modern methods to detect serum-specific immunoglobulin E (ssIgE), it is unclear if ssIgE testing could substitute for IDST. To determine the efficacy of ssIgE testing and IDST when added to SPT in diagnosing environmental allergic sensitizations. SPT, IDST, and ssIgE testing to nine common environmental allergens were analyzed in 75 patients with oculonasal symptoms who presented to our allergy clinics in the Bronx, New York, between January 2014 and May 2015. A total of 651 SPT and 499 ssIgE tests were independently performed and revealed 162 (25%) and 127 (25%) sensitizations, respectively. When SPT results were negative, IDST results revealed 108 of 452 additional sensitizations (24%). In contrast, when SPT results were negative, ssIgE test results only revealed 9% additional sensitizations. When both SPT and IDST results were negative, ssIgE testing only detected 3% of additional sensitizations, and ssIgE levels were typically low in these cases (median, 1.25 kU/L; range, 0.357-4.47 kU/L). When both SPT and ssIgE test results were negative, IDST results detected 15% additional sensitizations. IDST detected more additional environmental sensitizations compared with ssIgE testing. IDST, therefore, may be useful when the SPT and/or ssIgE testing results were negative, but the exposure history indicated relevant allergic sensitization. Serology added only a little more information if both SPT and IDST results were negative but may be useful in combination with SPT if IDST cannot be performed.

Hydraulic tomography offers improved imaging of heterogeneity in fractured rocks.

PubMed

Illman, Walter A

2014-01-01

Fractured rocks have presented formidable challenges for accurately predicting groundwater flow and contaminant transport. This is mainly due to our difficulty in mapping the fracture-rock matrix system, their hydraulic properties and connectivity at resolutions that are meaningful for groundwater modeling. Over the last several decades, considerable effort has gone into creating maps of subsurface heterogeneity in hydraulic conductivity (K) and specific storage (Ss ) of fractured rocks. Developed methods include kriging, stochastic simulation, stochastic inverse modeling, and hydraulic tomography. In this article, I review the evolution of various heterogeneity mapping approaches and contend that hydraulic tomography, a recently developed aquifer characterization technique for unconsolidated deposits, is also a promising approach in yielding robust maps (or tomograms) of K and Ss heterogeneity for fractured rocks. While hydraulic tomography has recently been shown to be a robust technique, the resolution of the K and Ss tomograms mainly depends on the density of pumping and monitoring locations and the quality of data. The resolution will be improved through the development of new devices for higher density monitoring of pressure responses at discrete intervals in boreholes and potentially through the integration of other data from single-hole tests, borehole flowmeter profiling, and tracer tests. Other data from temperature and geophysical surveys as well as geological investigations may improve the accuracy of the maps, but more research is needed. Technological advances will undoubtedly lead to more accurate maps. However, more effort should go into evaluating these maps so that one can gain more confidence in their reliability. © 2013, National Ground Water Association.

Hydraulic tomography offers improved imaging of heterogeneity in fractured rocks

NASA Astrophysics Data System (ADS)

Illman, W. A.

2013-12-01

Fractured rocks have presented formidable challenges for accurately predicting groundwater flow and contaminant transport. This is mainly due to our difficulty in mapping the fracture-rock matrix system, their hydraulic properties and connectivity at resolutions that are meaningful for groundwater flow and especially transport modeling. Over the last several decades, considerable effort has gone into creating maps of subsurface heterogeneity in hydraulic conductivity (K) and specific storage (Ss) of fractured rocks. Developed methods include kriging, stochastic simulation, stochastic inverse modeling, and hydraulic tomography. In this presentation, I review the evolution of various heterogeneity mapping approaches and contend that hydraulic tomography, a recently developed aquifer characterization technique for unconsolidated deposits, is also a promising approach in yielding robust maps (or tomograms) of K and Ss heterogeneity for fractured rocks. While hydraulic tomography has recently been shown to be a robust technique, the resolution of the K and Ss tomograms mainly depends on the density of pumping and monitoring locations and the quality of data. The resolution will be improved through the development of new devices for higher density monitoring of pressure responses at discrete intervals in boreholes and potentially through the integration of other data from single-hole tests, borehole flowmeter profiling and tracer tests. Other data from temperature and geophysical surveys as well as geological investigations may improve the accuracy of the maps, but more research is needed. Technological advances will undoubtedly lead to more accurate maps. However, more effort should go into evaluating these maps so that one can gain more confidence in their reliability.

NASA software specification and evaluation system: Software verification/validation techniques

NASA Technical Reports Server (NTRS)

1977-01-01

NASA software requirement specifications were used in the development of a system for validating and verifying computer programs. The software specification and evaluation system (SSES) provides for the effective and efficient specification, implementation, and testing of computer software programs. The system as implemented will produce structured FORTRAN or ANSI FORTRAN programs, but the principles upon which SSES is designed allow it to be easily adapted to other high order languages.

Deficiency of slow skeletal muscle troponin T causes atrophy of type I slow fibres and decreases tolerance to fatigue.

PubMed

Wei, Bin; Lu, Yingru; Jin, J-P

2014-03-15

The total loss of slow skeletal muscle troponin T (ssTnT encoded by TNNT1 gene) due to a nonsense mutation in codon Glu(180) causes a lethal form of recessively inherited nemaline myopathy (Amish nemaline myopathy, ANM). To investigate the pathogenesis and muscle pathophysiology of ANM, we studied the phenotypes of partial and total loss of ssTnT in Tnnt1 gene targeted mice. An insertion of neomycin resistance cassette in intron 10 of Tnnt1 gene caused an approximately 60% decrease in ssTnT protein expression whereas cre-loxP-mediated deletion of exons 11-13 resulted in total loss of ssTnT, as seen in ANM muscles. In diaphragm and soleus muscles of the knockdown and knockout mouse models, we demonstrated that ssTnT deficiency resulted in significantly decreased levels of other slow fibre-specific myofilament proteins whereas fast fibre-specific myofilament proteins were increased correspondingly. Immunohistochemical studies revealed that ssTnT deficiency produced significantly smaller type I slow fibres and compensatory growth of type II fast fibres. Along with the slow fibre atrophy and the changes in myofilament protein isoform contents, ssTnT deficiency significantly reduced the tolerance to fatigue in soleus muscle. ssTnT-deficient soleus muscle also contains significant numbers of small-sized central nuclei type I fibres, indicating active regeneration. The data provide strong support for the essential role of ssTnT in skeletal muscle function and the causal effect of its loss in the pathology of ANM. This observation further supports the hypothesis that the function of slow fibres can be restored in ANM patients if a therapeutic supplement of ssTnT is achieved.

Deficiency of slow skeletal muscle troponin T causes atrophy of type I slow fibres and decreases tolerance to fatigue

PubMed Central

Wei, Bin; Lu, Yingru; Jin, J-P

2014-01-01

The total loss of slow skeletal muscle troponin T (ssTnT encoded by TNNT1 gene) due to a nonsense mutation in codon Glu180 causes a lethal form of recessively inherited nemaline myopathy (Amish nemaline myopathy, ANM). To investigate the pathogenesis and muscle pathophysiology of ANM, we studied the phenotypes of partial and total loss of ssTnT in Tnnt1 gene targeted mice. An insertion of neomycin resistance cassette in intron 10 of Tnnt1 gene caused an approximately 60% decrease in ssTnT protein expression whereas cre-loxP-mediated deletion of exons 11–13 resulted in total loss of ssTnT, as seen in ANM muscles. In diaphragm and soleus muscles of the knockdown and knockout mouse models, we demonstrated that ssTnT deficiency resulted in significantly decreased levels of other slow fibre-specific myofilament proteins whereas fast fibre-specific myofilament proteins were increased correspondingly. Immunohistochemical studies revealed that ssTnT deficiency produced significantly smaller type I slow fibres and compensatory growth of type II fast fibres. Along with the slow fibre atrophy and the changes in myofilament protein isoform contents, ssTnT deficiency significantly reduced the tolerance to fatigue in soleus muscle. ssTnT-deficient soleus muscle also contains significant numbers of small-sized central nuclei type I fibres, indicating active regeneration. The data provide strong support for the essential role of ssTnT in skeletal muscle function and the causal effect of its loss in the pathology of ANM. This observation further supports the hypothesis that the function of slow fibres can be restored in ANM patients if a therapeutic supplement of ssTnT is achieved. PMID:24445317

Genetic Basis of Sjögren's Syndrome. How Strong is the Evidence?

PubMed Central

Anaya, Juan-Manuel; Delgado-Vega, Angélica María; Castiblanco, John

2006-01-01

Sjögren's syndrome (SS) is a late-onset chronic autoimmune disease (AID) affecting the exocrine glands, mainly the salivary and lachrymal. Genetic studies on twins with primary SS have not been performed, and only a few case reports describing twins have been published. The prevalence of primary SS in siblings has been estimated to be 0.09% while the reported general prevalence of the disease is approximately 0.1%. The observed aggregation of AIDs in families of patients with primary SS is nevertheless supportive for a genetic component in its etiology. In the absence of chromosomal regions identified by linkage studies, research has focused on candidate gene approaches (by biological plausibility) rather than on positional approaches. Ancestral haplotype 8.1 as well as TNF, IL10 and SSA1 loci have been consistently associated with the disease although they are not specific for SS. In this review, the genetic component of SS is discussed on the basis of three known observations: (a) age at onset and sex-dependent presentation, (b) familial clustering of the disease, and (c) dissection of the genetic component. Since there is no strong evidence for a specific genetic component in SS, a large international and collaborative study would be suitable to assess the genetics of this disorder. PMID:17162364

Aetiology of Bacteraemia as a Risk Factor for Septic Shock at the Onset of Febrile Neutropaenia in Adult Cancer Patients

PubMed Central

Rosa, Regis Goulart; Goldani, Luciano Zubaran

2014-01-01

Septic shock (SS) at the onset of febrile neutropaenia (FN) is an emergency situation that is associated with high morbidity and mortality. The impact of the specific aetiology of bloodstream infections (BSIs) in the development of SS at the time of FN is not well established. The aim of this study was to evaluate the association between the aetiology of BSIs and SS at the time of FN in hospitalised adult cancer patients. This prospective cohort study was performed at a single tertiary hospital from October 2009 to August 2011. All adult cancer patients admitted consecutively to the haematology ward with FN were evaluated. A stepwise logistic regression was conducted to verify the association between the microbiological characteristics of BSIs and SS at the onset of FN. In total, 307 cases of FN in adult cancer patients were evaluated. There were 115 cases with documented BSI. A multivariate analysis showed that polymicrobial bacteraemia (P = 0.01) was associated with SS. The specific blood isolates independently associated with SS were viridans streptococci (P = 0.02) and Escherichia coli (P = 0.01). Neutropaenic cancer patients with polymicrobial bacteraemia or BSI by viridans streptococci or Escherichia coli are at increased risk for SS at the time of FN. PMID:24804223

The particle size distribution, density, and specific surface area of welding fumes from SMAW and GMAW mild and stainless steel consumables.

PubMed

Hewett, P

1995-02-01

Particle size distributions were measured for fumes from mild steel (MS) and stainless steel (SS); shielded metal arc welding (SMAW) and gas metal arc welding (GMAW) consumables. Up to six samples of each type of fume were collected in a test chamber using a micro-orifice uniform deposit (cascade) impactor. Bulk samples were collected for bulk fume density and specific surface area analysis. Additional impactor samples were collected using polycarbonate substrates and analyzed for elemental content. The parameters of the underlying mass distributions were estimated using a nonlinear least squares analysis method that fits a smooth curve to the mass fraction distribution histograms of all samples for each type of fume. The mass distributions for all four consumables were unimodal and well described by a lognormal distribution; with the exception of the GMAW-MS and GMAW-SS comparison, they were statistically different. The estimated mass distribution geometric means for the SMAW-MS and SMAW-SS consumables were 0.59 and 0.46 micron aerodynamic equivalent diameter (AED), respectively, and 0.25 micron AED for both the GMAW-MS and GMAW-SS consumables. The bulk fume densities and specific surface areas were similar for the SMAW-MS and SMAW-SS consumables and for the GMAW-MS and GMAW-SS consumables, but differed between SMAW and GMAW. The distribution of metals was similar to the mass distributions. Particle size distributions and physical properties of the fumes were considerably different when categorized by welding method. Within each welding method there was little difference between MS and SS fumes.

Sleep spindle alterations in patients with Parkinson's disease

PubMed Central

Christensen, Julie A. E.; Nikolic, Miki; Warby, Simon C.; Koch, Henriette; Zoetmulder, Marielle; Frandsen, Rune; Moghadam, Keivan K.; Sorensen, Helge B. D.; Mignot, Emmanuel; Jennum, Poul J.

2015-01-01

The aim of this study was to identify changes of sleep spindles (SS) in the EEG of patients with Parkinson's disease (PD). Five sleep experts manually identified SS at a central scalp location (C3-A2) in 15 PD and 15 age- and sex-matched control subjects. Each SS was given a confidence score, and by using a group consensus rule, 901 SS were identified and characterized by their (1) duration, (2) oscillation frequency, (3) maximum peak-to-peak amplitude, (4) percent-to-peak amplitude, and (5) density. Between-group comparisons were made for all SS characteristics computed, and significant changes for PD patients vs. control subjects were found for duration, oscillation frequency, maximum peak-to-peak amplitude and density. Specifically, SS density was lower, duration was longer, oscillation frequency slower and maximum peak-to-peak amplitude higher in patients vs. controls. We also computed inter-expert reliability in SS scoring and found a significantly lower reliability in scoring definite SS in patients when compared to controls. How neurodegeneration in PD could influence SS characteristics is discussed. We also note that the SS morphological changes observed here may affect automatic detection of SS in patients with PD or other neurodegenerative disorders (NDDs). PMID:25983685

Materials for Consideration in Standardized Canister Design Activities.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bryan, Charles R.; Ilgen, Anastasia Gennadyevna; Enos, David George

2014-10-01

This document identifies materials and material mitigation processes that might be used in new designs for standardized canisters for storage, transportation, and disposal of spent nuclear fuel. It also addresses potential corrosion issues with existing dual-purpose canisters (DPCs) that could be addressed in new canister designs. The major potential corrosion risk during storage is stress corrosion cracking of the weld regions on the 304 SS/316 SS canister shell due to deliquescence of chloride salts on the surface. Two approaches are proposed to alleviate this potential risk. First, the existing canister materials (304 and 316 SS) could be used, but themore » welds mitigated to relieve residual stresses and/or sensitization. Alternatively, more corrosion-resistant steels such as super-austenitic or duplex stainless steels, could be used. Experimental testing is needed to verify that these alternatives would successfully reduce the risk of stress corrosion cracking during fuel storage. For disposal in a geologic repository, the canister will be enclosed in a corrosion-resistant or corrosion-allowance overpack that will provide barrier capability and mechanical strength. The canister shell will no longer have a barrier function and its containment integrity can be ignored. The basket and neutron absorbers within the canister have the important role of limiting the possibility of post-closure criticality. The time period for corrosion is much longer in the post-closure period, and one major unanswered question is whether the basket materials will corrode slowly enough to maintain structural integrity for at least 10,000 years. Whereas there is extensive literature on stainless steels, this evaluation recommends testing of 304 and 316 SS, and more corrosion-resistant steels such as super-austenitic, duplex, and super-duplex stainless steels, at repository-relevant physical and chemical conditions. Both general and localized corrosion testing methods would be used to establish corrosion rates and component lifetimes. Finally, it is unlikely that the aluminum-based neutron absorber materials that are commonly used in existing DPCs would survive for 10,000 years in disposal environments, because the aluminum will act as a sacrificial anode for the steel. We recommend additional testing of borated and Gd-bearing stainless steels, to establish general and localized corrosion resistance in repository-relevant environmental conditions.« less

Multiscale analysis of information dynamics for linear multivariate processes.

PubMed

Faes, Luca; Montalto, Alessandro; Stramaglia, Sebastiano; Nollo, Giandomenico; Marinazzo, Daniele

2016-08-01

In the study of complex physical and physiological systems represented by multivariate time series, an issue of great interest is the description of the system dynamics over a range of different temporal scales. While information-theoretic approaches to the multiscale analysis of complex dynamics are being increasingly used, the theoretical properties of the applied measures are poorly understood. This study introduces for the first time a framework for the analytical computation of information dynamics for linear multivariate stochastic processes explored at different time scales. After showing that the multiscale processing of a vector autoregressive (VAR) process introduces a moving average (MA) component, we describe how to represent the resulting VARMA process using statespace (SS) models and how to exploit the SS model parameters to compute analytical measures of information storage and information transfer for the original and rescaled processes. The framework is then used to quantify multiscale information dynamics for simulated unidirectionally and bidirectionally coupled VAR processes, showing that rescaling may lead to insightful patterns of information storage and transfer but also to potentially misleading behaviors.

Single-walled carbon nanotubes based chemiresistive genosensor for label-free detection of human rheumatic heart disease

NASA Astrophysics Data System (ADS)

Singh, Swati; Kumar, Ashok; Khare, Shashi; Mulchandani, Ashok; Rajesh

2014-11-01

A specific and ultrasensitive, label free single-walled carbon nanotubes (SWNTs) based chemiresistive genosensor was fabricated for the early detection of Streptococcus pyogenes infection in human causing rheumatic heart disease. The mga gene of S. pyogenes specific 24 mer ssDNA probe was covalently immobilized on SWNT through a molecular bilinker, 1-pyrenemethylamine, using carbodiimide coupling reaction. The sensor was characterized by the current-voltage (I-V) characteristic curve and scanning electron microscopy. The sensing performance of the sensor was studied with respect to changes in conductance in SWNT channel based on hybridization of the target S. pyogenes single stranded genomic DNA (ssG-DNA) to its complementary 24 mer ssDNA probe. The sensor shows negligible response to non-complementary Staphylococcus aureus ssG-DNA, confirming the specificity of the sensor only with S. pyogenes. The genosensor exhibited a linear response to S. pyogenes G-DNA from 1 to1000 ng ml-1 with a limit of detection of 0.16 ng ml-1.

Quality assessment of roof-harvested rainwater in the West Bank, Palestinian Authority.

PubMed

Daoud, A K; Swaileh, K M; Hussein, R M; Matani, M

2011-09-01

Rain harvesting is becoming more common in the Palestinian Territories as a result of drinking water scarcity. Although it might pose serious human health risk, this water is being consumed without treatment in many areas of the West Bank. The present study evaluates the physicochemical and microbial quality of harvested rainwater that is used as potable water in the West Bank. Samples from roof-harvested rainwater storage tanks (n = 42) were collected in summer (SS) 2006/winter (WS) 2007. Physicochemical parameters measured were: temperature, pH, electrical conductivity, salinity, total dissolved solids, turbidity, nitrate, copper and lead. With few exceptions, all these parameters were within WHO guideline values. All samples (100%) were found to contain coliforms and to be heavily contaminated with heterotrophic bacteria. About 67% of all samples were contaminated with fecal coliforms. Specific PCR technique confirmed the presence of five pathogenic microorganisms that can be ordered according to their prevalence as: Citrobacter (83%) > Acinetobacter (78%) > Aeromonas (52%) > Pseudomonas and Campylobacter (7%). Prevalence of microorganisms in SS was higher than in WS. Although the physicochemical quality of most harvested rainwater samples was in accordance with WHO guidelines for drinking water, stored rainwater was significantly contaminated with bacteria resulting in significant human health risk from infectious diseases.

Effect of tension-free vaginal tape and TVT-obturator on lower urinary tract symptoms other than stress urinary incontinence.

PubMed

Ballert, Katie N; Kanofsky, Jamie A; Nitti, Victor W

2008-03-01

Variable effects on lower urinary tract symptoms (LUTS) other than stress urinary incontinence (SUI) have been reported after tension-free vaginal tape (TVT). We measured the effect of TVT on LUTS using the American Urological Association Symptom Index (AUASI). Patients undergoing TVT completed the AUASI pre- and post-operatively. Total scores (TS), storage scores (SS), and voiding scores (VS) were compared overall and among patients with SUI vs mixed urinary incontinence (MUI) and those who underwent TVT vs TVT-obturator (TVT-O). The mean change in TS and SS was -3.6 and -3.0. Mean reductions in TS and SS were significant in all patient subsets with no change in VS. There was no significant difference in the mean changes in TS between patients with SUI vs MUI or those undergoing TVT vs TVT-O. LUTS are improved after TVT in most patients. In general, voiding symptoms were not adversely affected.

Suppression of Virus Specific Immune Responses by IL-10 in Acute Dengue Infection

PubMed Central

Malavige, Gathsaurie Neelika; Jeewandara, Chandima; Alles, K. M. Luckmaal; Salimi, Maryam; Gomes, Laksiri; Kamaladasa, Achala; Jayaratne, S. D.; Ogg, Graham Stuart

2013-01-01

Background Elevated IL-10 has been shown to be associated with severe dengue infection (DI). We proceeded to investigate the role of IL-10 in the pathogenesis of acute DI. Materials and methods Ex vivo and cultured IFNγ ELISpot assays for dengue virus (DENV) NS3 protein and non dengue viral proteins were carried out in 26 patients with acute DI (16 with dengue haemorrhagic fever) and 12 healthy dengue seropositive individuals from Sri Lanka. DENV serotype specific (SS) responses were determined by using a panel of SS peptides. Results Serum IL-10 level were significantly higher (p = 0.02) in those who did not have in vitro responses to DENV-SS peptides (mean 144.2 pg/ml) when compared to those who responded (mean 75.7 pg/ml). DENV-NS3 specific ex vivo IFNγ ELISpot responses were also significantly lower (p = 0.0001) in those who did not respond to DENV-SS peptides (mean 42 SFU/million PBMCs) when compared to those who responded to DENV-SS peptides (mean 1024 SFU/million PBMCs). Serum IL-10 levels correlated significantly (p = 0.03) and inversely (Spearmans R = −0.45) with ex vivo DENV-NS3 specific responses but not with ex vivo non DENV specific responses (Spearmans R = −014, p = 0.52). Blockage of IL-10 in vitro significantly increased (p = 0.04) the ex vivo IFNγ ELISpot DENV-NS3 specific responses but had no effect on responses to non DENV proteins. Conclusion IL-10 appears to contribute to the pathogenesis of acute dengue infections by inhibiting DENV-specific T cell responses, which can be restored by blocking IL-10. PMID:24040431

Sex-specific differences in the severity of symptoms and recovery rate following sports-related concussion in young athletes.

PubMed

Berz, Kate; Divine, Jon; Foss, Kim Barber; Heyl, Rachel; Ford, Kevin R; Myer, Gregory D

2013-05-01

While research on adult recovery from concussion indicates sex-specific symptoms and recovery rates, there is little existing data on younger patient populations. To determine sex-specific differences in the severity of presenting symptoms and recovery rate between groups of young athletes who presented ≤ 7 or > 7 days after sports-related concussion. This study was a retrospective review of athletes aged 9 to 17 years who were referred for evaluation of a sports-related concussion over a 24-month period. The study groups were divided by sex and post-injury presentation to the clinic at ≤ 7 days and > 7 days from the date of injury. Athletes with learning disabilities were excluded from the study and data analysis. Age, height, and weight were recorded for each subject. Each subject also reported their initial degree of confusion, amnesia, or loss of consciousness, and whether a helmet was worn when the injury was sustained. A 22-item post-concussion symptom score (SS) scale was completed by both groups on initial assessment (SS1) and follow-up visit (SS2). The recovery rate (SSR) was calculated as (SS2-SS1)/days between SS2 and SS1. Sex and group comparisons for SS1 and SSR were performed using 2 × 2 analysis of variance. A similar analysis was also performed for effects of sex on SS1 and SSR in patients who were not wearing a helmet. Thirty-seven athletes aged 15.0 ± 1.9 years were evaluated. Males, regardless of day of presentation, had a lower SS1 evaluation than females (15.8 vs 30.9; P < 0.05). Males without helmets did not differ from females without helmets, but this was not significantly different (14.1 vs 29.6; P = 0.1). There was not a significant difference in SS1 evaluation between the groups who presented at ≤ 7 or > 7 days. The overall mean SSR was -1.2/day, with no significant difference seen between groups or sex. There were no significant differences in degree of loss of consciousness, amnesia, confusion, or age between the sexes or groups. Whether presenting at ≤ 7 or > 7 days following a sports-related concussion, female athletes reported a higher SS1 evaluation. With SSR being similar between sexes, the current data suggest that young, female athletes may take longer to become symptom free following sports-related concussion. This information may be an important factor in returning a young athlete to sport after sports-related concussion.

A method to estimate groundwater depletion from confining layers

USGS Publications Warehouse

Konikow, Leonard F.; Neuzil, Christopher E.

2007-01-01

Although depletion of storage in low‐permeability confining layers is the source of much of the groundwater produced from many confined aquifer systems, it is all too frequently overlooked or ignored. This makes effective management of groundwater resources difficult by masking how much water has been derived from storage and, in some cases, the total amount of water that has been extracted from an aquifer system. Analyzing confining layer storage is viewed as troublesome because of the additional computational burden and because the hydraulic properties of confining layers are poorly known. In this paper we propose a simplified method for computing estimates of confining layer depletion, as well as procedures for approximating confining layer hydraulic conductivity (K) and specific storage (Ss) using geologic information. The latter makes the technique useful in developing countries and other settings where minimal data are available or when scoping calculations are needed. As such, our approach may be helpful for estimating the global transfer of groundwater to surface water. A test of the method on a synthetic system suggests that the computational errors will generally be small. Larger errors will probably result from inaccuracy in confining layer property estimates, but these may be no greater than errors in more sophisticated analyses. The technique is demonstrated by application to two aquifer systems: the Dakota artesian aquifer system in South Dakota and the coastal plain aquifer system in Virginia. In both cases, depletion from confining layers was substantially larger than depletion from the aquifers.

Effect of 1-methylcyclopropene on tomato flavour components, shelf life and decay as influenced by harvest maturity and storage temperature.

PubMed

Baldwin, Elizabeth; Plotto, Anne; Narciso, Jan; Bai, Jinhe

2011-04-01

In Florida, tomatoes are harvested green (GR), which includes mature green (MG) and immature green (IG) fruits, and stored at low temperature (13 °C), resulting in poor flavour. Flavour improvement might be achieved if fruits were harvested with some colour (to eliminate IG fruits) and/or stored at higher temperature with the ripening inhibitor 1-methylcyclopropene (1-MCP). 'Florida 47' tomatoes were harvested at GR (MG + IG), breaker (BR), turning (TR) and pink (PK) stages, treated (+) or not (-) with 1-MCP and stored at 13 and/or 18 °C. 1-MCP treatment resulted in a gain of up to 6 days of shelf life depending on harvest maturity and storage temperature. Storage at 18 °C rather than 13 °C resulted in an increase in internal red colour, soluble solids (SS)/titratable acidity (TA) ratio and levels of many volatiles studied. The shelf life of BR (+) MCP fruits stored at 13 °C was similar to that of MG fruits. IG fruits exhibited lowest levels of SS, TA and ten volatiles compared with BR fruits. Harvesting tomatoes with colour (BR), thereby eliminating IG fruits, and treating with 1-MCP resulted in better quality with adequate shelf life. This article is a US Government work and is in the public domain in the USA. Published 2011 by John Wiley & Sons, Ltd.

Relationships between starch synthase I and branching enzyme isozymes determined using double mutant rice lines

PubMed Central

2014-01-01

Background Starch is the most important carbohydrate in plant storage tissues. Multiple isozymes in at least four enzyme classes are involved in starch biosynthesis. Some of these isozymes are thought to interact and form complexes for efficient starch biosynthesis. Of these enzyme classes, starch synthases (SSs) and branching enzymes (BEs) play particularly central roles. Results We generated double mutant lines (ss1/be1 and ss1 L /be2b) between SSI (the largest component of total soluble SS activity) and BEI or BEIIb (major BEs in developing rice endosperm) to explore the relationships among these isozymes. The seed weight of ss1/be1 was comparable to that of wild type, although most ss1/be2b seeds were sterile and no double recessive plants were obtained. The seed weight of the double recessive mutant line ss1 L /be2b, derived from the leaky ss1 mutant (ss1 L ) and be2b, was higher than that of the single be2b mutant. Analyses of the chain-length distribution of amylopectin in ss1/be1 endosperm revealed additive effects of SSI and BEI on amylopectin structure. Chain-length analysis indicated that the BEIIb deficiency significantly reduced the ratio of short chains in amylopectin of ss1 L /be2b. The amylose content of endosperm starch of ss1/be1 and ss1 L /be2b was almost the same as that of wild type, whereas the endosperm starch of be2b contained more amylose than did that of wild type. SSI, BEI, and BEIIb deficiency also affected the extent of binding of other isozymes to starch granules. Conclusions Analysis of the chain-length distribution in amylopectin of the double mutant lines showed that SSI and BEI or BEIIb primarily function independently, and branching by BEIIb is followed by SSI chain elongation. The increased amylose content in be2b was because of reduced amylopectin biosynthesis; however, the lower SSI activity in this background may have enhanced amylopectin biosynthesis as a result of a correction of imbalance between the branching and elongation found in the single mutant. The fact that a deficiency of SSI, BEI, or BEIIb affected the affinity of other starch biosynthetic isozymes for the starch granule implies that there is a close interaction among SSI, BEI and BEIIb during amylopectin biosynthesis in rice endosperm. PMID:24670252

Relationships between starch synthase I and branching enzyme isozymes determined using double mutant rice lines.

PubMed

Abe, Natsuko; Asai, Hiroki; Yago, Hikari; Oitome, Naoko F; Itoh, Rumiko; Crofts, Naoko; Nakamura, Yasunori; Fujita, Naoko

2014-03-26

Starch is the most important carbohydrate in plant storage tissues. Multiple isozymes in at least four enzyme classes are involved in starch biosynthesis. Some of these isozymes are thought to interact and form complexes for efficient starch biosynthesis. Of these enzyme classes, starch synthases (SSs) and branching enzymes (BEs) play particularly central roles. We generated double mutant lines (ss1/be1 and ss1L/be2b) between SSI (the largest component of total soluble SS activity) and BEI or BEIIb (major BEs in developing rice endosperm) to explore the relationships among these isozymes. The seed weight of ss1/be1 was comparable to that of wild type, although most ss1/be2b seeds were sterile and no double recessive plants were obtained. The seed weight of the double recessive mutant line ss1L/be2b, derived from the leaky ss1 mutant (ss1L) and be2b, was higher than that of the single be2b mutant. Analyses of the chain-length distribution of amylopectin in ss1/be1 endosperm revealed additive effects of SSI and BEI on amylopectin structure. Chain-length analysis indicated that the BEIIb deficiency significantly reduced the ratio of short chains in amylopectin of ss1L/be2b. The amylose content of endosperm starch of ss1/be1 and ss1L/be2b was almost the same as that of wild type, whereas the endosperm starch of be2b contained more amylose than did that of wild type. SSI, BEI, and BEIIb deficiency also affected the extent of binding of other isozymes to starch granules. Analysis of the chain-length distribution in amylopectin of the double mutant lines showed that SSI and BEI or BEIIb primarily function independently, and branching by BEIIb is followed by SSI chain elongation. The increased amylose content in be2b was because of reduced amylopectin biosynthesis; however, the lower SSI activity in this background may have enhanced amylopectin biosynthesis as a result of a correction of imbalance between the branching and elongation found in the single mutant. The fact that a deficiency of SSI, BEI, or BEIIb affected the affinity of other starch biosynthetic isozymes for the starch granule implies that there is a close interaction among SSI, BEI and BEIIb during amylopectin biosynthesis in rice endosperm.

Risk of Sex-Specific Cancers in Opposite-Sex and Same-Sex Twins in Denmark and Sweden

PubMed Central

Ahrenfeldt, Linda J.; Skytthe, Axel; Möller, Sören; Czene, Kamila; Adami, Hans-Olov; Mucci, Lorelei A.; Kaprio, Jaakko; Petersen, Inge; Christensen, Kaare; Lindahl-Jacobsen, Rune

2016-01-01

Background Increasing evidence shows that some cancers originate in utero. It is hypothesized that elevated exposure to some steroid hormones might increase cancer risk and that hormone transfer between twin fetuses could result in different prenatal exposure to testosterone. Methods This large-scale prospective twin study compared opposite-sex (OS) and same-sex (SS) twins to test the impact of intrauterine exposures on cancer risk. On the basis of the Danish and Swedish twin and cancer registries, we calculated incidence rate ratios for OS and SS twins, whereas standardized incidence ratios (SIR) with 95% confidence intervals (CI) were calculated for OS/SS twins compared with the general population. Results Atotal of 18,001 cancers were identified during 1943–2009. No significant differences were observed between OS and SS twins, neither for the sex-specific cancers nor for cancer at all sites. All-cause cancer was slightly reduced for OS and SS twins compared with the general population, significant for OS males (SIR, 0.95; 95% CI, 0.92–0.98) and for SS males and females (SIR, 0.97; 95% CI, 0.94–0.99). Conclusions Our data suggest that having a male co-twin—which may entail higher exposure to prenatal testosterone—does not increase the risk of sex-specific cancers in OS females. Furthermore, the study supports that twinning per se is not a risk factor of cancer. Impact Findings are reassuring, as they fail to provide evidence for the hypothesis that endocrine or other difference in the in utero milieu affects the risk of sex-specific cancers. PMID:26282631

The effects of different durations of static stretching within a comprehensive warm-up on voluntary and evoked contractile properties.

PubMed

Reid, Jonathan C; Greene, Rebecca; Young, James D; Hodgson, Daniel D; Blazevich, Anthony J; Behm, David G

2018-05-02

Evidence for performance decrements following prolonged static stretching (SS) has led to a paradigm shift in stretching routines within a warm-up. Rather than SS, dynamic stretching (DS) and dynamic activity (DA) have replaced SS within warm-up routines. The objective of the present study was to compare the effect of differing lower limb SS durations (30 [SS30s], 60 [SS60s] or 120 s [SS120s] of SS per muscle group or no-stretch control) within a comprehensive warm-up protocol consisting of aerobic activity, DS and DA. Sixteen male participants completed the four stretching conditions in a randomized order, after a 5-min low-intensity (cycle) warm-up and before a DS/DA component on separate days. Tests included passive hip and knee ranges of motion (ROM), maximum voluntary knee extensor/flexor force, force produced at 100 ms (F100), vertical jump height and evoked knee extensor contractile properties. For hip flexion (hamstrings) ROM, SS120s provided the largest increase (5.6-11.7%) followed by SS60s (4.3-11.4%), control (4.4-10.6%) and SS30s (3.6-11.1%). For knee flexion (quadriceps) ROM, SS30s provided the largest increase (9.3-18.2%) followed by SS120s (6.5-16.3%), SS60s (7.2-15.2%) and control (6.3-15.2%). There were decreases in quadriceps F100 following SS in SS120s (29.6%) only. There were increases in vertical jump performance in the control (6.2%), SS60s (4.6%) and SS30s (3.3%). While 120 s SS per muscle increased ROM, even within a comprehensive warm-up routine, it also elicited notable performance decrements. However, moderate durations of SS were observed to improve ROM whilst either having negligible or beneficial (but not detrimental) effects on specific aspects of athletic performance.

The N-terminal Part of Arabidopsis thaliana Starch Synthase 4 Determines the Localization and Activity of the Enzyme.

PubMed

Raynaud, Sandy; Ragel, Paula; Rojas, Tomás; Mérida, Ángel

2016-05-13

Starch synthase 4 (SS4) plays a specific role in starch synthesis because it controls the number of starch granules synthesized in the chloroplast and is involved in the initiation of the starch granule. We showed previously that SS4 interacts with fibrillins 1 and is associated with plastoglobules, suborganelle compartments physically attached to the thylakoid membrane in chloroplasts. Both SS4 localization and its interaction with fibrillins 1 were mediated by the N-terminal part of SS4. Here we show that the coiled-coil region within the N-terminal portion of SS4 is involved in both processes. Elimination of this region prevents SS4 from binding to fibrillins 1 and alters SS4 localization in the chloroplast. We also show that SS4 forms dimers, which depends on a region located between the coiled-coil region and the glycosyltransferase domain of SS4. This region is highly conserved between all SS4 enzymes sequenced to date. We show that the dimerization seems to be necessary for the activity of the enzyme. Both dimerization and the functionality of the coiled-coil region are conserved among SS4 proteins from phylogenetically distant species, such as Arabidopsis and Brachypodium This finding suggests that the mechanism of action of SS4 is conserved among different plant species. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Plasma cholesterol-lowering and transient liver dysfunction in mice lacking squalene synthase in the liver[S

PubMed Central

Nagashima, Shuichi; Yagyu, Hiroaki; Tozawa, Ryuichi; Tazoe, Fumiko; Takahashi, Manabu; Kitamine, Tetsuya; Yamamuro, Daisuke; Sakai, Kent; Sekiya, Motohiro; Okazaki, Hiroaki; Osuga, Jun-ichi; Honda, Akira; Ishibashi, Shun

2015-01-01

Squalene synthase (SS) catalyzes the biosynthesis of squalene, the first specific intermediate in the cholesterol biosynthetic pathway. To test the feasibility of lowering plasma cholesterol by inhibiting hepatic SS, we generated mice in which SS is specifically knocked out in the liver (L-SSKO) using Cre-loxP technology. Hepatic SS activity of L-SSKO mice was reduced by >90%. In addition, cholesterol biosynthesis in the liver slices was almost eliminated. Although the hepatic squalene contents were markedly reduced in L-SSKO mice, the hepatic contents of cholesterol and its precursors distal to squalene were indistinguishable from those of control mice, indicating the presence of sufficient centripetal flow of cholesterol and/or its precursors from the extrahepatic tissues. L-SSKO mice showed a transient liver dysfunction with moderate hepatomegaly presumably secondary to increased farnesol production. In a fed state, the plasma total cholesterol and triglyceride were significantly reduced in L-SSKO mice, primarily owing to reduced hepatic VLDL secretion. In a fasted state, the hypolipidemic effect was lost. mRNA expression of liver X receptor α target genes was reduced, while that of sterol-regulatory element binding protein 2 target genes was increased. In conclusion, liver-specific ablation of SS inhibits hepatic cholesterol biosynthesis and induces hypolipidemia without increasing significant mortality. PMID:25755092

Environmental Assessment: Installation of Thermally Stable Jet Fuel (JPTS) Above Ground Storage System Westover Air Reserve Base, Chicopee, Massachusetts

DTIC Science & Technology

2004-06-30

gasoline fuels is a result ofleaking USTs in the Aqua System Site (SS-19) to the north. Volatile petroleum hydrocarbon ( VPH ) contamination from the...in- situ enhanced bioremediation plan wilJ be implemented to reduce the concentrations of VPH that are present in soils in the groundwater saturated

Assessment of nailfold capillaroscopy by x 30 digital epiluminescence (dermoscopy) in patients with Raynaud phenomenon.

PubMed

Beltrán, E; Toll, A; Pros, A; Carbonell, J; Pujol, R M

2007-05-01

Dermoscopy is a useful tool for dermatologists to study melanocytic lesions. Its possible usefulness in the assessment of capillary nailfold morphological changes (capillaroscopy) has recently been advocated. To assess the practical utility of digital epiluminescence microscopy as a capillaroscopic instrument in patients with Raynaud phenomenon (RP). To compare the sensitivity and specificity rates obtained by epiluminescence microscopy with those previously reported with conventional capillaroscopic devices. Fifty-six consecutive patients with primary RP (PRP; n = 5) or secondary RP (SRP; n = 51) (11 men and 45 women in total) were included in the study. A control group of 10 healthy subjects was also evaluated. Twenty-six patients (46%) had systemic sclerosis (SS), 12 (21%) presystemic sclerosis (pre-SS), one (2%) dermatopolymyositis-SS, one (2%) mixed connective tissue disease, two (4%) Sjögren syndrome, two (4%) an overlap syndrome, one (2%) rheumatoid arthritis and six (11%) other connective tissue diseases. Capillary nailfold changes were studied using a nonportable digital epiluminescence device (magnification x 30). Following a systematized protocol, capillary nailfold morphology, density and distribution were evaluated. Several capillaroscopic patterns were identified (normal, sclerodermic, nonspecific, nondiagnostic) as previously defined. A possible relationship between capillary nailfold changes and the intensity of RP or the presence of associated autoimmune diseases was assessed. The sclerodermic pattern showed a sensitivity of 76.9% and a specificity of 90.9% in SS. A typical capillaroscopic SS pattern was observed in 73% of cases of limited SS and in 82% of cases of diffuse SS. Patients with Sjögren syndrome and dermatopolymyositis-SS showed a nonspecific capillaroscopic pattern. All patients with PRP presented a normal capillaroscopic pattern. A normal capillaroscopic pattern was also observed in 11 of 12 patients with pre-SS. In one of two patients presenting severe sclerodactyly and in all patients showing hand oedema (three of 56), capillaroscopic changes could not be evaluated. Avascular areas correlated significantly with severe RP (P < 0.002), bone resorption (P < 0.007) and diffuse SS (P < 0.008). Digital epiluminescence seems to be a useful and reliable technique in the evaluation of capillary nailfold morphological changes. This technical variation allows the identification of specific capillaroscopic patterns associated with connective tissue diseases. It also permits us to differentiate PRP from SRP. The results obtained with this technique are similar to those previously reported using standard capillaroscopy devices.

Performance comparison between 8 and 14 bit-depth imaging in polarization-sensitive swept-source optical coherence tomography

NASA Astrophysics Data System (ADS)

Lu, Zenghai; Kasaragoda, Deepa K.; Matcher, Stephen J.

2011-03-01

We compare true 8 and 14 bit-depth imaging of SS-OCT and polarization-sensitive SS-OCT (PS-SS-OCT) at 1.3μm wavelength by using two hardware-synchronized high-speed data acquisition (DAQ) boards. The two DAQ boards read exactly the same imaging data for comparison. The measured system sensitivity at 8-bit depth is comparable to that for 14-bit acquisition when using the more sensitive of the available full analog input voltage ranges of the ADC. Ex-vivo structural and birefringence images of an equine tendon sample indicate no significant differences between images acquired by the two DAQ boards suggesting that 8-bit DAQ boards can be employed to increase imaging speeds and reduce storage in clinical SS-OCT/PS-SS-OCT systems. We also compare the resulting image quality when the image data sampled with the 14-bit DAQ from human finger skin is artificially bit-reduced during post-processing. However, in agreement with the results reported previously, we also observe that in our system that real-world 8-bit image shows more artifacts than the image acquired by numerically truncating to 8-bits from the raw 14-bit image data, especially in low intensity image area. This is due to the higher noise floor and reduced dynamic range of the 8-bit DAQ. One possible disadvantage is a reduced imaging dynamic range which can manifest itself as an increase in image artefacts due to strong Fresnel reflection.

Label-free DNA hybridization detection and single base-mismatch discrimination using CE-ICP-MS assay.

PubMed

Li, Yan; Sun, Shao-kai; Yang, Jia-lin; Jiang, Yan

2011-12-07

Detecting a specific DNA sequence and discriminating single base-mismatch is critical to clinical diagnosis, paternity testing, forensic sciences, food and drug industry, pathology, genetics, environmental monitoring, and anti-bioterrorism. To this end, capillary electrophoresis (CE) coupled with the inductively coupled plasma mass spectrometry (ICP-MS) method is developed using the displacing interaction between the target ssDNA and the competitor Hg(2+) for the first time. The thymine-rich capture ssDNA 1 is interacted with the competitor Hg(2+), forming an assembled complex in a hairpin-structure between the thymine bases arrangement at both sides of the capture ssDNA 1. In the presence of a target ssDNA with stronger affinity than that of the competitor Hg(2+), the energetically favorable hybridization between capture ssDNA 1 and the target ssDNA destroys the hairpin-structure and releases the competitor as free Hg(2+), which was then read out and accurately quantified by CE-ICP-MS assay. Under the optimal CE separation conditions, free Hg(2+) ions and its capture ssDNA 1 adduct were baseline separated and detected on-line by ICP-MS; the increased peak intensity of free Hg(2+) against the concentration of perfectly complementary target ssDNA was linear over the concentration range of 30-600 nmol L(-1) with a limit of detection of 8 nmol L(-1) (3s, n = 11) in the pre-incubated mixture containing 1 μmol L(-1) Hg(2+) and 0.2 μmol L(-1) capture ssDNA 1. This new assay method is simple in design since any target ssDNA binding can in principle result in free Hg(2+) release by 6-fold Hg(2+) signal amplification, avoiding oligonucleotide labeling or assistance by excess signal transducer and signal reporter to read out the target. Due to element-specific detection of ICP-MS in our assay procedure, the interference from the autofluorescence of substrata was eliminated.

Validity and reliability of a Nigerian-Yoruba version of the stroke-specific quality of life scale 2.0.

PubMed

Odetunde, Marufat Oluyemisi; Akinpelu, Aderonke Omobonike; Odole, Adesola Christiana

2017-10-19

Psychometric evidence is necessary to establish scientific integrity and clinical usefulness of translations and cultural adaptations of the Stroke-Specific Quality of Life (SS-QoL) scale. However, the limited evidence on psychometrics of Yoruba version of SS-QoL 2.0 (SS-QoL(Y)) is a significant shortcoming. This study assessed the test-retest reliability, internal consistency, convergent, divergent, discriminant and known-group validity of the SS-QoL(Y). Yoruba version of the WHOQoL-BREF was used to test the convergent and divergent validity of the SS-QoL(Y) among 100 consenting stroke survivors. The WHOQoL-BREF and SS-QoL(Y) was administered randomly in order to eliminate bias. The test-retest reliability of the SS-QoL(Y) was carried out among 68 of the respondents within an interval of 7 days. All respondents were purposively recruited from selected secondary and tertiary health facilities in South-west Nigeria. Data were analysed using descriptive statistics of mean and standard deviation, and inferential statistics of Spearman correlation, Cronbach's alpha, Intra-class Correlation Coefficient (ICC), Independent t-test and One-way ANOVA. Alpha level was set at p < 0.05. The physical health, psychological health, social relationship and environment domains on WHOQoL-BREF with correlation coefficient that ranged from 0.214 to 0.360 showed significant correlation with similar domains on SS-QoL(Y). Dissimilar domains between the two scales had r values from 0.035 to 0.366. Discriminant validity of SS-QoL(Y) showed that items' r value ranged from 0.711 to 0.920 with their hypothesized domains. The scale demonstrated moderate to strong test-retest reliability with Intra-class correlation coefficient (ICC) for the domains and overall scores (r = 0.47 to 0.81) and moderate to high internal consistency (Cronbach's alpha =0.61 to 0.82) for domains scores. These correlations were also significant for the domains and overall scores (p < 0.05). There were no significant differences across different age groups or gender for the domains or overall scores of SS-QoL(Y). Discriminant and known-group validity, test-retest reliability and internal consistency of the Yoruba version of the Stroke Specific Quality of Life 2.0 are adequate while the convergent and divergent validity are low but acceptable. The SS-QoL(Y) is recommended for assessing health-related quality of life among Yoruba stroke survivors.

Development of Single-Stranded DNA Aptamers for Specific Bisphenol A Detection

PubMed Central

Jo, Minjoung; Ahn, Ji-Young; Lee, Joohyung; Lee, Seram; Hong, Sun Woo; Yoo, Jae-Wook; Kang, Jeehye; Dua, Pooja

2011-01-01

The development of reagents with high affinity and specificity to small molecules is crucial for the high-throughput detection of chemical compounds, such as toxicants or pollutants. Aptamers are short and single-stranded (ss) oligonucleotides able to recognize target molecules with high affinity. Here, we report the selection of ssDNA aptamers that bind to Bisphenol A (BPA), an environmental hormone. Using SELEX process, we isolated high affinity aptamers to BPA from a 1015 random library of 60 mer ssDNAs. The selected aptamers bound specifically to BPA, but not to structurally similar molecules, such as Bisphenol B with one methyl group difference, or 4,4′-Bisphenol with 2 methyl groups difference. Using these aptamers, we developed an aptamer-based sol–gel biochip and detected BPA dissolved in water. This novel BPA aptamer-based detection can be further applied to the universal and high-specificity detection of small molecules. PMID:21413891

Sensitivity enhancement in swept-source optical coherence tomography by parametric balanced detector and amplifier

PubMed Central

Kang, Jiqiang; Wei, Xiaoming; Li, Bowen; Wang, Xie; Yu, Luoqin; Tan, Sisi; Jinata, Chandra; Wong, Kenneth K. Y.

2016-01-01

We proposed a sensitivity enhancement method of the interference-based signal detection approach and applied it on a swept-source optical coherence tomography (SS-OCT) system through all-fiber optical parametric amplifier (FOPA) and parametric balanced detector (BD). The parametric BD was realized by combining the signal and phase conjugated idler band that was newly-generated through FOPA, and specifically by superimposing these two bands at a photodetector. The sensitivity enhancement by FOPA and parametric BD in SS-OCT were demonstrated experimentally. The results show that SS-OCT with FOPA and SS-OCT with parametric BD can provide more than 9 dB and 12 dB sensitivity improvement, respectively, when compared with the conventional SS-OCT in a spectral bandwidth spanning over 76 nm. To further verify and elaborate their sensitivity enhancement, a bio-sample imaging experiment was conducted on loach eyes by conventional SS-OCT setup, SS-OCT with FOPA and parametric BD at different illumination power levels. All these results proved that using FOPA and parametric BD could improve the sensitivity significantly in SS-OCT systems. PMID:27446655

Effects of topical fluoride prophylactic agents on the mechanical properties of orthodontic nickel-titanium closed coil springs and stainless steel closed coil springs

NASA Astrophysics Data System (ADS)

Carpenter, Brittany Gelene

The purpose of this study was to investigate the effects of topical fluoride prophylactic agents on the mechanical unloading properties of nickel-titanium (NiTi) and stainless steel (SS) closed coil springs. Spring were stored at 37°C under static load in phosphate buffered saline (PBS) and treated with either neutral sodium fluoride (NaF) or acidulated phosphate fluoride (APF) five days per week for two minutes. Mechanical testing was done in a dH2O bath at 37°C at 0-, 1-, 4-, 8-, and 12 weeks. Unloading forces for NiTi and SS springs were measured at 9-, 6-, and 3 mm and 2-, 1.5-, and 1 mm, respectively. Scanning electron microscopy was used to evaluate surface topography of selected springs after 12 weeks. Based on a 1-Factor ANOVA and Dunnett's post hoc, 3M NiTi springs showed a significant decrease (p <0.01) in the unloading force at each extension following exposure to both fluoride treatments, but only after 12 weeks. The AO NiTi springs showed a significant decrease in unloading force at each extension after 12 weeks following exposure to NaF. However, with SS springs, there was no significant effect of either fluoride treatment on the SS springs at any extension or time point. SS also springs showed no significant surface topography changes, irrespective of storage conditions, which correlates with the lack of fluoride effects on SS mechanical property effects. In contrast, while there were NiTi surface topography changes (pitting and mottling) following PBS+APF exposure, those changes could not be directly linked to the observed changes in mechanical properties. Results suggest topical fluoride used with NiTi springs could potentially lead to prolonged treatment time due to decreased unloading properties. However, topical fluoride used with SS springs should not affect treatment duration.

Single-walled carbon nanotubes based chemiresistive genosensor for label-free detection of human rheumatic heart disease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Swati; Kumar, Ashok, E-mail: rajesh-csir@yahoo.com, E-mail: ashokigib@rediffmail.com; Academy of Scientific and Innovative Research

A specific and ultrasensitive, label free single-walled carbon nanotubes (SWNTs) based chemiresistive genosensor was fabricated for the early detection of Streptococcus pyogenes infection in human causing rheumatic heart disease. The mga gene of S. pyogenes specific 24 mer ssDNA probe was covalently immobilized on SWNT through a molecular bilinker, 1-pyrenemethylamine, using carbodiimide coupling reaction. The sensor was characterized by the current-voltage (I-V) characteristic curve and scanning electron microscopy. The sensing performance of the sensor was studied with respect to changes in conductance in SWNT channel based on hybridization of the target S. pyogenes single stranded genomic DNA (ssG-DNA) to itsmore » complementary 24 mer ssDNA probe. The sensor shows negligible response to non-complementary Staphylococcus aureus ssG-DNA, confirming the specificity of the sensor only with S. pyogenes. The genosensor exhibited a linear response to S. pyogenes G-DNA from 1 to1000 ng ml{sup −1} with a limit of detection of 0.16 ng ml{sup −1}.« less

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.

PubMed

Kouno, Takahide; Silvas, Tania V; Hilbert, Brendan J; Shandilya, Shivender M D; Bohn, Markus F; Kelch, Brian A; Royer, William E; Somasundaran, Mohan; Kurt Yilmaz, Nese; Matsuo, Hiroshi; Schiffer, Celia A

2017-04-28

Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 Å. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A-ssDNA complex defines the 5'-3' directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics.

Space station utilization and commonality

NASA Technical Reports Server (NTRS)

Butler, John

1986-01-01

Several potential ways of utilizing the space station, including utilization of learning experiences (such as operations), utilization of specific elements of hardware which can be largely common between the SS and Mars programs, and utilization of the on-orbit SS for transportation node functions were identified and discussed. The probability of using the SS in all of these areas seems very good. Three different ways are discussed of utilizing the then existing Low Earth Orbit (LEO) SS for operational support during assembly and checkout of the Mars Space Vehicle (SV): attaching the SV to the SS; allowing the SV to co-orbit near the SS; and a hybrid of the first 2 ways. Discussion of each of these approaches is provided, and the conclusion is reached that either the co-orbiting or hybrid approach might be preferable. Artists' conception of the modes are provided, and sketches of an assembly system concept (truss structure and subsystems derivable from the SS) which could be used for co-orbiting on-orbit assembly support are provided.

Discovery of Plant Phenolic Compounds That Act as Type III Secretion System Inhibitors or Inducers of the Fire Blight Pathogen, Erwinia amylovora

PubMed Central

Khokhani, Devanshi; Zhang, Chengfang; Li, Yan; Wang, Qi; Zeng, Quan; Yamazaki, Akihiro; Hutchins, William; Zhou, Shan-Shan

2013-01-01

Erwinia amylovora causes a devastating disease called fire blight in rosaceous plants. The type III secretion system (T3SS) is one of the important virulence factors utilized by E. amylovora in order to successfully infect its hosts. By using a green fluorescent protein (GFP) reporter construct combined with a high-throughput flow cytometry assay, a library of phenolic compounds and their derivatives was studied for their ability to alter the expression of the T3SS. Based on the effectiveness of the compounds on the expression of the T3SS pilus, the T3SS inhibitors 4-methoxy-cinnamic acid (TMCA) and benzoic acid (BA) and one T3SS inducer, trans-2-(4-hydroxyphenyl)-ethenylsulfonate (EHPES), were chosen for further study. Both the T3SS inhibitors (TMCA and BA) and the T3SS inducer (EHPES) were found to alter the expression of T3SS through the HrpS-HrpL pathway. Additionally, TMCA altered T3SS expression through the rsmBEa-RsmAEa system. Finally, we found that TMCA and BA weakened the hypersensitive response (HR) in tobacco by suppressing the T3SS of E. amylovora. In our study, we identified phenolic compounds that specifically targeted the T3SS. The T3SS inhibitor may offer an alternative approach to antimicrobial therapy by targeting virulence factors of bacterial pathogens. PMID:23770912

Discovery of plant phenolic compounds that act as type III secretion system inhibitors or inducers of the fire blight pathogen, Erwinia amylovora.

PubMed

Khokhani, Devanshi; Zhang, Chengfang; Li, Yan; Wang, Qi; Zeng, Quan; Yamazaki, Akihiro; Hutchins, William; Zhou, Shan-Shan; Chen, Xin; Yang, Ching-Hong

2013-09-01

Erwinia amylovora causes a devastating disease called fire blight in rosaceous plants. The type III secretion system (T3SS) is one of the important virulence factors utilized by E. amylovora in order to successfully infect its hosts. By using a green fluorescent protein (GFP) reporter construct combined with a high-throughput flow cytometry assay, a library of phenolic compounds and their derivatives was studied for their ability to alter the expression of the T3SS. Based on the effectiveness of the compounds on the expression of the T3SS pilus, the T3SS inhibitors 4-methoxy-cinnamic acid (TMCA) and benzoic acid (BA) and one T3SS inducer, trans-2-(4-hydroxyphenyl)-ethenylsulfonate (EHPES), were chosen for further study. Both the T3SS inhibitors (TMCA and BA) and the T3SS inducer (EHPES) were found to alter the expression of T3SS through the HrpS-HrpL pathway. Additionally, TMCA altered T3SS expression through the rsmBEa-RsmAEa system. Finally, we found that TMCA and BA weakened the hypersensitive response (HR) in tobacco by suppressing the T3SS of E. amylovora. In our study, we identified phenolic compounds that specifically targeted the T3SS. The T3SS inhibitor may offer an alternative approach to antimicrobial therapy by targeting virulence factors of bacterial pathogens.

alpha(4)beta(7) independent pathway for CD8(+) T cell-mediated intestinal immunity to rotavirus.

PubMed

Kuklin, N A; Rott, L; Darling, J; Campbell, J J; Franco, M; Feng, N; Müller, W; Wagner, N; Altman, J; Butcher, E C; Greenberg, H B

2000-12-01

Rotavirus (RV), which replicates exclusively in cells of the small intestine, is the most important cause of severe diarrhea in young children worldwide. Using a mouse model, we show that expression of the intestinal homing integrin alpha(4)ss(7) is not essential for CD8(+) T cells to migrate to the intestine or provide immunity to RV. Mice deficient in ss7 expression (ss7(-/-)) and unable to express alpha(4)ss(7) integrin were found to clear RV as quickly as wild-type (wt) animals. Depletion of CD8(+) T cells in ss7(-/-) animals prolonged viral shedding, and transfer of immune ss7(-/-) CD8(+) T cells into chronically infected Rag-2-deficient mice resolved RV infection as efficiently as wt CD8(+) T cells. Paradoxically, alpha(4)ss(7)(hi) memory CD8(+) T cells purified from wt mice that had been orally immunized cleared RV more efficiently than alpha(4)ss(7)(low) CD8(+) T cells. We explained this apparent contradiction by demonstrating that expression of alpha(4)ss(7) on effector CD8(+) T cells depends upon the site of initial antigen exposure: oral immunization generates RV-specific CD8(+) T cells primarily of an alpha(4)ss(7)(hi) phenotype, but subcutaneous immunization yields both alpha(4)ss(7)(hi) and alpha(4)ss(7)(low) immune CD8(+) T cells with anti-RV effector capabilities. Thus, alpha(4)ss(7) facilitates normal intestinal immune trafficking to the gut, but it is not required for effective CD8(+) T cell immunity.

Beyond solicitousness: a comprehensive review on informal pain-related social support.

PubMed

Bernardes, Sónia F; Forgeron, Paula; Fournier, Karine; Reszel, Jessica

2017-11-01

Adults with chronic pain cite social support (SS) as an important resource. Research has mostly focused on general SS or pain-specific solicitousness, resulting in a limited understanding of the role of SS in pain experiences. Drawing on SS theoretical models, this review aimed to understand how pain-related SS has been conceptualized and measured and how its relationship with pain experiences has been investigated. Arksey and O'Malley scoping review framework guided the study. A database search (2000-2015) was conducted in PsycINFO, CINAHL, MEDLINE, and EMBASE using a combination of subject headings/keywords on pain and SS; 3864 citations were screened; 101 full texts were assessed for eligibility; references of 52 papers were hand searched. Fifty-three studies were included. Most studies were either a-theoretical or drew upon the operant conditioning model. There are several self-report measures and observational systems to operationalize pain-related SS. However, the Multidimensional Pain Inventory remains the most often used, accounting for the centrality of the concept of solicitousness in the literature. Most studies focused on individuals with chronic pain self-report of spousal pain-related SS and investigated its main effects on pain outcomes. Only a minority investigated the role of pain SS within the stress and coping process (as a buffer or mediator). Little is known about mediating pathways, contextual modulation of the effectiveness of SS exchanges, and there are practically no SS-based intervention studies. Drawing on general SS models, the main gaps in pain-related SS research are discussed and research directions for moving this literature beyond solicitousness are proposed.

[How has social status been measured in health research? A review of the international literature].

PubMed

Cabieses, Báltica; Zitko, Pedro; Pinedo, Rafael; Espinoza, Manuel; Albor, Christo

2011-06-01

Social status (SS) is a multidimensional variable that is used widely in health research. There is no single optimal method for estimating social status. Rather, in each case the measurement may vary depending on the research subject, the base theory considered, the population of interest, the event of interest and, in some cases, the available information. This literature review develops the following topics related to SS measurement, based on the international scientific sources available electronically: i) identification of the role of SS in the context of social epidemiology research, ii) description of the principal indicators and methodological approaches used to measure SS in health research, and iii) analysis of the distinct difficulties of SS measurement in specific populations such as ethnic groups, women, children, the elderly, and in rural vs. urban contexts. The review finally makes it possible to describe some of the implications of SS measurement in Latin American countries.

AtlasT4SS: a curated database for type IV secretion systems.

PubMed

Souza, Rangel C; del Rosario Quispe Saji, Guadalupe; Costa, Maiana O C; Netto, Diogo S; Lima, Nicholas C B; Klein, Cecília C; Vasconcelos, Ana Tereza R; Nicolás, Marisa F

2012-08-09

The type IV secretion system (T4SS) can be classified as a large family of macromolecule transporter systems, divided into three recognized sub-families, according to the well-known functions. The major sub-family is the conjugation system, which allows transfer of genetic material, such as a nucleoprotein, via cell contact among bacteria. Also, the conjugation system can transfer genetic material from bacteria to eukaryotic cells; such is the case with the T-DNA transfer of Agrobacterium tumefaciens to host plant cells. The system of effector protein transport constitutes the second sub-family, and the third one corresponds to the DNA uptake/release system. Genome analyses have revealed numerous T4SS in Bacteria and Archaea. The purpose of this work was to organize, classify, and integrate the T4SS data into a single database, called AtlasT4SS - the first public database devoted exclusively to this prokaryotic secretion system. The AtlasT4SS is a manual curated database that describes a large number of proteins related to the type IV secretion system reported so far in Gram-negative and Gram-positive bacteria, as well as in Archaea. The database was created using the RDBMS MySQL and the Catalyst Framework based in the Perl programming language and using the Model-View-Controller (MVC) design pattern for Web. The current version holds a comprehensive collection of 1,617 T4SS proteins from 58 Bacteria (49 Gram-negative and 9 Gram-Positive), one Archaea and 11 plasmids. By applying the bi-directional best hit (BBH) relationship in pairwise genome comparison, it was possible to obtain a core set of 134 clusters of orthologous genes encoding T4SS proteins. In our database we present one way of classifying orthologous groups of T4SSs in a hierarchical classification scheme with three levels. The first level comprises four classes that are based on the organization of genetic determinants, shared homologies, and evolutionary relationships: (i) F-T4SS, (ii) P-T4SS, (iii) I-T4SS, and (iv) GI-T4SS. The second level designates a specific well-known protein families otherwise an uncharacterized protein family. Finally, in the third level, each protein of an ortholog cluster is classified according to its involvement in a specific cellular process. AtlasT4SS database is open access and is available at http://www.t4ss.lncc.br.

Usefulness of layer-specific strain for identifying complex CAD and predicting the severity of coronary lesions in patients with non-ST-segment elevation acute coronary syndrome: Compared with Syntax score.

PubMed

Zhang, Li; Wu, Wei-Chun; Ma, Hong; Wang, Hao

2016-11-15

Layer-specific strain allows the assessment of the function of every layer of myocardium. To evaluate the changes of non-ST-segment elevation acute coronary syndrome(NSTE-ACS) patients with and without complex coronary artery disease(CAD) by layer-specific strain and determine if myocardial strain can identify complex CAD and assess the severity of coronary lesions as defined by Syntax score (SS). A total of 139 patients undergoing coronary angiography due to suspected NSTE-ACS were prospectively enrolled. Echocardiography was performed 1h before angiography. Global longitudinal strain (GLS), territorial longitudinal strain (TLS), global circumferential strain (GCS) and territorial circumferential strain (TCS) of the three layers of LV wall were assessed by two-dimensional (2D) speckle tracking echocardiography (STE) with layer-specific myocardial deformation quantitative analysis based on the perfusion territories of the three major coronary arteries in an 18-segment model of LV. SS was used for predicting the severity of coronary lesions in patients with complex CAD. 78 had complex CAD, 32 had 1- or 2-vessel disease and 29 had no significant coronary stenosis confirmed by coronary angiography. According to SS value, 78 complex CAD subjects were subdivided into three groups, 24 in group SS 1 (SS≤22), 26 in group SS 2 (SS 23-32) and 28 in group SS 3 (SS≥33). Compared to the other two groups without complex CAD, patients with NSTE-ACS due to complex CAD had worse function in all 3 myocardial layers assessed by GLS, TLS, GCS and TCS. Endocardial GLS and TLS (all, P<0.01) were most affected. The absolute differences between endocardial and epicardial GLS and TLS were lower in magnitude in patients with complex CAD than in those without (all, P<0.001), and the more complex of coronary lesion, the lower magnitude of the parameters(all, P<0.001). Endocardial GLS and TLS were closely correlated with SS value(r=-0.751 and r=-0.753, respectively; P<0.001). By receiver-operating characteristic curve analysis, endocardial GLS and TLS demonstrated the highest area under curve, showing better diagnostic accuracy (endocardial GLS: value<-21.35% had 72% sensitivity, 84% specificity and area under the curve ¼0.846; endocardial TLS: value<-20.15% had 72% sensitivity, 88% specificity and area under the curve ¼0.852) than GCS, TCS, mid-myocardial and epicardial GLS, and TLS(all, P<0.05). Strains, particularly endocardial GLS and TLS measurement by 2DSTE might enable a non-invasive method to identify complex CAD and predict the severity of coronary lesions in patients with NSTE-ACS. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A new source of resistance to 2-furaldehyde from Scheffersomyces (Pichia) stipitis for sustainable lignocellulose-to-biofuel conversion.

PubMed

Wang, Xu; Lewis Liu, Z; Zhang, Xiaoping; Ma, Menggen

2017-06-01

Aldehyde inhibitory compounds derived from lignocellulosic biomass pretreatment have been identified as a major class of toxic chemicals that interfere with microbial growth and subsequent fermentation for advanced biofuel production. Development of robust next-generation biocatalyst is a key for a low-cost biofuel production industry. Scheffersomyces (Pichia) stipitis is a naturally occurring C-5 sugar utilization yeast; however, little is known about the genetic background underlying its potential tolerance to biomass conversion inhibitors. We investigated and identified five uncharacterized putative aryl-alcohol dehydrogenase genes (SsAADs) from this yeast as a new source of resistance against biomass fermentation inhibitor 2-furaldehyde (furfural) by gene expression, gene cloning, and direct enzyme assay analysis using partially purified proteins. All five proteins from S. stipitis showed furfural reduction using cofactor NADH. An optimum active temperature was observed at 40 °C for SsAad1p; 30 °C for SsAad3p, SsAad4p, and SsAad5p; and 20 °C for SsAad2p. SsAad2p, SsAad3p, and SsAad4p showed tolerance to a wide range of pH from 4.5 to 8, but SsAad1p and SsAad5p were sensitive to pH changes beyond 7. Genes SsAAD2, SsAAD3, and SsAAD4 displayed significantly enhanced higher levels of expression in response to the challenge of furfural. Their encoding proteins also showed higher levels of specific activity toward furfural and were suggested as core functional enzymes contributing aldehyde resistance in S. stipitis.

Is extra-glandular organ damage in primary Sjögren's syndrome related to the presence of systemic auto-antibodies and/or hypergammaglobulinemia? A long-term cohort study with 110 patients from the Netherlands.

PubMed

Ter Borg, Evert-Jan; Kelder, Johannes Cornelis

2017-07-01

To test the hypothesis that systemic auto-antibodies or hypergammaglobulinemia are related to the prevalence of extra-glandular tissue organ damage (EGOD) in primary Sjögren's syndrome (SS). A real practice-based investigation of a relatively large (n = 110) Dutch cohort of primary SS patients systematically followed up in a large non-academic hospital. After a follow up of mean 8.2 years a significant correlation was found between disease duration and the prevalence of EGOD. We did not observe a relationship between the total number or type of systemic auto-antibodies or hypergammaglobulinemia and the total number of EGOD. However, there was a correlation between the prevalence of polyneuropathy (PNP) and antinuclear antibodies (ANA) as well as anti-Ro/SS-A positivity and there was an inverse relationship between the presence of anti-Ro/SS-A antibodies and primary biliary cirrhosis (PBC). All PBC cases were anti-Ro/SS-A and anti-La/SS-B negative but ANA positive. There was a trend for a higher occurrence of pleuro-pulmonary disease in the ANA negative cases. Although we did not find a relationship between the total number or type of systemic auto-antibodies and the total number of EGOD, there were correlations between specific systemic auto-antibodies and specific types of EGOD. The presence of ANA and anti-Ro/SS-A was associated with the occurrence of PNP, as well as was the absence of anti-Ro/SS-A with PBC. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

Spleen Stiffness Is Superior to Liver Stiffness for Predicting Esophageal Varices in Chronic Liver Disease: A Meta-Analysis.

PubMed

Ma, Xiaowen; Wang, Le; Wu, Hao; Feng, Yuemin; Han, Xibiao; Bu, Haoran; Zhu, Qiang

2016-01-01

Liver stiffness (LS) and spleen stiffness (SS) are two most widely accessible non-invasive parameters for predicting esophageal varices (EV), but the reported accuracy of the two predictors have been inconsistent across studies. This meta-analysis aims to evaluate the diagnostic performance of LS and SS measurement for detecting EV in patients with chronic liver disease (CLD), and compare their accuracy. Pubmed/Medline, Embase, Cochrane Library and Ovid were searched for all studies assessing SS and LS simultaneously in EV diagnosis. A total of 16 studies including 1892 patients were included in this meta-analysis, and the pooled statistical parameters were calculated using the bivariate mixed effects models. In detection of any EV, for LS measurement, the summary sensitivity was 0.83 (95% confidence interval [CI]: 0.78-0.87), and the specificity was 0.66 (95% CI: 0.60-0.72). While for SS measurement, the pooled sensitivity and specificity was 0.88 (95% CI: 0.83-0.92) and 0.78 (95% CI: 0.73-0.83). The summary receiver operating characteristic (SROC) curve values of LS and SS were 0.81 (95% CI: 0.77-0.84) and 0.88 (95% CI: 0.85-0.91) respectively, and the results had statistical significance (P<0.01). The diagnostic odds ratio (DOR) of SS (25.73) was significantly higher than that of LS (9.54), with the relative DOR value was 2.48 (95%CI: 1.10-5.60), P<0.05. Under current techniques, SS is significantly superior to LS for identifying the presence of EV in patients with CLD. SS measurement may help to select patients for endoscopic screening.

Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production.

PubMed

Kick, Benjamin; Hensler, Samantha; Praetorius, Florian; Dietz, Hendrik; Weuster-Botz, Dirk

2017-04-01

The bacteriophage M13 has found frequent applications in nanobiotechnology due to its chemically and genetically tunable protein surface and its ability to self-assemble into colloidal membranes. Additionally, its single-stranded (ss) genome is commonly used as scaffold for DNA origami. Despite the manifold uses of M13, upstream production methods for phage and scaffold ssDNA are underexamined with respect to future industrial usage. Here, the high-cell-density phage production with Escherichia coli as host organism was studied in respect of medium composition, infection time, multiplicity of infection, and specific growth rate. The specific growth rate and the multiplicity of infection were identified as the crucial state variables that influence phage amplification rate on one hand and the concentration of produced ssDNA on the other hand. Using a growth rate of 0.15 h -1 and a multiplicity of infection of 0.05 pfu cfu -1 in the fed-batch production process, the concentration of pure isolated M13 ssDNA usable for scaffolded DNA origami could be enhanced by 54% to 590 mg L -1 . Thus, our results help enabling M13 production for industrial uses in nanobiotechnology. Biotechnol. Bioeng. 2017;114: 777-784. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Interactions between integrin receptors and fibronectin are required for calvarial osteoblast differentiation in vitro

NASA Technical Reports Server (NTRS)

Moursi, A. M.; Globus, R. K.; Damsky, C. H.

1997-01-01

We previously showed that anti-fibronectin antibodies or soluble fibronectin fragments containing the central cell-binding domain inhibit formation of mineralized nodules by fetal calvarial osteoblasts in vitro. These findings suggest a critical role for fibronectin in osteoblast differentiation and morphogenesis. In this study we tested the hypothesis that fibronectin's effects on osteogenesis are mediated via direct interactions with integrin receptors for fibronectin on osteoblasts. Immunocytochemical analysis identified the integrin fibronectin receptor alpha5ss1 in fetal rat calvarial tissue and in cultured osteoblasts at all stages of differentiation. Three other integrins, alpha3ss1, alpha8ss1 and alphavss3, which can bind fibronectin, as well as other matrix components, were also identified in tissue and at all stages of cell culture. Immunoprecipitation data showed that alpha5ss1 levels are constant throughout osteoblast differentiation whereas levels of alpha3ss1 and alpha8ss1 decline in mature mineralized cultures. To determine whether integrin fibronectin receptors are required for osteoblast formation of mineralized nodules, we examined the extent of nodule formation in the presence and absence of function-perturbing anti-integrin antibodies. The antibodies were present continuously in cultures beginning at confluence (day 3), and nodule formation was measured at days 10 and 20. An anti-alpha5 integrin subunit antibody reduced nodule formation to less than 5% of control values at both time points. Inhibition of nodule formation was reversible and did not affect cell attachment and viability. Function-perturbing antibodies against alpha3ss1 and alpha8ss1 also reduced nodule formation, to less than 20% of control values. In contrast, function-perturbing antibodies to alphavss3 and alphavss5 did not affect nodule formation, indicating that the inhibitions noted were indeed specific. To determine the effect of antibody treatment on gene expression, steady-state mRNA expression was examined and found to be suppressed for osteoblast markers alkaline phosphatase and osteocalcin. Together, these results indicate that direct osteoblast interactions with the extracellular matrix are mediated by a select group of integrin receptors that includes alpha5ss1, alpha3ss1 and alpha8ss1. We further conclude that the specific alpha5ss1 fibronectin receptor mediates critical interactions between osteoblasts and fibronectin required for both bone morphogenesis and osteoblast differentiation.

Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications

PubMed Central

Hong, Ka Lok

2015-01-01

Molecular recognition elements (MREs) can be short sequences of single-stranded DNA, RNA, small peptides, or antibody fragments. They can bind to user-defined targets with high affinity and specificity. There has been an increasing interest in the identification and application of nucleic acid molecular recognition elements, commonly known as aptamers, since they were first described in 1990 by the Gold and Szostak laboratories. A large number of target specific nucleic acids MREs and their applications are currently in the literature. This review first describes the general methodologies used in identifying single-stranded DNA (ssDNA) aptamers. It then summarizes advancements in the identification and biosensing application of ssDNA aptamers specific for bacteria, viruses, their associated molecules, and selected chemical toxins. Lastly, an overview of the basic principles of ssDNA aptamer-based biosensors is discussed. PMID:26199940

Modeling the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands.

PubMed

Salter, Jason D; Smith, Harold C

2018-05-23

The 11-member APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like) family of zinc-dependent cytidine deaminases bind to RNA and single-stranded DNA (ssDNA) and, in specific contexts, modify select (deoxy)cytidines to (deoxy)uridines. In this review, we describe advances made through high-resolution co-crystal structures of APOBECs bound to mono- or oligonucleotides that reveal potential substrate-specific binding sites at the active site and non-sequence-specific nucleic acid binding sites distal to the active site. We also discuss the effect of APOBEC oligomerization on functionality. Future structural studies will need to address how ssDNA binding away from the active site may enhance catalysis and the mechanism by which RNA binding may modulate catalytic activity on ssDNA. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Analysis and Design of Crew Sleep Station for ISS

NASA Technical Reports Server (NTRS)

Keener, John F.; Paul, Thomas; Eckhardt, Bradley; Smith, Fredrick

2002-01-01

This paper details the analysis and design of the Temporary Sleep Station (TeSS) environmental control system for International Space Station (ISS). The TeSS will provide crewmembers with a private and personal space, to accommodate sleeping, donning and doffing of clothing, personal communication and performance of recreational activities. The need for privacy to accommodate these activities requires adequate ventilation inside the TeSS. This study considers whether temperature, carbon dioxide, and humidity within the TeSS remain within crew comfort and safety levels for various expected operating scenarios. Evaluation of these scenarios required the use and integration of various simulation codes. An approach was adapted for this study, whereby results from a particular code were integrated with other codes when necessary. Computational Fluid Dynamics (CFD) methods were used to evaluate the flow field inside the TeSS, from which local gradients for temperature, velocity, and species concentration such as CO (sub 2) could be determined. A model of the TeSS, containing a human, as well as equipment such as a laptop computer, was developed in FLUENT, a finite-volume code. Other factors, such as detailed analysis of the heat transfer through the structure, radiation, and air circulation from the TeSS to the US Laboratory Aisle, where the TeSS is housed, were considered in the model. A complementary model was developed in G189A, a code which has been used by NASA/JSC for environmental control systems analyses since the Apollo program. Boundary conditions were exchanged between the FLUENT and G189A TeSS models. G189A provides human respiration rates to the FLUENT model, while the FLUENT model provides local convective heat transfer coefficients to G189A model. An additional benefit from using an approach with both a systems simulation and CFD model, is the capability to verify the results of each model by comparison to the results of the other model. The G189A and FLUENT models were used to evaluate various ventilation designs for the TeSS over a range of operating conditions with varying crew metabolic load, equipment operating modes, ventilation flow rates, and with the TeSS doors open and closed. Results from the study were instrumental in the optimization of a design for the TeSS ventilation hardware. A special case was considered where failure of the TeSS ventilation system occurred. In this case, a study was conducted in order to determine the time required for the CO (sub 2) concentration inside the TeSS to increase to ISS limit values under transient conditions. A lumped-capacitance code, SINDA-FLUINT was used in this case to provide accurate predictions of the human reaction to the TeSS cabin conditions including core and skin temperatures and body heat storage. A simple two-dimensional CFD model of a crewmember inside the TeSS was developed in FLUENT in order to determine the volume envelope of the respired air from the human, which maintained a minimum velocity profile. This volume was then used in the SINDA-FLUINT model to facilitate the calculations of CO (sub 2) concentrations, dry bulb temperatures and humidity levels inside the TeSS.

Profile of lower urinary tract symptoms in the male and their impact on quality of life.

PubMed

Cambronero, J; Arlandis, S; Errando, C; Mora, A M

2013-01-01

Following current European Guidelines, Lower Urinary Tract Symptoms (LUTS) are produced by several causes and, thus, thorough clinical assessment should be undertaken for a correct therapeutic management. This study was conducted in order to assess the symptoms profile and their impact on Health-Related Quality of Life (HRQL) of male patients attending urology outpatient clinics. Epidemiological, cross-sectional study including adult male patients (n=826) presenting with at least one de novo previously untreated LUTS. Socio-demographic and clinical variables were collected. Patients completed IPSS, Bladder Control Self-Assessment Questionnaire (B-SAQ) and SF-12 questionnaires. Mean age (SD) was 65 (10) years. A combination of storage, voiding and post-micturition symptoms were present in 69% of subjects and 30% showed >2 urgency episodes and >6 micturitions daily (storage symptoms -SS- sub-population). Storage symptoms were the reason for consultation in 86%. Mean peak urinary flow (Q(max)) was 11.4 mL/s, in 44% of patients,prostate volume was 20-40 mL and 91% showed moderate or severe symptoms on IPSS with an overall mean (SD) score of 17 (7). SS sub-population had higher B-SAQ scores (6,9 vs 4,8 for symptoms; 7,8 vs 5,1 for bother), and worse HRQL (IPSS item 8). These findings support the importance of addressing treatment adequately according to patient profile, bothersomeness and impact on HRQL. Copyright © 2012 AEU. Published by Elsevier Espana. All rights reserved.

Soil Microbial Functional and Fungal Diversity as Influenced by Municipal Sewage Sludge Accumulation

PubMed Central

Frąc, Magdalena; Oszust, Karolina; Lipiec, Jerzy; Jezierska-Tys, Stefania; Nwaichi, Eucharia Oluchi

2014-01-01

Safe disposal of municipal sewage sludge is a challenging global environmental concern. The aim of this study was to assess the response of soil microbial functional diversity to the accumulation of municipal sewage sludge during landfill storage. Soil samples of a municipal sewage sludge (SS) and from a sewage sludge landfill that was 3 m from a SS landfill (SS3) were analyzed relative to an undisturbed reference soil. Biolog EcoPlatesTM were inoculated with a soil suspension, and the Average Well Color Development (AWCD), Richness (R) and Shannon-Weaver index (H) were calculated to interpret the results. The fungi isolated from the sewage sludge were identified using comparative rDNA sequencing of the LSU D2 region. The MicroSEQ® ID software was used to assess the raw sequence files, perform sequence matching to the MicroSEQ® ID-validated reference database and create Neighbor-Joining trees. Moreover, the genera of fungi isolated from the soil were identified using microscopic methods. Municipal sewage sludge can serve as a habitat for plant pathogens and as a source of pathogen strains for biotechnological applications. PMID:25170681

Soil microbial functional and fungal diversity as influenced by municipal sewage sludge accumulation.

PubMed

Frąc, Magdalena; Oszust, Karolina; Lipiec, Jerzy; Jezierska-Tys, Stefania; Nwaichi, Eucharia Oluchi

2014-08-28

Safe disposal of municipal sewage sludge is a challenging global environmental concern. The aim of this study was to assess the response of soil microbial functional diversity to the accumulation of municipal sewage sludge during landfill storage. Soil samples of a municipal sewage sludge (SS) and from a sewage sludge landfill that was 3 m from a SS landfill (SS3) were analyzed relative to an undisturbed reference soil. Biolog EcoPlatesTM were inoculated with a soil suspension, and the Average Well Color Development (AWCD), Richness (R) and Shannon-Weaver index (H) were calculated to interpret the results. The fungi isolated from the sewage sludge were identified using comparative rDNA sequencing of the LSU D2 region. The MicroSEQ® ID software was used to assess the raw sequence files, perform sequence matching to the MicroSEQ® ID-validated reference database and create Neighbor-Joining trees. Moreover, the genera of fungi isolated from the soil were identified using microscopic methods. Municipal sewage sludge can serve as a habitat for plant pathogens and as a source of pathogen strains for biotechnological applications.

Receptor binding of somatostatin-14 and somatostatin-28 in rat brain: differential modulation by nucleotides and ions.

PubMed

Srikant, C B; Dahan, A; Craig, C

1990-02-04

The tissue-selective binding of the two principal bioactive forms of somatostatin, somatostatin-14 (SS-14) and somatostatin-28 (SS-28), their ability to modulate cAMP-dependent and -independent regulation of post-receptor events to different degrees and the documentation of specific labelling of SS receptor subtypes with SS-28 but not SS-14 in discrete regions of rat brain suggest the existence of distinct SS-14 and SS-28 binding sites. Receptor binding of SS-14 ligands has been shown to be modulated by nucleotides and ions, but the effect of these agents on SS-28 binding has not been studied. In the present study we investigated the effects of adenine and guanine nucleotides as well as monovalent and divalent cations on rat brain SS receptors quantitated with radioiodinated analogs of SS-14 ([125I-Tyr11]SS14, referred to in this paper as SS-14) and SS-28 ([Leu8, D-Trp22, 125I-Tyr25] SS-28, referred to as LTT* SS-28) in order to determine if distinct receptor sites for SS-14 and SS-28 could be distinguished on the basis of their modulation by nucleotides and ions. GTP as well as ATP exerted a dose-dependent inhibition (over a concentration range of 10(-7)-10(-3) M) of the binding of the two radioligands. The nucleotide inhibition of binding resulted in a decrease the Bmax of the SS receptors, the binding affinity remaining unaltered. GTP (10(-4) M) decreased the Bmax of LTT* SS-28 binding sites to a greater extent than ATP (145 +/- 10 and 228 +/- 16 respectively, compared to control value of 320 +/- 20 pmol mg-1). Under identical conditions GTP was less effective than ATP in reducing the number of T* SS-14 binding sites (Bmax = 227 +/- 8 and 182 +/- 15, respectively, compared to 340 +/- 15 pmol mg-1 in the absence of nucleotides). Monovalent cations inhibited the binding of both radioligands, Li+ and Na+ inhibited the binding of T* SS-14 to a greater extent than K+. The effect of divalent cations on the other hand was varied. At low concentration (2 mM) Mg2+, Ba2+, Mn2+, Ca2+ and Co2+ augmented the binding of both T* SS-14 and LTT* SS-28, while higher than 4 mM Co2+ inhibited binding of both ligands. LTT* SS-28 binding was reduced in the presence of high concentrations of Ba2+ and Mn2+ also. Interestingly Ca2+ at higher than 10 mM preferentially inhibited LTT* SS-28 binding and increased the affinity of SS-14 but not SS-28 for LTT* SS-28 binding sites.(ABSTRACT TRUNCATED AT 400 WORDS)

Molecular Analysis of the Human Autoantibody Response to α-Fodrin in Sjögren’s Syndrome Reveals Novel Apoptosis-Induced Specificity

PubMed Central

Maruyama, Toshiaki; Saito, Ichiro; Hayashi, Yoshio; Kompfner, Elizabeth; Fox, Robert I.; Burton, Dennis R.; Ditzel, Henrik J.

2004-01-01

Lymphocyte infiltration of salivary and lacrimal glands leading to diminished secretion and gland destruction as a result of apoptosis is thought to be pivotal in the pathogenesis of Sjögren’s syndrome (SS). The cytoskeletal protein α-fodrin is cleaved during this apoptotic process, and a strong antibody (Ab) response is elicited to a 120-kd fragment of cleaved α-fodrin in the majority of SS patients, but generally not in other diseases in which apoptosis also occurs. Little is known about the anti-α-fodrin autoantibody response on a molecular level. To address this issue, IgG phage display libraries were generated from the bone marrow of two SS donors and a panel of anti-α-fodrin IgGs was isolated by selection on α-fodrin immunoblots. All of the human monoclonal Abs (hmAbs) reacted with a 150-kd fragment and not with the 120-kd fragment or intact α-fodrin, indicating that the epitope recognized became exposed after α-fodrin cleavage. Analysis of a large panel of SS patients (defined by the strict San Diego diagnostic criteria) showed that 25% of SS sera exhibited this 150-kd α-fodrin specificity. The hmAbs stained human cultured salivary acinar cells and the staining was redistributed to surface blebs during apoptosis. They also stained inflamed acinar/ductal epithelial cells in SS salivary tissue biopsies, and only partially co-localized with monoclonal Abs recognizing the full-length α-fodrin. Our study shows that in SS patients, neoepitopes on the 150-kd cleaved product of α-fodrin become exposed to the immune system, frequently eliciting anti-150-kd α-fodrin Abs in addition to the previously reported anti-120-kd Abs. The anti-150-kd α-fodrin hmAbs may serve as valuable reagents for the study of SS pathogenesis and diagnostic analyses of SS salivary gland tissue. PMID:15215161

The sequential hypothesis of sleep function. IV. A correlative analysis of sleep variables in learning and nonlearning rats.

PubMed

Langella, M; Colarieti, L; Ambrosini, M V; Giuditta, A

1992-02-01

Female adult rats were trained for a two-way active avoidance task (4 h), and allowed free sleep (3 h). Control rats (C) were left in their home cages during the acquisition period. Dural electrodes and an intraventricular cannula, implanted one week in advance, were used for EEG recording during the period of sleep and for the injection of [3H]thymidine at the beginning of the training session, respectively. Rats were killed at the end of the sleep period, and the DNA-specific activity was determined in the main brain regions and in liver. Correlations among sleep, behavioral and biochemical variables were assessed using Spearman's nonparametric method. In learning rats (L), the number of avoidances was negatively correlated with SS-W variables, and positively correlated with SS-PS variables (episodes of synchronized sleep followed by wakefulness or paradoxical sleep, respectively) and with PS variables. An inverse pattern of correlations was shown by the number of escapes or freezings. No correlations occurred in rats unable to achieve the learning criterion (NL). In L rats, the specific activity of brain DNA was negatively correlated with SS-W variables and positively correlated with SS-PS variables, while essentially no correlation concerned PS variables. On the other hand, in NL rats, comparable correlations were positive with SS-W variables and negative with SS-PS and PS variables. Few and weak correlations occurred in C rats. The data support a role of SS in brain information processing, as postulated by the sequential hypothesis on the function of sleep. In addition, they suggest that the elimination of nonadaptive memory traces may require several SS-W episodes and a terminal SS-PS episode. During PS episodes, adaptive memory traces cleared of nonadaptive components may be copied in more suitable brain sites.

Anti-calponin-3 autoantibodies: a new specificity in patients with Sjögren's syndrome.

PubMed

Birnbaum, Julius; Hoke, Ahmet; Lalji, Aliya; Calabresi, Peter; Bhargava, Pavan; Casciola-Rosen, Livia

2018-05-11

Autoantibodies are clinically useful for phenotyping patients across the spectrum of autoimmune rheumatic diseases. Using serum from a patient with Sjögren's Syndrome (SS), we detected a new specificity by immunoblotting. The purpose of this study was to identify this autoantibody and to evaluate its disease specificity. A prominent 40 kDa band was detected when immunoblots were performed using a SS patient serum and lysate from rat dorsal root ganglia (DRG). Using two-dimensional gel electrophoresis and liquid chromatography tandem mass spectrometry peptide sequencing, the autoantigen was identified as calponin-3. Anti-calponin-3 antibodies were assayed by ELISA using sera from patients with primary SS (n=209), systemic lupus erythematosus (SLE, n=138), myositis (n=138), multiple sclerosis (MS, n=44) and healthy controls (n=46). Expression of calponin-3 was assessed by immunohistochemistry. These studies identified calponin-3 as a new autoantigen. Anti-calponin-3 antibodies were detected in 23/209 (11.0%) SS patients, 12/138 (8.7%) SLE patients, 7/138 (5.1%) myositis patients, 3/44 (6.8%) MS patients, and 1/46 (2.2%) healthy controls. Amongst SS patients, the frequency of anti-calponin-3 antibodies was highest in those with neuropathies (7/39, 17.9%). In this subset, the frequency of anti-calponin-3 antibodies differed significantly from the controls (p=0.02). Calponin-3 was expressed primarily in perineuronal satellite cells but not in DRG neurons. Calponin-3 is a novel autoantigen. Antibodies against this protein are found in SS, and associate with the subset of patients experiencing neuropathies. Intriguingly, we found that calponin-3 is expressed in DRG perineuronal satellite cells, suggesting that these may be one of the targets in SS. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Biologics formulation factors affecting metal leachables from stainless steel.

PubMed

Zhou, Shuxia; Schöneich, Christian; Singh, Satish K

2011-03-01

An area of increasing concern and scientific scrutiny is the potential contamination of drug products by leachables entering the product during manufacturing and storage. These contaminants may either have a direct safety impact on the patients or act indirectly through the alteration of the physicochemical properties of the product. In the case of biotherapeutics, trace amounts of metal contaminants can arise from various sources, but mainly from contact with stainless steel (ss). The effect of the various factors, buffer species, solution fill volume per unit contact surface area, metal chelators, and pH, on metal leachables from contact with ss over time were investigated individually. Three major metal leachables, iron, chromium, and nickel, were monitored by inductively coupled plasma-mass spectrometry because they are the major components of 316L ss. Iron was primarily used to evaluate the effect of each factor since it is the most abundant. It was observed that each studied factor exhibited its own effect on metal leachables from contact with ss. The effect of buffer species and pH exhibited temperature dependence over the studied temperature range. The metal leachables decreased with the increased fill volume (mL) per unit contact ss surface area (cm(2)) but a plateau was achieved at approximately 3 mL/cm(2). Metal chelators produced the strongest effect in facilitating metal leaching. In order to minimize the metal leachables and optimize biological product stability, each formulation factor must be evaluated for its impact, to balance its risk and benefit in achieving the target drug product shelf life. © 2011 American Association of Pharmaceutical Scientists

ELISA subtypization of anti-ENA autoantibodies in clinical management of autoimmune diseases in Bosnia and Herzegovina.

PubMed

Subasic, Djemo; Karamehic, Jasenko; Gavrankapetanovic, Faris; Hodzic, Harun; Kasumovic, Mersija; Delic-Sarac, Marina; Prljaca-Zecevic, Lamija

2009-01-01

The basis of autoimmune diseases such as SLE (Systemic Lupus Eritematodes), Sjogren's syndrome, scleroderma, dermatomyositis and polymiositis is the creation of auto-antibodies to the following specific extractable nuclear antigens (ENA):Jo-1, Ssl-70, SS-A, SS-B, Sm and Sm/RNPs. Some of these antigens are in fact enzymes (Jo-1-histidil-tRNA synthetase, Scl-70-topoisomerase) which are inhibited by specific autoantibodies--this leads to disturbance in the metabolism of DNA and protein biosynthesis. During 2009, we analyzed total of 87 serum samples of patients suspected for autoimmune disorder using ANA-IFA and ELISA-ENA-6 methods. After establishing IFA-ANA positivity (83.9%), all serum specimens; ANA positive and negative, were subtypized by ELISA ENA-6 test. Analysis showed the highest incidence of anti-SS-A (56%), and incidence of anti-SS-B (29.8%), anti-Sm/ RNP (11.5%), anti-Jo-1 (2.3%) and anti-Scl-70 (1,1%) auto-antibodies. Also, 78.5% of IFA-ANA negative serum specimens showed high level of positivity (212.50 and 277.0 IU/ml) to SS-A (78.5%) and SS-B (21.4%) antigenes using ELISA-ENA-6 subtypization. Following these results, we conclude that it is necessary to introduce Western blot confirmation testing. After comparing with other clinical findings, we diagnosed the following autoimmune diseases: SLE, Sjogren's syndrome and dermatomiosytis.

Chemostat studies of bacteriophage M13 infected Escherichia coli JM109 for continuous ssDNA production.

PubMed

Kick, Benjamin; Behler, Karl Lorenz; Severin, Timm Steffen; Weuster-Botz, Dirk

2017-09-20

Steady state studies in a chemostat enable the control of microbial growth rate at defined reaction conditions. The effects of bacteriophage M13 infection on maximum growth rate of Escherichia coli JM109 were studied in parallel operated chemostats on a milliliter-scale to analyze the steady state kinetics of phage production. The bacteriophage infection led to a decrease in maximum specific growth rate of 15% from 0.74h -1 to 0.63h -1 . Under steady state conditions, a constant cell specific ssDNA formation rate of 0.15±0.004 mg ssDNA g CDW -1 h -1 was observed, which was independent of the growth rate. Using the estimated kinetic parameters for E. coli infected with bacteriophage M13, the ssDNA concentration in the steady state could be predicted as function of the dilution rate and the glucose concentration in the substrate. Scalability of milliliter-scale data was approved by steady state studies on a liter-scale at a selected dilution rate. An ssDNA space-time yield of 5.7mgL -1 h -1 was achieved with increased glucose concentration in the feed at a dilution rate of 0.3h -1 , which is comparable to established fed-batch fermentation with bacteriophage M13 for ssDNA production. Copyright © 2017 Elsevier B.V. All rights reserved.

DETECTION OF TREATMENT-NAIVE CHOROIDAL NEOVASCULARIZATION IN AGE-RELATED MACULAR DEGENERATION BY SWEPT SOURCE OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY.

PubMed

Ahmed, Daniel; Stattin, Martin; Graf, Alexandra; Forster, Julia; Glittenberg, Carl; Krebs, Ilse; Ansari-Shahrezaei, Siamak

2017-09-04

To compare the detection rate of choroidal neovascularization (CNV) in treatment-naive neovascular age-related macular degeneration by swept source optical coherence tomography angiography (SS-OCTA, Topcon's DRI Triton) working at 1,050 nm wavelength versus fluorescence angiography. Cross-sectional analysis of 156 eyes (107 neovascular age-related macular degeneration and 49 dry AMD) in 98 patients, previously diagnosed by multimodal imaging using fluorescein (FA) and indocyanine green angiography (Heidelberg's Spectralis) in a tertiary retina center, evaluated by SS-OCTA 4.5 mm × 4.5 mm and 6 mm × 6 mm macular cubes. Main outcome measures were sensitivity and specificity of SS-OCTA in AMD. Potential factors influencing CNV detection rate were analyzed. Swept source optical coherence tomography angiography detected CNV in 81 of 107 eyes, resulting in a sensitivity of 75.7%. In 49 eyes with dry AMD, no CNV could be identified (specificity 100%). A statistical significance was calculated for nondetection of treatment-naive CNV by SS-OCTA in pigment epithelial detachment over 400 μm (P = 0.0238). Topcon's SS-OCTA was not able to detect all CNV lesions. Large pigment epithelial detachments were associated with signal loss. Fluorescence angiography still remains the gold standard, but the tested SS-OCTA device can be considered as a feasible additional diagnostic tool in AMD.

Short and long sympathetic-sensory feedback loops in white fat

PubMed Central

Ryu, Vitaly

2014-01-01

We previously demonstrated white adipose tissue (WAT) innervation using the established WAT retrograde sympathetic nervous system (SNS)-specific transneuronal viral tract tracer pseudorabies virus (PRV152) and showed its role in the control of lipolysis. Conversely, we demonstrated WAT sensory innervation using the established anterograde sensory system (SS)-specific transneuronal viral tracer, the H129 strain of herpes simplex virus-1, with sensory nerves showing responsiveness with increases in WAT SNS drive. Several brain areas were part of the SNS outflow to and SS inflow from WAT between these studies suggesting SNS-SS feedback loops. Therefore, we injected both PRV152 and H129 into inguinal WAT (IWAT) of Siberian hamsters. Animals were perfused on days 5 and 6 postinoculation after H129 and PRV152 injections, respectively, and brains, spinal cords, sympathetic, and dorsal root ganglia (DRG) were processed for immunohistochemical detection of each virus across the neuroaxis. The presence of H129+PRV152-colocalized neurons (∼50%) in the spinal segments innervating IWAT suggested short SNS-SS loops with significant coinfections (>60%) in discrete brain regions, signifying long SNS-SS loops. Notably, the most highly populated sites with the double-infected neurons were the medial part of medial preoptic nucleus, medial preoptic area, hypothalamic paraventricular nucleus, lateral hypothalamus, periaqueductal gray, oral part of the pontine reticular nucleus, and the nucleus of the solitary tract. Collectively, these results strongly indicate the neuroanatomical reality of the central SNS-SS feedback loops with short loops in the spinal cord and long loops in the brain, both likely involved in the control of lipolysis or other WAT pad-specific functions. PMID:24717676

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity

PubMed Central

Kouno, Takahide; Silvas, Tania V.; Hilbert, Brendan J.; Shandilya, Shivender M. D.; Bohn, Markus F.; Kelch, Brian A.; Royer, William E.; Somasundaran, Mohan; Kurt Yilmaz, Nese; Matsuo, Hiroshi; Schiffer, Celia A.

2017-01-01

Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 Å. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A–ssDNA complex defines the 5′–3′ directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics. PMID:28452355

Isotope labeling for studying RNA by solid-state NMR spectroscopy.

PubMed

Marchanka, Alexander; Kreutz, Christoph; Carlomagno, Teresa

2018-04-12

Nucleic acids play key roles in most biological processes, either in isolation or in complex with proteins. Often they are difficult targets for structural studies, due to their dynamic behavior and high molecular weight. Solid-state nuclear magnetic resonance spectroscopy (ssNMR) provides a unique opportunity to study large biomolecules in a non-crystalline state at atomic resolution. Application of ssNMR to RNA, however, is still at an early stage of development and presents considerable challenges due to broad resonances and poor dispersion. Isotope labeling, either as nucleotide-specific, atom-specific or segmental labeling, can resolve resonance overlaps and reduce the line width, thus allowing ssNMR studies of RNA domains as part of large biomolecules or complexes. In this review we discuss the methods for RNA production and purification as well as numerous approaches for isotope labeling of RNA. Furthermore, we give a few examples that emphasize the instrumental role of isotope labeling and ssNMR for studying RNA as part of large ribonucleoprotein complexes.

Drug distribution and stability in extemporaneous preparations of meloxicam and carprofen after dilution and suspension at two storage temperatures.

PubMed

Hawkins, Michelle G; Karriker, Margo J; Wiebe, Valerie; Taylor, Ian T; Kass, Philip H

2006-09-15

To determine dispersion uniformity and stability of meloxicam and carprofen in extemporaneous preparations stored for 28 days. Prospective study. Meloxicam and carprofen (commercial formulations) were compounded (day 0) with deionized water (DW), 1% methylcellulose gel (MCG), MCG and simple syrup (SS; 1:1 mixture), or a suspending and flavoring vehicle combination (SFVC; 1:1 mixture) to nominal drug concentrations of 0.25, 0.5, or 1.0 mg/mL and 1.25, 2.5, or 5.0 mg/mL, respectively. Preparations were stored at approximately 4 degrees C (39.2 degrees F) or 22 degrees C (71.6 degrees F). For each preparation, drug concentrations were determined and drug stability was evaluated at intervals during storage; on days 0 and 28, pH values were measured and bacterial cultures were initiated. In meloxicam-DW, meloxicam-MCG (0.25 mg/mL), and meloxicam-MCG (0.5 mg/mL) preparations, drug distribution was uniform (coefficient of variation < 10%); > 90% of the original drug concentration was maintained for 28 days. Despite uniform drug distribution of the carprofen-SFVC preparations, most retained > or = 90% of the original drug concentration for only 21 days. Use of the MCG-SS combination resulted in foamy preparations of unacceptable variability. After 28 days, pH decreased slightly in meloxicam-DW and meloxicam-MCG preparations (0.17 +/- 0.04 and 0.21 +/- 0.04, respectively). Carprofen-SFVC (2.5 mg/mL) and carprofen-MCG-SS (5.0 mg/mL) preparations stored at 22 degrees C for 28 days yielded bacterial growth. DW, MCG, and the SFVC can be used successfully for extemporaneous preparation of meloxicam and carprofen for administration to small exotic animals. Refrigeration is recommended for preparations of meloxicam-DW and carprofen-SFVC.

Order-picking in deep cold--physiological responses of younger and older females. Part 2: body core temperature and skin surface temperature.

PubMed

Baldus, Sandra; Kluth, Karsten; Strasser, Helmut

2012-01-01

So far, it was unclear to what extent working in deep cold-storage depots has an influence on female order-pickers body core temperature and skin surface temperature considering different age groups. Physiological effects of order-picking in a chill room (+3°C) and cold store (-24°C) were examined on 30 female subjects (Ss), classified in two age groups (20- to 35- year-olds and 40- to 65-year-olds). The body core temperature was taken every 15 min at the tympanum and the skin surface temperature was recorded continuously at seven different positions. Working in the chill room induced a decrease of the body core temperature up to 0.5K in comparison to the value at the outset for both age groups which could be compensated by all Ss during the breaks. Working in the cold store caused a decline up to 1.1K for the younger Ss and 1.3K for the older Ss. A complete warming-up during the breaks was often not possible. Regarding the skin surface temperature, working in the chill room can be considered as unproblematic, whereas significantly lower temperatures at nose, fingers and toes, associated with substantial negative subjective sensations, were recorded while working in the cold store.

Equilibrious Strand Exchange Promoted by DNA Conformational Switching

NASA Astrophysics Data System (ADS)

Wu, Zhiguo; Xie, Xiao; Li, Puzhen; Zhao, Jiayi; Huang, Lili; Zhou, Xiang

2013-01-01

Most of DNA strand exchange reactions in vitro are based on toehold strategy which is generally nonequilibrium, and intracellular strand exchange mediated by proteins shows little sequence specificity. Herein, a new strand exchange promoted by equilibrious DNA conformational switching is verified. Duplexes containing c-myc sequence which is potentially converted into G-quadruplex are designed in this strategy. The dynamic equilibrium between duplex and G4-DNA is response to the specific exchange of homologous single-stranded DNA (ssDNA). The SER is enzyme free and sequence specific. No ATP is needed and the displaced ssDNAs are identical to the homologous ssDNAs. The SER products and exchange kenetics are analyzed by PAGE and the RecA mediated SER is performed as the contrast. This SER is a new feature of G4-DNAs and a novel strategy to utilize the dynamic equilibrium of DNA conformations.

Controlled Assembly of Ag Nanoparticles and Carbon Nanotube Hybrid Structures for Biosensing

DTIC Science & Technology

2010-01-01

to∼190 kΩ. The same device was again washed with DI water and treated with the thiolated ssDNA in high salt buffer. After a 2 h treatment, the device...after the cleaning only thiolated DNA should be present on the device, whereas the nonspecifically bound DNA as well as the buffer salts should be...ssDNA molecules for 2 h. Specific immobiliza- tion of thiolated ssDNA (sequence: 50thiol_TCATAC AGCTAGATA ACC AAAGA) was carried out in high salt

Isolation of the sex-determining gene Sex-lethal (Sxl) in Penaeus (Litopenaeus) vannamei (Boone, 1931) and characterization of its embryogenic, gametogenic, and tissue-specific expression.

PubMed

López-Cuadros, Itzia; García-Gasca, Alejandra; Gomez-Anduro, Gracia; Escobedo-Fregoso, Cristina; Llera-Herrera, Raúl A; Ibarra, Ana M

2018-08-20

The Pacific white shrimp Penaeus vannamei is the most cultured shrimp species around the world. Because females grow larger than males, the culture of 'only females' is of great interest, but knowledge on sex determination and differentiation is required for producing only females. In an effort to obtain information associated with reproduction in P. vannamei, transcriptomic data from female gonads was generated, and partial sequences of a transcript were identified as Sex-lethal (Sxl). Its characterization indicated that, differently from other penaeids in which this gene has been isolated, there are six isoforms of the Sxl transcript in P. vannamei (PvanSxl 1-6). These isoforms result from alternative splicing at three splice sites (SS1, SS2, SS3). The first splice-site is unique to P. vannamei, as it has not been reported for other Arthropod species; the second splice-site (SS2) is common among crustaceans, and the third splice-site (SS3) is also unique to P. vannamei and when spliced-out, it is always together with SS2. All isoforms are expressed during embryogenesis as well as gametogenesis of both genders. The two shorter isoforms, PvanSxl-5 and PvanSxl-6, which result from the splicing of SS2 and SS3, were found mostly expressed in adult testis, but PvanSxl-6 was also expressed in oocytes during gametogenesis. During oogenesis, the second largest isoform, PvanSxl-2, which splices-out only SS1, and PvanSxl-4 that splices-out SS1 and SS2 were highly expressed. These two isoforms were also highly expressed during embryonic development. In situ hybridization allowed pinpointing more specifically the cells where the PvanSxl transcripts were expressed. During embryogenesis, hybridization was observed from the one-cell stage embryo to late gastrula. In the female gonad in previtellogenesis, hybridization occurred in the nucleus of oocytes, whereas in secondary vitellogenesis the transcript also hybridized cytoplasmic granules and cortical crypts. Finally, in situ hybridization corroborated the expression of PvanSxl also in the male gonad during spermatogenesis, mostly occurring in the cytoplasm from spermatogonia and spermatocytes. Copyright © 2018 Elsevier B.V. All rights reserved.

Circulating auto-antibodies against nuclear and non-nuclear antigens in primary Sjögren's syndrome: prevalence and clinical significance in 335 patients.

PubMed

Nardi, Norma; Brito-Zerón, Pilar; Ramos-Casals, Manuel; Aguiló, Sira; Cervera, Ricard; Ingelmo, Miguel; Font, Josep

2006-05-01

The aim of this study was to analyze the prevalence and clinical significance of circulating auto-antibodies against nuclear and non-nuclear antigens in a large cohort of Spanish patients with primary Sjögren's syndrome (SS). We studied 335 patients diagnosed with primary SS seen consecutively in our department since 1994 and tested for anti-nuclear antibodies (ANA), anti-Ro/SS-A, anti-La/SS-B, anti-Sm, anti-ribonucleoprotein (anti-RNP), anti-smooth muscle antibodies (anti-SMA), anti-parietal cell antibodies (anti-PCA), anti-liver-kidney microsome type-1 (anti-LKM-1) antibodies and anti-mitochondrial antibodies (AMA). ANA were detected in 278 (83%) patients. The association of positive ANA with the presence of anti-Ro/SS-A and anti-La/SS-B antibodies reached statistical significance at a titre of ANA >1/80 (p<0.001), while the presence of anti-Sm and anti-RNP was associated with positive ANA at a titre > or =1/320 (p=0.037 for Sm and p=0.016 for RNP). ANA titres correlated with the number of positive antibodies against specific nuclear antigens (p<0.001) but not with the number of positive antibodies against non-nuclear antigens. We found positive anti-Ro/SS-A antibodies in 111 (33%) patients, anti-La/SS-B in 78 (23%), anti-RNP in 8 (2%) and anti-Sm in 4 (1%). Anti-SMA antibodies were detected in 208 (62%) patients, with no significant associations with clinical or analytical SS features, while anti-PCA antibodies were found in 90 (27%) patients and were associated with a higher prevalence of thyroiditis and liver involvement. AMA were detected in 28 (8%) patients, although only 14 presented clinical and/or analytical evidence of liver involvement. No patient presented anti-LKM antibodies. ANA play a central role in the immunological expression of primary SS, due to their frequency and close association with the underlying presence of one or more anti-ENA antibodies. Positivity for antibodies against non-nuclear antigens such as anti-PCA and AMA suggests an association with some organ-specific autoimmune diseases (thyroiditis and primary biliary cirrhosis), while the presence of anti-SMA, in spite of their high prevalence, has no clinical significance in primary SS.

The Body Dysmorphic Disorder Symptom Scale: Development and preliminary validation of a self-report scale of symptom specific dysfunction.

PubMed

Wilhelm, Sabine; Greenberg, Jennifer L; Rosenfield, Elizabeth; Kasarskis, Irina; Blashill, Aaron J

2016-06-01

The Body Dysmorphic Disorder Symptom Scale (BDD-SS) is a new self-report measure used to examine the severity of a wide variety of symptoms associated with body dysmorphic disorder (BDD). The BDD-SS was designed to differentiate, for each group of symptoms, the number of symptoms endorsed and their severity. This report evaluates and compares the psychometric characteristics of the BDD-SS in relation to other measures of BDD, body image, and depression in 99 adult participants diagnosed with BDD. Total scores of the BDD-SS showed good reliability and convergent validity and moderate discriminant validity. Analyses of the individual BDD-SS symptom groups confirmed the reliability of the checking, grooming, weight/shape, and cognition groups. The current findings indicate that the BDD-SS can be quickly administered and used to examine the severity of heterogeneous BDD symptoms for research and clinical purposes. Copyright © 2016. Published by Elsevier Ltd.

Visualization of the Serratia Type VI Secretion System Reveals Unprovoked Attacks and Dynamic Assembly

PubMed Central

Gerc, Amy J.; Diepold, Andreas; Trunk, Katharina; Porter, Michael; Rickman, Colin; Armitage, Judith P.; Stanley-Wall, Nicola R.; Coulthurst, Sarah J.

2015-01-01

Summary The Type VI secretion system (T6SS) is a bacterial nanomachine that fires toxic proteins into target cells. Deployment of the T6SS represents an efficient and widespread means by which bacteria attack competitors or interact with host organisms and may be triggered by contact from an attacking neighbor cell as a defensive strategy. Here, we use the opportunist pathogen Serratia marcescens and functional fluorescent fusions of key components of the T6SS to observe different subassemblies of the machinery simultaneously and on multiple timescales in vivo. We report that the localization and dynamic behavior of each of the components examined is distinct, revealing a multi-stage and dynamic assembly process for the T6SS machinery. We also show that the T6SS can assemble and fire without needing a cell contact trigger, defining an aggressive strategy that broadens target range and suggesting that activation of the T6SS is tailored to survival in specific niches. PMID:26387948

The effect of ice slushy ingestion and mouthwash on thermoregulation and endurance performance in the heat.

PubMed

Burdon, Catriona A; Hoon, Matthew W; Johnson, Nathan A; Chapman, Phillip G; O'Connor, Helen T

2013-10-01

The purpose of this study was to establish whether sensory factors associated with cold-beverage ingestion exert an ergogenic effect on endurance performance independent of thermoregulatory or cardiovascular factors. Ten males performed three trials involving 90 min of steady state cycling (SS; 62% VO2max) in the heat (32.1 ± 0.9 °C, 40 ± 2.4% relative humidity) followed by a 4 kJ/kg body mass time trial (TT). During SS, participants consumed an identical volume (260 ± 38 g) of sports beverage (7.4% carbohydrate) every 15 min as either ice slushy (-1 °C; ICE), thermoneutral liquid (37 °C; CON), or thermoneutral liquid consumption with expectorated ice slushy mouthwash (WASH). Rectal temperature, hydration status, heart rate, and skin blood flow were not different between trials. Gastrointestinal (pill) temperature was lower in ICE (35.6 ± 2.7 °C) versus CON (37.4 ± 0.7 °C, p = .05). Heat storage tended to be lower with ICE during SS (14.7 ± 8.4 W.m(-2), p = .08) and higher during TT (68.9 ± 38.6 W.m(-2), p = .03) compared with CON (22.1 ± 6.6 and 31.4 ± 27.6 W.m(-2)). ICE tended to lower the rating of perceived exertion (RPE, 12.9 ± 0.6, p = .05) and improve thermal comfort (TC, 4.5 ± 0.2; p = .01) vs. CON (13.8 ± 1.0 and 5.2 ± 0.2 respectively). WASH RPE (13.0 ± 0.8) and TC (4.8 ± 0.2) tended to be lower versus CON (p = .07 and p = .09 respectively). ICE improved performance (18:28 ± 1:03) compared with CON (20:24 ± 1:46) but not WASH (19:45 ± 1:43). Improved performance with ICE ingestion likely resulted from the creation of a gastrointestinal heat sink, reducing SS heat storage. Although the benefits of cold-beverage consumption are more potent when there is ingestion, improved RPE, TC, and meaningful performance improvement with WASH supports an independent sensory effect of presenting a cold stimulus to the mouth.

Symptom severity scale of the DSM5 for schizophrenia, and other psychotic disorders: diagnostic validity and clinical feasibility.

PubMed

Ritsner, Michael S; Mar, Maria; Arbitman, Marina; Grinshpoon, Alexander

2013-06-30

Innovations in DSM5 include dimensional diagnosis of schizophrenia (SZ) and other psychotic (OP) disorders using the symptom severity scale (SS-DSM5). We evaluated the psychometric properties and diagnostic validity of the SS-DSM5 scale using a cross-sectional design and an unselected convenience unselected sample of 314 inpatients and outpatients with SZ/OP and mood disorders who received standard care in routine clinical practice. The SS-DSM5 scale, the Clinical Global Impression-Severity scale (CGI-S), the Positive and Negative Syndrome Scale (PANSS), and the Bech-Rafaelsen Mania Scale (BRMS) were administered. Factor structure, reliability, internal consistency, convergent and diagnostic ability of the DSM5-SS were evaluated. Factor analysis indicated two latent factors underlying the SS-DSM5 (Psychotic and Deficit sub-scales). Cronbach's alpha was >0.70. Convergent validity of the SS-DSM5 was highly significant. Patients with SZ/PO disorders were correctly diagnosed (77.9%) using the SS-DSM5 scale (72% using PANSS). The agreement of the diagnostic decisions between the SS-DSM5 and PANSS was substantial for SZ/PO disorders (Kappa=0.75). Classifying participants with SZ/PO versus mood disorders using SS-DSM5 provided a sensitivity of 95%, and specificity of 34%. Thus, this study suggests that the SS-DSM5 has acceptable psychometric properties and that its use in clinical practice and research is feasible in clinical settings. The dimensional option for the diagnosis of schizophrenia and related disorders using SS-DSM5 is discussed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A novel fluorescent DNA sensor for ultrasensitive detection of Helicobacter pylori.

PubMed

Liu, Ziping; Su, Xingguang

2017-01-15

In this work, a novel fluorescent DNA sensor for ultrasensitive detection of Helicobacter pylori (H. pylori) DNA was developed. This strategy took advantage of DNA hybridization between single-stranded DNA (ssDNA, which had been designed as an aptamer specific for H. pylori DNA) and the complementary target H. pylori DNA, and the feature that ssDNA bound to graphene oxide (GO) with significantly higher affinity than double-stranded DNA (dsDNA). ssDNA were firstly covalent conjugated with CuInS 2 quantum dots (QDs) by reaction between the carboxy group of QDs and amino group modified ssDNA, forming ssDNA-QDs genosensor. In the absence of the complementary target H. pylori DNA, GO could adsorb ssDNA-QDs DNA sensor and efficiently quench the fluorescence of ssDNA-QDs. While the complementary target H. pylori DNA was introduced, the ssDNA-QDs preferentially bound with the H. pylori DNA. The formation of dsDNA would alter the conformation of ssDNA and disturb the interaction between ssDNA and GO. Thus, the dsDNA-QDs/GO system exhibited a stronger fluorescence emission than that of the ssDNA-QDs/GO system. Under the optimized conditions, a linear correlation was established between the fluorescence intensity ratio I/I 0 and the concentration of H. pylori DNA in the range of 1.25-875pmolL -1 with a detection limit of 0.46pmolL -1 . The proposed method was applied to the determination of H. pylori DNA sequence in milk samples with satisfactory results. Copyright © 2016 Elsevier B.V. All rights reserved.

Detection of human T lymphotropic virus type-I bZIP factor and tax in the salivary glands of Sjögren's syndrome patients.

PubMed

Nakamura, Hideki; Hasegawa, Hiroo; Sasaki, Daisuke; Takatani, Ayuko; Shimizu, Toshimasa; Kurushima, Shota; Horai, Yoshiro; Nakashima, Yoshikazu; Nakamura, Tatsufumi; Fukuoka, Junya; Kawakami, Atsushi

2018-03-20

To detect HTLV-I bZIP factor (HBZ), tax and relevant molecules in labial salivary glands (LSGs) from patients with Sjögren's syndrome (SS). The expressions of HBZ and tax in T cell lines and LSGs were analysed by in situ hybridization (ISH) or real time PCR. The expressions of forkhead box P3 (Foxp3) and p65 in immunohistochemistry were quantified. After specificity of ISH probes was determined in 5 T cell lines, in LSGs from an adult T-cell leukemia (ATL) patient and 3 HTLV-I-associated myelopathy (HAM)-SS patients, both HBZ and tax signals were detected in infiltrating mononuclear cells (MNCs) and ducts, and HBZ and tax were dominantly expressed in MNCs of ATL and HAM-SS, respectively. HBZ was dominantly observed in LSGs from 8 HTLV-I asymptomatic carrier (AC)-SS patients; faint expression of HBZ was observed in LSGs from 5 HTLV-I-seronegative SS patients. No cell adhesion molecule 1(CADM1) expressed in LSGs from the ATL patient. Although Foxp3 expression was observed in LSG MNCs of all of the SS patients, the ATL patient's expression was significantly greater than that of the AC-SS (p<0.01) and HTLV-I-seronegative SS (p<0.01) patients. The Foxp3 expression was similar in ATL and HAMSS, but significantly higher in HAM-SS than AC-SS (p<0.05). p65 was expressed in LSG MNC nuclei from all SS patients and co-expressed with Foxp3. The expressions of Foxp3 in ducts differed according to HTLV-I infection. These results suggest that HBZ-mediated Foxp3 expression is partly associated with the pathogenesis of HTLV-I-seropositive SS.

Comparative genomics of two super-shedder isolates of Escherichia coli O157:H7

PubMed Central

Katani, Robab; Cote, Rebecca; Kudva, Indira T.; DebRoy, Chitrita; Arthur, Terrance M.

2017-01-01

Shiga toxin-producing Escherichia coli O157:H7 (O157) are zoonotic foodborne pathogens and of major public health concern that cause considerable intestinal and extra-intestinal illnesses in humans. O157 colonize the recto-anal junction (RAJ) of asymptomatic cattle who shed the bacterium into the environment through fecal matter. A small subset of cattle, termed super-shedders (SS), excrete O157 at a rate (≥ 104 CFU/g of feces) that is several orders of magnitude greater than other colonized cattle and play a major role in the prevalence and transmission of O157. To better understand microbial factors contributing to super-shedding we have recently sequenced two SS isolates, SS17 (GenBank accession no. CP008805) and SS52 (GenBank accession no. CP010304) and shown that SS isolates display a distinctive strongly adherent phenotype on bovine rectal squamous epithelial cells. Here we present a detailed comparative genomics analysis of SS17 and SS52 with other previously characterized O157 strains (EC4115, EDL933, Sakai, TW14359). The results highlight specific polymorphisms and genomic features shared amongst SS strains, and reveal several SNPs that are shared amongst SS isolates, including in genes involved in motility, adherence, and metabolism. Finally, our analyses reveal distinctive patterns of distribution of phage-associated genes amongst the two SS and other isolates. Together, the results of our comparative genomics studies suggest that while SS17 and SS52 share genomic features with other lineage I/II isolates, they likely have distinct recent evolutionary histories. Future comparative and functional genomic studies are needed to decipher the precise molecular basis for super shedding in O157. PMID:28797098

Comparative genomics of two super-shedder isolates of Escherichia coli O157:H7.

PubMed

Katani, Robab; Cote, Rebecca; Kudva, Indira T; DebRoy, Chitrita; Arthur, Terrance M; Kapur, Vivek

2017-01-01

Shiga toxin-producing Escherichia coli O157:H7 (O157) are zoonotic foodborne pathogens and of major public health concern that cause considerable intestinal and extra-intestinal illnesses in humans. O157 colonize the recto-anal junction (RAJ) of asymptomatic cattle who shed the bacterium into the environment through fecal matter. A small subset of cattle, termed super-shedders (SS), excrete O157 at a rate (≥ 104 CFU/g of feces) that is several orders of magnitude greater than other colonized cattle and play a major role in the prevalence and transmission of O157. To better understand microbial factors contributing to super-shedding we have recently sequenced two SS isolates, SS17 (GenBank accession no. CP008805) and SS52 (GenBank accession no. CP010304) and shown that SS isolates display a distinctive strongly adherent phenotype on bovine rectal squamous epithelial cells. Here we present a detailed comparative genomics analysis of SS17 and SS52 with other previously characterized O157 strains (EC4115, EDL933, Sakai, TW14359). The results highlight specific polymorphisms and genomic features shared amongst SS strains, and reveal several SNPs that are shared amongst SS isolates, including in genes involved in motility, adherence, and metabolism. Finally, our analyses reveal distinctive patterns of distribution of phage-associated genes amongst the two SS and other isolates. Together, the results of our comparative genomics studies suggest that while SS17 and SS52 share genomic features with other lineage I/II isolates, they likely have distinct recent evolutionary histories. Future comparative and functional genomic studies are needed to decipher the precise molecular basis for super shedding in O157.

Usefulness of antibodies and minor salivary gland biopsy in the study of sicca syndrome in daily clinical practice.

PubMed

Santiago, Maria Lida; Seisdedos, Maria Renata; Garcia Salinas, Rodrigo Nicolás; Catalán Pellet, Antonio; Villalón, Liliana; Secco, Anastasia

2015-01-01

To assess the association between histologic findings in the minor salivary gland biopsy (MSGB) and anti La (La/SS-B)y antiRo antibodies (Ro/SS-A), antinuclear antibodies (ANA) and Rheumatoid Factor (RF),and compare the value of the latter as diagnostic tests with MSGB, considered as the gold standard. Patients with suspected Primary Sjögren Syndrome (PSS) referred for MSGB were included. Antibody measurements were performed. Grade III and IV biopsy results were considered positive. Two hundred and eighteen (218) patients were included, 95% females, with a median age of 54 years and 12 months median duration of sicca symptoms. 36 of the biopsies were positive. 33% of patients had positive anti Ro/SS-A anti La/SS-B antibodies, 62% had positive ANA, and 31% positive RF. A statistically significant association was found between MSGB and anti Ro/SS-A anti La/SS-B, ANA and RF. ANA were the most sensitive antibodies (84%. 95% CI: 75- 92), and the most specific were: Anti Ro/ SS-A and/or anti La/ SS-B (78%. 95% CI: 71-85) and RF (78%. 95% CI: 69-87). On PSS clinical suspicion, anti Ro/ SS-A y anti La/ SS-B antibodies have a great value to achieve the diagnosis, with MSGB useful for diagnosis of seronegative patients. The results also suggest the importance of ANA and RF for PSS classification. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

Ectopic Overexpression of SsCBF1, a CRT/DRE-Binding Factor from the Nightshade Plant Solanum lycopersicoides, Confers Freezing and Salt Tolerance in Transgenic Arabidopsis

PubMed Central

Zhang, Lili; Li, Zhenjun; Li, Jingfu; Wang, Aoxue

2013-01-01

The C-repeat (CRT)/dehydration-responsive element (DRE) binding factor (CBF/DREB1) transcription factors play a key role in cold response. However, the detailed roles of many plant CBFs are far from fully understood. A CBF gene (SsCBF1) was isolated from the cold-hardy plant Solanum lycopersicoides. A subcellular localization study using GFP fusion protein indicated that SsCBF1 is localized in the nucleus. We delimited the SsCBF1 transcriptional activation domain to the C-terminal segment comprising amino acid residues 193–228 (SsCBF1193–228). The expression of SsCBF1 could be dramatically induced by cold, drought and high salinity. Transactivation assays in tobacco leaves revealed that SsCBF1 could specifically bind to the CRT cis-elements in vivo to activate the expression of downstream reporter genes. The ectopic overexpression of SsCBF1 conferred increased freezing and high-salinity tolerance and late flowering phenotype to transgenic Arabidopsis. RNA-sequencing data exhibited that a set of cold and salt stress responsive genes were up-regulated in transgenic Arabidopsis. Our results suggest that SsCBF1 behaves as a typical CBF to contribute to plant freezing tolerance. Increased resistance to high-salinity and late flowering phenotype derived from SsCBF1 OE lines lend more credence to the hypothesis that plant CBFs participate in diverse physiological and biochemical processes related to adverse conditions. PMID:23755095

A novel engineered interchain disulfide bond in the constant region enhances the thermostability of adalimumab Fab.

PubMed

Nakamura, Hitomi; Oda-Ueda, Naoko; Ueda, Tadashi; Ohkuri, Takatoshi

2018-01-01

We constructed a system for expressing the Fab of the therapeutic human monoclonal antibody adalimumab at a yield of 20 mg/L in the methylotrophic yeast Pichia pastoris. To examine the contribution of interchain disulfide bonds to conformational stability, we prepared adalimumab Fab from which the interchain disulfide bond at the C-terminal region at both the CH 1 and CL domains was deleted by substitution of Cys with Ala (Fab ΔSS ). DSC measurements showed that the Tm values of Fab ΔSS were approximately 5 °C lower than those of wild-type Fab, suggesting that the interchain disulfide bond contributes to conformational thermostability. Using computer simulations, we designed a novel interchain disulfide bond outside the C-terminal region to increase the stability of Fab ΔSS . The resulting Fab (mutSS Fab ΔSS ) had the mutations H:V177C and L:Q160C in Fab ΔSS , confirming the formation of the disulfide bond between CH 1 and CL. The thermostability of mutSS Fab ΔSS was approximately 5 °C higher than that of Fab ΔSS . Therefore, the introduction of the designed interchain disulfide bond enhanced the thermostability of Fab ΔSS and mitigated the destabilization caused by partial reduction of the interchain disulfide bond at the C-terminal region, which occurs in site-specific modification such as PEGylation. Copyright © 2017 Elsevier Inc. All rights reserved.

Ehrlichia chaffeensis Tandem Repeat Proteins and Ank200 are Type 1 Secretion System Substrates Related to the Repeats-in-Toxin Exoprotein Family

PubMed Central

Wakeel, Abdul; den Dulk-Ras, Amke; Hooykaas, Paul J. J.; McBride, Jere W.

2011-01-01

Ehrlichia chaffeensis has type 1 and 4 secretion systems (T1SS and T4SS), but the substrates have not been identified. Potential substrates include secreted tandem repeat protein (TRP) 47, TRP120, and TRP32, and the ankyrin repeat protein, Ank200, that are involved in molecular host–pathogen interactions including DNA binding and a network of protein–protein interactions with host targets associated with signaling, transcriptional regulation, vesicle trafficking, and apoptosis. In this study we report that E. chaffeensis TRP47, TRP32, TRP120, and Ank200 were not secreted in the Agrobacterium tumefaciens Cre recombinase reporter assay routinely used to identify T4SS substrates. In contrast, all TRPs and the Ank200 proteins were secreted by the Escherichia coli complemented with the hemolysin secretion system (T1SS), and secretion was reduced in a T1SS mutant (ΔTolC), demonstrating that these proteins are T1SS substrates. Moreover, T1SS secretion signals were identified in the C-terminal domains of the TRPs and Ank200, and a detailed bioinformatic analysis of E. chaffeensis TRPs and Ank200 revealed features consistent with those described in the repeats-in-toxins (RTX) family of exoproteins, including glycine- and aspartate-rich tandem repeats, homology with ATP-transporters, a non-cleavable C-terminal T1SS signal, acidic pIs, and functions consistent with other T1SS substrates. Using a heterologous E. coli T1SS, this investigation has identified the first Ehrlichia T1SS substrates supporting the conclusion that the T1SS and corresponding substrates are involved in molecular host–pathogen interactions that contribute to Ehrlichia pathobiology. Further investigation of the relationship between Ehrlichia TRPs, Ank200, and the RTX exoprotein family may lead to a greater understanding of the importance of T1SS substrates and specific functions of T1SS in the pathobiology of obligately intracellular bacteria. PMID:22919588

Isolation of a new ssDNA aptamer against staphylococcal enterotoxin B based on CNBr-activated sepharose-4B affinity chromatography.

PubMed

Hedayati Ch, Mojtaba; Amani, Jafar; Sedighian, Hamid; Amin, Mohsen; Salimian, Jafar; Halabian, Raheleh; Imani Fooladi, Abbas Ali

2016-09-01

Staphylococcus aureus are potent human pathogens possessing arsenal of virulence factors. Staphylococcal food poisoning (SFP) and respiratory infections mediated by staphylococcal enterotoxin B (SEB) are common clinical manifestations. Many diagnostic techniques are based on serological detection and quantification of SEB in different food and clinical samples. Aptamers are known as new therapeutic and detection tools which are available in different ssDNA, dsDNA and protein structures. In this study, we used a new set of ssDNA aptamers against SEB. The methods used included preparation of a dsDNA library using standard SEB protein as the target analyte, affinity chromatography matrix in microfuge tubes, SELEX procedures to isolate specific ssDNA-aptamer as an affinity ligand, aptamer purification using ethanol precipitation method, affinity binding assay using ELISA, aptamer cloning and specificity test. Among 12 readable sequences, three of them were selected as the most appropriate aptamer because of their affinity and specificity to SEB. This study presents a new set of ssDNA aptamer with favorable selectivity to SEB through 12 rounds of SELEX. Selected aptamers were used to detect SEB in infected serum samples. Results showed that SEB c1 aptamer (2 µg SEB/100 nM aptamer) had favorable specificity to SEB (kd  = 2.3 × 10(-11) ). In conclusion, aptamers can be considered as useful tools for detecting and evaluating SEB. The results showed that affinity chromatography was an affordable assay with acceptable accuracy to isolate sensitive and selective novel aptamers. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Flame oxidation of stainless steel felt enhances anodic biofilm formation and current output in bioelectrochemical systems.

PubMed

Guo, Kun; Donose, Bogdan C; Soeriyadi, Alexander H; Prévoteau, Antonin; Patil, Sunil A; Freguia, Stefano; Gooding, J Justin; Rabaey, Korneel

2014-06-17

Stainless steel (SS) can be an attractive material to create large electrodes for microbial bioelectrochemical systems (BESs), due to its low cost and high conductivity. However, poor biocompatibility limits its successful application today. Here we report a simple and effective method to make SS electrodes biocompatible by means of flame oxidation. Physicochemical characterization of electrode surface indicated that iron oxide nanoparticles (IONPs) were generated in situ on an SS felt surface by flame oxidation. IONPs-coating dramatically enhanced the biocompatibility of SS felt and consequently resulted in a robust electroactive biofilm formation at its surface in BESs. The maximum current densities reached at IONPs-coated SS felt electrodes were 16.5 times and 4.8 times higher than the untreated SS felts and carbon felts, respectively. Furthermore, the maximum current density achieved with the IONPs-coated SS felt (1.92 mA/cm(2), 27.42 mA/cm(3)) is one of the highest current densities reported thus far. These results demonstrate for the first time that flame oxidized SS felts could be a good alternative to carbon-based electrodes for achieving high current densities in BESs. Most importantly, high conductivity, excellent mechanical strength, strong chemical stability, large specific surface area, and comparatively low cost of flame oxidized SS felts offer exciting opportunities for scaling-up of the anodes for BESs.

Mainstream smoke and sidestream smoke affect the cardiac differentiation of mouse embryonic stem cells discriminately.

PubMed

Cheng, Wei; Zhou, Ren; Feng, Yan; Wang, Yan

2016-05-16

Epidemiology studies suggest that maternal smoking and passive smoking have strongly resulted in the occurrence of congenital heart defects (CHD) in offspring. Cigarette smoke (CS) can be divided into mainstream smoke (MS) and sidestream smoke (SS); CS chemistry study indicates that significant differences exist in the composition of MS and SS. Therefore, MS and SS were suspected to process toxicity dissimilarly. However, much less was known about the difference in the developmental effects induced by MS and SS. In the current study, heart development was mimicked by mouse embryonic stem cells (ESCs) differentiation. After MS and SS exposure, by tracing the bone morphogenetic protein (BMP)-Smad4 signalling pathway, interruption of downstream gene expression was observed, including Gata4, Mef2c and Nkx2.5, as well as myosin heavy chain and myosin light chain. Specifically, SS caused inhibition of Gata4 expression, even at non-cytotoxic concentration. Further, SS-induced hypoacetylation in promoter regions of Gata4 reflected the orchestration of CS-gene modulation-epigenetic regulation. Even though SS induced apoptosis in ESC-derived cardiomyocytes, the partial clearance in cells with down-regulated Gata4 caused these cells to survive and undergo further differentiation, which laid potential risk for abnormal heart development. These data uncovered the difference between MS and SS on heart development preliminarily. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Recombination in Eukaryotic Single Stranded DNA Viruses

PubMed Central

Martin, Darren P.; Biagini, Philippe; Lefeuvre, Pierre; Golden, Michael; Roumagnac, Philippe; Varsani, Arvind

2011-01-01

Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution. PMID:21994803

MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction.

PubMed

Fang, Chao; Shang, Yi; Xu, Dong

2018-05-01

Protein secondary structure prediction can provide important information for protein 3D structure prediction and protein functions. Deep learning offers a new opportunity to significantly improve prediction accuracy. In this article, a new deep neural network architecture, named the Deep inception-inside-inception (Deep3I) network, is proposed for protein secondary structure prediction and implemented as a software tool MUFOLD-SS. The input to MUFOLD-SS is a carefully designed feature matrix corresponding to the primary amino acid sequence of a protein, which consists of a rich set of information derived from individual amino acid, as well as the context of the protein sequence. Specifically, the feature matrix is a composition of physio-chemical properties of amino acids, PSI-BLAST profile, and HHBlits profile. MUFOLD-SS is composed of a sequence of nested inception modules and maps the input matrix to either eight states or three states of secondary structures. The architecture of MUFOLD-SS enables effective processing of local and global interactions between amino acids in making accurate prediction. In extensive experiments on multiple datasets, MUFOLD-SS outperformed the best existing methods and other deep neural networks significantly. MUFold-SS can be downloaded from http://dslsrv8.cs.missouri.edu/~cf797/MUFoldSS/download.html. © 2018 Wiley Periodicals, Inc.

The effect of somatostatin analogs on secretion of growth, pancreatic, and gastrointestinal hormones in man.

PubMed

Adrian, T E; Barnes, A J; Long, R G; O'Shaughnessy, D J; Brown, M R; Rivier, J; Vale, W; Blackburn, A M; Bloom, S R

1981-10-01

The potency and specificity of somatostatin (SS) and four of its analogs were compared in seven patients with pancreatic endocrine tumors. The analogs tested were [D-Trp8]-SS, [D-Trp8, D-Cys14]-SS, Des-Asn5-[D-Trp8, D-Ser13]-SS, and Des (AA)1,2,4,5,12,13, [D-Trp8]-SS, and they did not show selective effects on the suppression of basal concentrations of GH, insulin, glucagon, pancreatic polypeptide, gastrin, gastric inhibitory peptide, motilin, enteroglucagon, or neurotensin. The observation that the potency of these analogs is similar to that of the parent molecule throws considerable light on the structure/activity relationship of the somatostatin molecule. Des-AA1,2,4,5,12,13, [D-Trp8]-Ss has been reported to have a prolonged action when administered sc. When administered iv, however, this octapeptide analog ws not long acting, suggesting that the prolonged action seen in the previous study was a result of delayed uptake from the injection site. An increment in plasma SS concentrations of 19 +/- 3 pmol/liter suppressed basal concentrations of GH, insulin, glucagon, and several gastrointestinal hormones by more than 50%, suggesting that even small changes in plasma SS levels may be physiologically important.

Single strand DNA functionalized single wall carbon nanotubes as sensitive electrochemical labels for arsenite detection.

PubMed

Wang, Yonghong; Wang, Ping; Wang, Yiqiang; He, Xiaoxiao; Wang, Kemin

2015-08-15

In this work, a simple and sensitive electrochemical strategy for arsenite detection based on the ability of arsenite bound to single-strand DNA (ssDNA) and the signal transduction of single wall carbon nanotubes (SWCNTs) is developed. To realize this purpose, the ssDNA/SWCNTs complexes were formed at first by making ssDNA wrapped around SWCNTs via π-stacking. In the presence of arsenite, the arsenite could strongly bind with the G/T bases of ssDNA and decrease the π-π interaction between ssDNA and SWCNTs, resulting in a certain amount of ssDNA dissociating from the complexes. The separated SWCNTs were selectively assembled on the self-assembled monolayer (SAM) modified Au electrode. Then the SWCNTs onto the SAM-modified Au electrode substantially restored heterogeneous electron transfer that was almost totally blocked by the SAM. The assembled SWCNTs could generate a considerably sensitive and specific tactic for signal transduction, which was related to the concentration of the arsenite. Through detecting the currents mediated by SWCNTs, a linear response to concentration of arsenite ranging from 0.5 to 10ppb and a detection limit of 0.5ppb was readily achieved with desirable specificity and sensitivity. Such a SWCNTs-based biosensor creates a simple, sensitive, nonradioactive route for detection of arsenite. In addition, this demonstration provides a new approach to fabrication of stable biosensors with favorable electrochemical properties believed to be appealing to electroanalytical applications. Copyright © 2015 Elsevier B.V. All rights reserved.

SS-mPEG chemical modification of recombinant phospholipase C for enhanced thermal stability and catalytic efficiency.

PubMed

Fang, Xian; Wang, Xueting; Li, Guiling; Zeng, Jun; Li, Jian; Liu, Jingwen

2018-05-01

PEGylation is one of the most promising and extensively studied strategies for improving the properties of proteins as well as enzymic physical and thermal stability. Phospholipase C, hydrolyzing the phospholipids offers tremendous applications in diverse fields. However, the poor thermal stability and higher cost of production have restricted its industrial application. This study focused on improving the stabilization of recombinant PLC by chemical modification with methoxypolyethylene glycol-Succinimidyl Succinate (SS-mPEG, MW 5000). PLC gene from isolate Bacillus cereus HSL3 was fused with SUMO, a novel small ubiquitin-related modifier expression vector and over expressed in Escherichia coli. The soluble fraction of SUMO-PLC reached 80% of the total recombinant protein. The enzyme exhibited maximum catalytic activity at 80 °C and was relatively thermostable at 40-70 °C. It showed extensive substrate specificity pattern and marked activity toward phosphatidylcholine, which made it a typical non-specific PLC for industrial purpose. SS-mPEG-PLC complex exhibited an enhanced thermal stability at 70-80 °C and the catalytic efficiency (K cat /K m ) had increased by 3.03 folds compared with free PLC. CD spectrum of SS-mPEG-PLC indicated a possible enzyme aggregation after chemical modification, which contributed to the higher thermostability of SS-mPEG-PLC. The increase of antiparallel β sheets in secondary structure also made it more stable than parallel β sheets. The presence of SS-mPEG chains on the enzyme molecule surface somewhat changed the binding rate of the substrates, leading to a significant improvement in catalytic efficiency. This study provided an insight into the addition of SS-mPEG for enhancing the industrial applications of phospholipase C at higher temperature. Copyright © 2018 Elsevier B.V. All rights reserved.

Detection of SYT-SSX mutant transcripts in formalin-fixed paraffin-embedded sarcoma tissues using one-step reverse transcriptase real-time PCR.

PubMed

Norlelawati, A T; Mohd Danial, G; Nora, H; Nadia, O; Zatur Rawihah, K; Nor Zamzila, A; Naznin, M

2016-04-01

Synovial sarcoma (SS) is a rare cancer and accounts for 5-10% of adult soft tissue sarcomas. Making an accurate diagnosis is difficult due to the overlapping histological features of SS with other types of sarcomas and the non-specific immunohistochemistry profile findings. Molecular testing is thus considered necessary to confirm the diagnosis since more than 90% of SS cases carry the transcript of t(X;18)(p11.2;q11.2). The purpose of this study is to diagnose SS at molecular level by testing for t(X;18) fusion-transcript expression through One-step reverse transcriptase real-time Polymerase Chain Reaction (PCR). Formalin-fixed paraffin-embedded tissue blocks of 23 cases of soft tissue sarcomas, which included 5 and 8 cases reported as SS as the primary diagnosis and differential diagnosis respectively, were retrieved from the Department of Pathology, Tengku Ampuan Afzan Hospital, Kuantan, Pahang. RNA was purified from the tissue block sections and then subjected to One-step reverse transcriptase real-time PCR using sequence specific hydrolysis probes for simultaneous detection of either SYT-SSX1 or SYT-SSX2 fusion transcript. Of the 23 cases, 4 cases were found to be positive for SYT-SSX fusion transcript in which 2 were diagnosed as SS whereas in the 2 other cases, SS was the differential diagnosis. Three cases were excluded due to failure of both amplification assays SYT-SSX and control β-2-microglobulin. The remaining 16 cases were negative for the fusion transcript. This study has shown that the application of One-Step reverse transcriptase real time PCR for the detection SYT-SSX transcript is feasible as an aid in confirming the diagnosis of synovial sarcoma.

Effect of Low-Temperature Sensitization on the Corrosion Behavior of AISI Type 304L SS Weld Metal in Simulated Groundwater

NASA Astrophysics Data System (ADS)

Suresh, Girija; Nandakumar, T.; Viswanath, A.

2018-04-01

The manuscript presents the investigations carried out on the effect of low-temperature sensitization (LTS) of 304L SS weld metal on its corrosion behavior in simulated groundwater, for its application as a canister material for long-term storage of nuclear vitrified high-level waste in geological repositories. AISI type 304L SS weld pad was fabricated by multipass gas tungsten arc welding process using 308L SS filler wire. The as-welded specimens were subsequently subjected to carbide nucleation and further to LTS at 500 °C for 11 days to simulate a temperature of 300 °C for 100-year life of the canister in geological repositories. Delta ferrite (δ-ferrite) content of the 304L SS weld metal substantially decreased on carbide nucleation treatment and further only a marginal decrease occurred on LTS treatment. The microstructure of the as-welded consisted of δ-ferrite as a minor phase distributed in austenite matrix. The δ-ferrite appeared fragmented in the carbide-nucleated and LTS-treated weld metal. The degree of sensitization measured by double-loop electrochemical potentokinetic reactivation method indicated an increase in carbide nucleation treatment when compared to the as-welded specimens, and further increase occurred on LTS treatment. Potentiodynamic anodic polarization investigations in simulated groundwater indicated a substantial decrease in the localized corrosion resistance of the carbide-nucleated and LTS 304L SS weld metals, when compared to the as-welded specimens. Post-experimental micrographs indicated pitting as the primary mode of attack in the as-welded, while pitting and intergranular corrosion (IGC) occurred in the carbide-nucleated weld metal. LTS-treated weld metal predominantly underwent IGC attack. The decrease in the localized corrosion resistance of the weld metal after LTS treatment was found to have a direct correlation with the degree of sensitization and the weld microstructure. The results are detailed in the manuscript.

Effect of Low-Temperature Sensitization on the Corrosion Behavior of AISI Type 304L SS Weld Metal in Simulated Groundwater

NASA Astrophysics Data System (ADS)

Suresh, Girija; Nandakumar, T.; Viswanath, A.

2018-05-01

The manuscript presents the investigations carried out on the effect of low-temperature sensitization (LTS) of 304L SS weld metal on its corrosion behavior in simulated groundwater, for its application as a canister material for long-term storage of nuclear vitrified high-level waste in geological repositories. AISI type 304L SS weld pad was fabricated by multipass gas tungsten arc welding process using 308L SS filler wire. The as-welded specimens were subsequently subjected to carbide nucleation and further to LTS at 500 °C for 11 days to simulate a temperature of 300 °C for 100-year life of the canister in geological repositories. Delta ferrite ( δ-ferrite) content of the 304L SS weld metal substantially decreased on carbide nucleation treatment and further only a marginal decrease occurred on LTS treatment. The microstructure of the as-welded consisted of δ-ferrite as a minor phase distributed in austenite matrix. The δ-ferrite appeared fragmented in the carbide-nucleated and LTS-treated weld metal. The degree of sensitization measured by double-loop electrochemical potentokinetic reactivation method indicated an increase in carbide nucleation treatment when compared to the as-welded specimens, and further increase occurred on LTS treatment. Potentiodynamic anodic polarization investigations in simulated groundwater indicated a substantial decrease in the localized corrosion resistance of the carbide-nucleated and LTS 304L SS weld metals, when compared to the as-welded specimens. Post-experimental micrographs indicated pitting as the primary mode of attack in the as-welded, while pitting and intergranular corrosion (IGC) occurred in the carbide-nucleated weld metal. LTS-treated weld metal predominantly underwent IGC attack. The decrease in the localized corrosion resistance of the weld metal after LTS treatment was found to have a direct correlation with the degree of sensitization and the weld microstructure. The results are detailed in the manuscript.

Non-covalent binding of nucleic acids with gold nanoparticles provides their stability and effective desorption in environment mimicking biological media.

PubMed

Epanchintseva, Anna; Dolodoev, Anton; Grigor'eva, Alina; Chelobanov, Boris; Pyshnyi, Dmitrii; Ryabchikova, Elena; Pyshnaya, Inna

2018-08-31

The ability of gold nanoparticles to bind different substances has resulted in the high interest of researchers determining their usage as a promising carrier of various biological substances including nucleic acids (NAs) for therapeutic applications. Most publications report covalent binding (conjugation) of an NA to spherical AuNPs via the Au-S bond. In this work, we obtained non-covalent associates of different ssDNA, ssRNA and siRNAs with spherical gold nanoparticles (AuNPs) and examined their physico-chemical properties and stability in media mimicking intracellular space (bacterial 'cytosol') and cell culture media (10% FBS in DMEM). The 'cytosol' was obtained from E. coli and possessed nuclease activity. For the first time, we used the phosphoryl guanidine (dimethylimidazolidin-2-imine, Dmi) group for modification of 3'-ends to enhance the stability of ssRNAs and siRNAs against nuclease destruction. Trying to evaluate the material balance, we analyzed the whole nucleotide species obtained after incubation of NA-AuNPs associates in 'cytosol' and FBS and evaluated the degree of NAs destruction, a share of full-size NAs remained on the surface of the AuNPs and in the solution. Native ss- and siRNAs, both free and in composition of non-covalent associates with AuNPs, were less resistant to degrading factors than ssDNA. The introduction of two Dmi-groups into the ssDNA increased its stability in 'cytosol' three times within 2.5 h. Dmi-modified siRNAs in non-covalent associates with AuNPs were two times more stable than unmodified siRNA within 4 h. We showed that non-covalent siRNA-AuNPs associates serve as a kind of storage for full-size NAs and thereby prolong their presence in nuclease-active media. Our study showed that non-covalent binding of siRNAs with a surface of AuNPs provides desorption of both strands, which is necessary for siRNA functioning in living cells, and could be considered as an important way to construct siRNA and ssDNA delivery systems based on AuNPs.

Identification and characterization of a type III secretion-associated chaperone in the type III secretion system 1 of Vibrio parahaemolyticus.

PubMed

Akeda, Yukihiro; Okayama, Kanna; Kimura, Tomomi; Dryselius, Rikard; Kodama, Toshio; Oishi, Kazunori; Iida, Tetsuya; Honda, Takeshi

2009-07-01

Vibrio parahaemolyticus causes human gastroenteritis. Genomic sequencing of this organism has revealed that it has two sets of type III secretion systems, T3SS1 and T3SS2, both of which are important for its pathogenicity. However, the mechanism of protein secretion via T3SSs is unknown. A characteristic of many effectors is that they require specific chaperones for efficient delivery via T3SSs; however, no chaperone has been experimentally identified in the T3SSs of V. parahaemolyticus. In this study, we identified candidate T3SS1-associated chaperones from genomic sequence data and examined their roles in effector secretion/translocation and binding to their cognate substrates. From these experiments, we concluded that there is a T3S-associated chaperone, VecA, for a cytotoxic T3SS1-dependent effector, VepA. Further analysis using pulldown and secretion assays characterized the chaperone-binding domain encompassing the first 30-100 amino acids and an amino terminal secretion signal encompassing the first 5-20 amino acids on VepA. These findings will provide a strategy to clarify how the T3SS1 of V. parahaemolyticus secretes its specific effectors.

A family longevity selection score: ranking sibships by their longevity, size, and availability for study.

PubMed

Sebastiani, Paola; Hadley, Evan C; Province, Michael; Christensen, Kaare; Rossi, Winifred; Perls, Thomas T; Ash, Arlene S

2009-12-15

Family studies of exceptional longevity can potentially identify genetic and other factors contributing to long life and healthy aging. Although such studies seek families that are exceptionally long lived, they also need living members who can provide DNA and phenotype information. On the basis of these considerations, the authors developed a metric to rank families for selection into a family study of longevity. Their measure, the family longevity selection score (FLoSS), is the sum of 2 components: 1) an estimated family longevity score built from birth-, gender-, and nation-specific cohort survival probabilities and 2) a bonus for older living siblings. The authors examined properties of FLoSS-based family rankings by using data from 3 ongoing studies: the New England Centenarian Study, the Framingham Heart Study, and screenees for the Long Life Family Study. FLoSS-based selection yields families with exceptional longevity, satisfactory sibship sizes and numbers of living siblings, and high ages. Parameters in the FLoSS formula can be tailored for studies of specific populations or age ranges or with different conditions. The first component of the FLoSS also provides a conceptually sound survival measure to characterize exceptional longevity in individuals or families in various types of studies and correlates well with later-observed longevity.

Classification and Morphological Parameters of the Scapular Spine

PubMed Central

Wang, Hua-Jun; Giambini, Hugo; Hou, Da-Biao; Huan, Song-Wei; Liu, Ning; Yang, Jie; Chen, Chao; Gao, Yan-Ping; Shang, Ru-Guo; Li, Yi-Kai; Zha, Zhen-gang

2015-01-01

Abstract Incidence of scapular spine (SS) fractures as a result of complications of reverse total shoulder arthroplasty is relatively high leading to inferior clinical outcomes and an increased risk of revision and dislocation. Fractures of SS because of trauma, including the acromion, constitute 6% to 23% of scapula fractures. The purpose of this study was to classify the SS and present specific geometrical parameters according to osteologic features. A total of 319 intact dry scapulae were collected and classified based on morphological characteristics and shape of the SS. Nine bony landmarks were also chosen and described for their relevance to regions of interest for scapular fixation. Five specific types of SS were noted and the most prevalent groups were Type 1 (Fusiform shape) (47.17%) and Type 5 (Horizontal S-shape) (19.18%). Overall, Types 3, 4, and 1 showed thicker landmark values compared to Type 5, with Type 2 having smaller values. Our classification into 5 distinct types allowed appreciation of the anatomical variance of SSs. The contours of Types 5 and 1 presented a more complex morphology and may lead to a worse surgical approach due to a fracture. As Types 2 and 5 were much thinner than the other types, these may be more susceptible to fractures. PMID:26559282

Live, attenuated Salmonella typhimurium vectoring Campylobacter antigens.

PubMed

Sizemore, Donata R; Warner, Beth; Lawrence, Julie; Jones, Amy; Killeen, Kevin P

2006-05-01

We describe the evaluation of three live, attenuated deltaphoP/Q Salmonella enteric serovar Typhimurium strains expressing PEB1 minus its signal sequence (PEB1-ss) from three different plasmids: a pBR-based asd plasmid, an arabinose-based runaway plasmid, which each expressed PEB1-ss in the bacterial cytosol, and a PEB1::HlyA fusion plasmid that directs secretion of PEB1-ss into the extracellular milieu. Serum IgG responses specific for PEB1-ss were induced by pBR-derived and runaway plasmids, with 100 and 90% seroconversion, respectively, at a 1:500 dilution of anti-sera as measured by Western blot analysis, while the PEB1-ss::HlyA fusion plasmid induced serum IgG in only 20% of the mice. Although significant levels of anti-PEB serum IgG were induced, no protection against oral Campylobacter jejuni challenge was observed.

A state-specific approach to multireference coupled electron-pair approximation like methods: Development and applications

NASA Astrophysics Data System (ADS)

Chattopadhyay, Sudip; Pahari, Dola; Mukherjee, Debashis; Mahapatra, Uttam Sinha

2004-04-01

The traditional multireference (MR) coupled-cluster (CC) methods based on the effective Hamiltonian are often beset by the problem of intruder states, and are not suitable for studying potential energy surface (PES) involving real or avoided curve crossing. State-specific MR-based approaches obviate this limitation. The state-specific MRCC (SS-MRCC) method developed some years ago [Mahapatra et al., J. Chem. Phys. 110, 6171 (1999)] can handle quasidegeneracy of varying degrees over a wide range of PES, including regions of real or avoided curve-crossing. Motivated by its success, we have suggested and explored in this paper a suite of physically motivated coupled electron-pair approximations (SS-MRCEPA) like methods, which are designed to capture the essential strength of the parent SS-MRCC method without significant sacrificing its accuracy. These SS-MRCEPA theories, like their CC counterparts, are based on complete active space, treat all the reference functions on the same footing and provide a description of potentially uniform precision of PES of states with varying MR character. The combining coefficients of the reference functions are self-consistently determined along with the cluster amplitudes themselves. The newly developed SS-MRCEPA methods are size-extensive, and are also size-consistent with localized orbitals. Among the various versions, there are two which are invariant with respect to the restricted rotations among doubly occupied and active orbitals separately. Similarity of performance of this latter and the noninvariant versions at the crossing points of the degenerate orbitals imply that the all the methods presented are rather robust with respect to the rotations among degenerate orbitals. Illustrative numerical applications are presented for PES of the ground state of a number of difficult test cases such as the model H4, H8 problems, the insertion of Be into H2, and Li2, where intruders exist and for a state of a molecule such as CH2, with pronounced MR character. Results obtained with SS-MRCEPA methods are found to be comparable in accuracy to the parent SS-MRCC and FCI/large scale CI results throughout the PES, which indicates the efficacy of our SS-MRCEPA methods over a wide range of geometries, despite their neglect of a host of complicated nonlinear terms, even when the traditional MR-based methods based on effective Hamiltonians fail due to intruders.

Nodule morphology, symbiotic specificity and association with unusual rhizobia are distinguishing features of the genus Listia within the southern African crotalarioid clade Lotononis s.l.

PubMed Central

Ardley, Julie K.; Reeve, Wayne G.; O'Hara, Graham W.; Yates, Ron J.; Dilworth, Michael J.; Howieson, John G.

2013-01-01

Background and Aims The legume clade Lotononis sensu lato (s.l.; tribe Crotalarieae) comprises three genera: Listia, Leobordea and Lotononis sensu stricto (s.s.). Listia species are symbiotically specific and form lupinoid nodules with rhizobial species of Methylobacterium and Microvirga. This work investigated whether these symbiotic traits were confined to Listia by determining the ability of rhizobial strains isolated from species of Lotononis s.l. to nodulate Listia, Leobordea and Lotononis s.s. hosts and by examining the morphology and structure of the resulting nodules. Methods Rhizobia were characterized by sequencing their 16S rRNA and nodA genes. Nodulation and N2 fixation on eight taxonomically diverse Lotononis s.l. species were determined in glasshouse trials. Nodules of all hosts, and the process of infection and nodule initiation in Listia angolensis and Listia bainesii, were examined by light microscopy. Key Results Rhizobia associated with Lotononis s.l. were phylogenetically diverse. Leobordea and Lotononis s.s. isolates were most closely related to Bradyrhizobium spp., Ensifer meliloti, Mesorhizobium tianshanense and Methylobacterium nodulans. Listia angolensis formed effective nodules only with species of Microvirga. Listia bainesii nodulated only with pigmented Methylobacterium. Five lineages of nodA were found. Listia angolensis and L. bainesii formed lupinoid nodules, whereas nodules of Leobordea and Lotononis s.s. species were indeterminate. All effective nodules contained uniformly infected central tissue. Listia angolensis and L. bainesii nodule initials occurred on the border of the hypocotyl and along the tap root, and nodule primordia developed in the outer cortical layer. Neither root hair curling nor infection threads were seen. Conclusions Two specificity groups occur within Lotononis s.l.: Listia species are symbiotically specific, while species of Leobordea and Lotononis s.s. are generally promiscuous and interact with rhizobia of diverse chromosomal and symbiotic lineages. The seasonally waterlogged habitat of Listia species may favour the development of symbiotic specificity. PMID:23712451

Cross-borehole slug test analysis in a fractured limestone aquifer

NASA Astrophysics Data System (ADS)

Audouin, Olivier; Bodin, Jacques

2008-01-01

SummaryThis work proposes new semi-analytical solutions for the interpretation of cross-borehole slug tests in fractured media. Our model is an extension of a previous work by Barker [Barker, J.A., 1988. A generalized radial flow model for hydraulic tests in fractured rock. Water Resources Research 24 (10), 1796-1804; Butler Jr., J.J., Zhan X., 2004. Hydraulic tests in highly permeable aquifers. Water Resources Research 40, W12402. doi:10.1029/2003/WR002998]. It includes inertial effects at both test and observation wells and a fractional flow dimension in the aquifer. The model has five fitting parameters: flow dimension n, hydraulic conductivity K, specific storage coefficient Ss, and effective lengths of test well Le and of observation well Leo. The results of a sensitivity analysis show that the most sensitive parameter is the flow dimension n. The model sensitivity to other parameters may be ranked as follows: K > Le ˜ Leo > Ss. The sensitivity to aquifer storage remains one or two orders of magnitude lower than that to other parameters. The model has been coupled to an automatic inversion algorithm for facilitating the interpretation of real field data. This inversion algorithm is based on a Gauss-Newton optimization procedure conditioned by re-scaled sensitivities. It has been used to interpret successfully cross-borehole slug test data from the Hydrogeological Experimental Site (HES) of Poitiers, France, consisting of fractured and karstic limestones. HES data provide flow dimension values ranging between 1.6 and 2.5, and hydraulic conductivity values ranging between 4.4 × 10 -5 and 7.7 × 10 -4 m s -1. These values are consistent with previous interpretations of single-well slug tests. The results of the sensitivity analysis are confirmed by calculations of relative errors on parameter estimates, which show that accuracy on n and K is below 20% and that on Ss is about one order of magnitude. The K-values interpreted from cross-borehole slug tests are one order of magnitude higher than those previously interpreted from interference pumping tests. These findings suggest that cross-borehole slug tests focus on preferential flowpath networks made by fractures and karstic channels, i.e. the head perturbation induced by a slug test propagates only through those flowpaths with the lowest hydraulic resistance. As a result, cross-borehole slug tests are expected to identify the hydrodynamic properties of karstic-channels and fracture flowpaths, and may be considered as complementary to pumping tests which more likely provide bulk properties of the whole fracture/karstic-channel/matrix system.

A distinct and divergent lineage of genomic island-associated Type IV Secretion Systems in Legionella.

PubMed

Wee, Bryan A; Woolfit, Megan; Beatson, Scott A; Petty, Nicola K

2013-01-01

Legionella encodes multiple classes of Type IV Secretion Systems (T4SSs), including the Dot/Icm protein secretion system that is essential for intracellular multiplication in amoebal and human hosts. Other T4SSs not essential for virulence are thought to facilitate the acquisition of niche-specific adaptation genes including the numerous effector genes that are a hallmark of this genus. Previously, we identified two novel gene clusters in the draft genome of Legionella pneumophila strain 130b that encode homologues of a subtype of T4SS, the genomic island-associated T4SS (GI-T4SS), usually associated with integrative and conjugative elements (ICE). In this study, we performed genomic analyses of 14 homologous GI-T4SS clusters found in eight publicly available Legionella genomes and show that this cluster is unusually well conserved in a region of high plasticity. Phylogenetic analyses show that Legionella GI-T4SSs are substantially divergent from other members of this subtype of T4SS and represent a novel clade of GI-T4SSs only found in this genus. The GI-T4SS was found to be under purifying selection, suggesting it is functional and may play an important role in the evolution and adaptation of Legionella. Like other GI-T4SSs, the Legionella clusters are also associated with ICEs, but lack the typical integration and replication modules of related ICEs. The absence of complete replication and DNA pre-processing modules, together with the presence of Legionella-specific regulatory elements, suggest the Legionella GI-T4SS-associated ICE is unique and may employ novel mechanisms of regulation, maintenance and excision. The Legionella GI-T4SS cluster was found to be associated with several cargo genes, including numerous antibiotic resistance and virulence factors, which may confer a fitness benefit to the organism. The in-silico characterisation of this new T4SS furthers our understanding of the diversity of secretion systems involved in the frequent horizontal gene transfers that allow Legionella to adapt to and exploit diverse environmental niches.

A Distinct and Divergent Lineage of Genomic Island-Associated Type IV Secretion Systems in Legionella

PubMed Central

Wee, Bryan A.; Woolfit, Megan; Beatson, Scott A.; Petty, Nicola K.

2013-01-01

Legionella encodes multiple classes of Type IV Secretion Systems (T4SSs), including the Dot/Icm protein secretion system that is essential for intracellular multiplication in amoebal and human hosts. Other T4SSs not essential for virulence are thought to facilitate the acquisition of niche-specific adaptation genes including the numerous effector genes that are a hallmark of this genus. Previously, we identified two novel gene clusters in the draft genome of Legionella pneumophila strain 130b that encode homologues of a subtype of T4SS, the genomic island-associated T4SS (GI-T4SS), usually associated with integrative and conjugative elements (ICE). In this study, we performed genomic analyses of 14 homologous GI-T4SS clusters found in eight publicly available Legionella genomes and show that this cluster is unusually well conserved in a region of high plasticity. Phylogenetic analyses show that Legionella GI-T4SSs are substantially divergent from other members of this subtype of T4SS and represent a novel clade of GI-T4SSs only found in this genus. The GI-T4SS was found to be under purifying selection, suggesting it is functional and may play an important role in the evolution and adaptation of Legionella. Like other GI-T4SSs, the Legionella clusters are also associated with ICEs, but lack the typical integration and replication modules of related ICEs. The absence of complete replication and DNA pre-processing modules, together with the presence of Legionella-specific regulatory elements, suggest the Legionella GI-T4SS-associated ICE is unique and may employ novel mechanisms of regulation, maintenance and excision. The Legionella GI-T4SS cluster was found to be associated with several cargo genes, including numerous antibiotic resistance and virulence factors, which may confer a fitness benefit to the organism. The in-silico characterisation of this new T4SS furthers our understanding of the diversity of secretion systems involved in the frequent horizontal gene transfers that allow Legionella to adapt to and exploit diverse environmental niches. PMID:24358157

[Effects of short-term deep vertically rotary tillage on topsoil structure of lime concretion black soil and wheat growth in Huang-Huai-Hai Plain, China].

PubMed

Zhai, Zhen; Li, Yu Yi; Zhang, Li; Pang, Bo; Pang, Huan Cheng; Wei, Ben Hui; Wang, Qing Wei; Qi, Shao Wei

2017-04-18

Annual rotary tillage can often create a compacted plough pan and shallow arable layer which hampers the high crop yield in Huang-Huai-Hai region. A brand new farming method named Vertically Rotary Tillage was introduced to solve this problem. One short-term field experiment was conducted to explore the effect of deep vertically rotary tillage on soil physical properties and photosynthetic characteristics at flowering stage of winter wheat. Two tillage treatments were designed including subsoiling tillage with 20 cm depth (SS 20 , CK) and deep vertically rotary tillage with 30 cm depth (DVR 30 ). The result showed that compared with SS 20 treatment, DVR 30 treatment could thoroughly break the plow pan and loose the arable layer. The soil bulk density at 10-20 cm and 20-30 cm layers under DVR 30 treatment was decreased by 9.5% and 11.2% respectively than that under SS 20 treatment. Meanwhile, the penetration resistance at 20-30 cm layer under DVR 30 treatment was also decreased by 42.3% than that under SS 20 treatment. Moreover, water infiltration under DVR 30 treatment and the soil water storage in the deep soil layers was then increased. The mass water content of soil increased significantly with the increase of soil depth. There was significant difference of mass water content of 30-40 cm 40-50 cm between SS 20 and DVR 30 . The mass water content 30-40 cm and 40-50 cm layers under DVR 30 treatment was increased by 16.9% and 10.6% compared with SS 20 treatment, respectively. Furthermore, DVR 30 treatment promoted the improvement of the photosynthetic capacity of wheat which could contribute to the dry matter accumulation of winter wheat. The net photosynthesis rate and SPAD at flowering stage of winter wheat leaves under DVR 30 treatment were increased by 1.3% and 15.5% respectively than that under SS 20 treatment, thereby the above and underground dry matter accumulation of winter wheat under DVR 30 was increased significantly. Due to all the superiority of DVR 30 treatment over SS 20 treatment showed above, the winter wheat yield under DVR 30 treatment was increased by 12.4% than that under SS 20 . It was concluded that deep vertically rotary tillage could provide a new and effective way to break up the compacted plough pan, build a reasonable soil structure and increase crop yield.

Ordered Self-Assembled Monolayers of Peptide Nucleic Acids with DNA Recognition Capability

NASA Astrophysics Data System (ADS)

Briones, C.; Mateo-Marti, E.; Gómez-Navarro, C.; Parro, V.; Román, E.; Martín-Gago, J. A.

2004-11-01

We report on the formation of ordered self-assembled monolayers (SAMs) of single-stranded peptide nucleic acids (ssPNA). In spite of their remarkable length (7nm) thiolated PNAs assemble standing up on gold surfaces similarly to the SAMs of short alkanethiols. SAMs of ssPNA recognize complementary nucleic acids, acting as specific biosensors that discriminate even a point mutation in target ssDNA. These results are obtained by surface characterization techniques that avoid labeling of the target molecule: x-ray photoemission, x-ray absorption and atomic force microscopy.

Antagonist effects of seglitide (MK 678) at somatostatin receptors in guinea-pig isolated right atria.

PubMed Central

Dimech, J.; Feniuk, W.; Humphrey, P. P.

1993-01-01

Somatostatin (SS) exerts a negative inotropic effect in isolated atria. Here we report that in guinea-pig isolated right atria, seglitide, a potent cyclic hexapeptide somatostatin agonist, behaves as a competitive somatostatin receptor antagonist with pA2 values against SS14, SS25 and SS28, of 6.50 +/- 0.40, 6.24 +/- 0.08 and 6.09 +/- 0.06, respectively. Seglitide had little or no effect on the negative inotropic action of carbachol or N6-cyclohexyladenosine. Our findings indicate that the receptor-response coupling characteristics of guinea-pig atria are such that in this preparation seglitide has low intrinsic activity and behaves specifically as a somatostatin receptor antagonist. PMID:8104651

[Construction and immunogenicity of recombinant porcine parvovirus-like particles with somatostatin].

PubMed

Zhang, Xuehua; Zheng, Qisheng; Chen, Jin; Xue, Gang; Hou, Hongyan; Hou, Jibo

2010-08-01

In order to obtain a virus-like particle vaccine both for porcine parvovirus (PPV) prevention and growth-promotion, VP2 gene of PPV NJ-a strain was amplified with PCR, and four copies of synthetic somatostatin gene were fused to the N-terminal of VP2 gene. The fused gene was cloned into pFast-HT A to construct the recombinant plasmid pFast-SS4-VP2, then the pFast-SS4-VP2 was transformed into DH10Bac competent cells and recombined with shuttle vector Bacmid, followed by identification with blue-white screening and PCR analysis for three cycles, and the positive recombinant was named as rBacmid-SS4-VP2. The positive Sf-9 cells were transfected with rBacmid-SS4-VP2 by Lipofectamine to produce recombinant baculovirus. When the cytopathic effect (CPE) was obvious, the transfected Sf-9 cell was harvested, and the positive recombinant virus was named as rBac-SS4-VP2. The insertion for the target gene into baculovirus genome was confirmed with PCR. SDS-PAGE and Western blotting revealed that the calculated protein of approximately 68 kDa was in the expressed in the insect cells. The Sf-9 cells infected with rBac-SS4-VP2 were stained positive against PPV antibody using the indirect immunofluorescence assay (IFA). Moreover, the virus particle self-assembly was observed under electron microscopy. 90 four-week-old mice were immunized by the recombinant protein coupled with different adjuvants alhydrogel, IMS and oil. VP2-specific ELISA antibodies, PPV-specific neutralizing antibody, somatostatin antibody and growth hormone levels were examined to evaluate the immunogenicity of this virus like particle. Results indicated that mice groups immunized rSS4-VP2 protein with alhydrogel and IMS developed similar humoral immune response comparing with inactived PPV vaccine. Mice group immunized with rSS4-VP2 generated higher level of SS antibody and growth hormone comparing with negative control, mice receiving rSS4-VP2 with alhydrogel developed the highest antibody titre than all other groups, while the oil group developed the lowest antibody level. This study provides not only a new rout for production of safe and effective virus like particle subunit vaccine, but also the foundations for peptide presentation and multivalent subunit vaccine design.

Sum frequency generation and solid-state NMR study of the structure, orientation, and dynamics of polystyrene-adsorbed peptides

PubMed Central

Weidner, Tobias; Breen, Nicholas F.; Li, Kun; Drobny, Gary P.; Castner, David G.

2010-01-01

The power of combining sum frequency generation (SFG) vibrational spectroscopy and solid-state nuclear magnetic resonance (ssNMR) spectroscopy to quantify, with site specificity and atomic resolution, the orientation and dynamics of side chains in synthetic model peptides adsorbed onto polystyrene (PS) surfaces is demonstrated in this study. Although isotopic labeling has long been used in ssNMR studies to site-specifically probe the structure and dynamics of biomolecules, the potential of SFG to probe side chain orientation in isotopically labeled surface-adsorbed peptides and proteins remains largely unexplored. The 14 amino acid leucine-lysine peptide studied in this work is known to form an α-helical secondary structure at liquid-solid interfaces. Selective, individual deuteration of the isopropyl group in each leucine residue was used to probe the orientation and dynamics of each individual leucine side chain of LKα14 adsorbed onto PS. The selective isotopic labeling methods allowed SFG analysis to determine the orientations of individual side chains in adsorbed peptides. Side chain dynamics were obtained by fitting the deuterium ssNMR line shape to specific motional models. Through the combined use of SFG and ssNMR, the dynamic trends observed for individual side chains by ssNMR have been correlated with side chain orientation relative to the PS surface as determined by SFG. This combination provides a more complete and quantitative picture of the structure, orientation, and dynamics of these surface-adsorbed peptides than could be obtained if either technique were used separately. PMID:20628016

Tetraterpene Synthase Substrate and Product Specificity in the Green Microalga Botryococcus braunii Race L.

PubMed

Thapa, Hem R; Tang, Su; Sacchettini, James C; Devarenne, Timothy P

2017-09-15

Recently, the biosynthetic pathway for lycopadiene, a C 40 tetraterpenoid hydrocarbon, was deciphered from the L race of Botryococcus braunii, an alga that produces hydrocarbon oils capable of being converted into combustible fuels. The lycopadiene pathway is initiated by the squalene synthase (SS)-like enzyme lycopaoctaene synthase (LOS), which catalyzes the head-to-head condensation of two C 20 geranylgeranyl diphosphate (GGPP) molecules to produce C 40 lycopaoctaene. LOS shows unusual substrate promiscuity for SS or SS-like enzymes by utilizing C 15 farnesyl diphosphate (FPP) and C 20 phytyl diphosphate in addition to GGPP as substrates. These three substrates can be combined by LOS individually or in combinations to produce six different hydrocarbons of C 30 , C 35 , and C 40 chain lengths. To understand LOS substrate and product specificity, rational mutagenesis experiments were conducted based on sequence alignment with several SS proteins as well as a structural comparison with the human SS (HSS) crystal structure. Characterization of the LOS mutants in vitro identified Ser276 and Ala288 in the LOS active site as key amino acids responsible for controlling substrate binding, and thus the promiscuity of this enzyme. Mutating these residues to those found in HSS largely converted LOS from lycopaoctaene production to C 30 squalene production. Furthermore, these studies were confirmed in vivo by expressing LOS in E. coli cells metabolically engineered to produce high FPP and GGPP levels. These studies also offer insights into tetraterpene hydrocarbon metabolism in B. braunii and provide a foundation for engineering LOS for robust production of specific hydrocarbons of a desired chain length.

[Fool's gold standards in language screening. Sensitivity and specificity of the Hessian child language screening test (Kindersprachscreening, KiSS)].

PubMed

Neumann, K; Holler-Zittlau, I; van Minnen, S; Sick, U; Zaretsky, Y; Euler, H A

2011-01-01

The German Kindersprachscreening (KiSS) is a universal speech and language screening test for large-scale identification of Hessian kindergarten children requiring special educational language training or clinical speech/language therapy. To calculate the procedural screening validity, 257 children (aged 4.0 to 4.5 years) were tested using KiSS and four language tests (Reynell Development Language Scales III, Patholinguistische Diagnostik, PLAKSS, AWST-R). The majority or consensus judgements of three speech-language professionals, based on the language test results, served as a reference criterion. The base (fail) rates of the professionals were either self-determined or preset based on known prevalence rates. Screening validity was higher for preset than for self-determined base rates due to higher inter-judge agreement. The confusion matrices of the overall index classification of the KiSS (speech-language abnormalities with educational or clinical needs) with the fixed base rate expert judgement about language impairment, including fluency or voice disorders, yielded a sensitivity of 88% and a specificity of 78%, for just language impairment 84% and 75%, respectively. Specificities for disorders requiring clinical diagnostics in the KiSS (language impairment alone or combined with fluency/voice disorders) related to the test-based consensus expert judgment was about 93%. Sensitivities were unsatisfactory because the differentiation between educational and clinical needs requires improvement. Since the judgement concordances between the speech-language professionals was only moderate, the development of a comprehensive German reference test for speech and language disorders with evidence-based algorithmic decision rules rather than subjective clinical judgement is advocated.

Replication of tobacco mosaic virus. VII. Further characterization of single- and double-stranded virus-related RNAs from TMV-infected plants.

PubMed

Palukaitis, P; García-Arenal, F; Sulzinski, M A; Zaitlin, M

1983-12-01

The single-stranded (ss) and double-stranded (ds) RNAs produced in tobacco tissue as a result of infection by tobacco mosaic virus (TMV) have been reinvestigated. 32P-labeled probes consisting of either cDNA or viral RNA, complementary to specific regions of either the viral RNA or its negative strand, respectively, were used in "Northern" hybridization experiments. Of the 10 ssRNA bands observed, all but four appeared to be artifacts of electrophoresis. These four RNAs were found on polyribosomes and are presumed to be true mRNAs; three were identified as the well-known genomic RNA, the I2-mRNA and the coat protein mRNA, or LMC. The fourth RNA species of MW approximately 1.2 x 10(6) had not previously been specifically identified as a subgenomic RNA of TMV. The viral RNA which gave rise to the six artifactual ssRNA bands was heterogeneous in size and was shown to be encapsidated in vivo. Upon electrophoresis, these heterogeneous RNA fragments comigrated approximately with plant rRNAs also present in the extracts, generating the observed artifactual bands. Four dsRNAs were also identified. From molecular weight and hybridization analyses, they appeared to be double-stranded forms of the above four polyribosome-associated ssRNAs. Attempts to translate proteins from the denatured dsRNAs in vitro were unsuccessful. A population of low-molecular-weight, TMV-specific ssRNAs, (+) and (-) in sequence, was generated during infection; however these RNAs were believed to be breakdown products.

Dynamics of single-stranded DNA tethered to a solid

NASA Astrophysics Data System (ADS)

Radiom, Milad; Paul, Mark R.; Ducker, William A.

2016-06-01

Tethering is used to deliver specific biological and industrial functions. For example, single-stranded DNA (ssDNA) is tethered to polymerases and long sequences of double-stranded DNA (dsDNA) during replication, and to solids in DNA microarrays. However, tethering ssDNA to a large object limits not only the available ssDNA conformations, but also the range of time-scales over which the mechanical responses of ssDNA are important. In this work we examine the effect of tethering by measurement of the mechanical response of ssDNA that is tethered at each end to two separate atomic force microscope cantilevers in aqueous solution. Thermal motion of the cantilevers drives the ends of the ssDNA chain at frequencies near 2 kHz. The presence of a tethered molecule makes a large difference to the asymmetric cross-correlation of two cantilevers, which enables resolution of the mechanical properties in our experiments. By analysis of the correlated motion of the cantilevers we extract the friction and stiffness of the ssDNA. We find that the measured friction is much larger than the friction that is usually associated with the unencumbered motion of ssDNA. We also find that the measured relaxation time, ∼30 μs, is much greater than prior measurements of the free-molecule relaxation time. We attribute the difference to the loss of conformational possibilities as a result of constraining the ends of the ssDNA.

Cultural Validation of the Maslach Burnout Inventory for Korean Students

ERIC Educational Resources Information Center

Shin, Hyojung; Puig, Ana; Lee, Jayoung; Lee, Ji Hee; Lee, Sang Min

2011-01-01

The purpose of this study was to examine the factorial validity of the MBI-SS in Korean students. Specifically, we investigated whether the original three-factor structure of the MBI-SS was appropriate for use with Korean students. In addition, by running multi-group structural equation model analyses with factorial invariance tests simultaneously…

The scientific results of the low energy portion of A-2

NASA Technical Reports Server (NTRS)

Garmire, G.

1979-01-01

Galactic phenomena observed using the HEAO 1 detectors are discussed. A source map of the soft X-ray sky is presented. Specific topics covered include the optical outburst of U Geminorum, low energy RS CVn stars, and the dwarf nova SS Cygni. Aspects of the SS Cygni pulsations are analyzed.

Sucrose metabolism and growth in transplanted loblolly pine seedlings

Treesearch

Shi-Jean S. Sung; C.C. Black; Paul P. Kormanik

1993-01-01

Loblolly pine (Pinus taeda L.) seedling height, root collar diameter, and the specific activities of three sucrose metabolizing enzymes, namely, sucrose synthase (SS), acid invertase, and neutral invertase, were measured to assess seedling responses to transplant stress. It was concluded that i) SS was the dominant enzyme for sucrose metabolism in...

RPA and POT1: friends or foes at telomeres?

PubMed

Flynn, Rachel Litman; Chang, Sandy; Zou, Lee

2012-02-15

Telomere maintenance in cycling cells relies on both DNA replication and capping by the protein complex shelterin. Two single-stranded DNA (ssDNA)-binding proteins, replication protein A (RPA) and protection of telomere 1 (POT1) play critical roles in DNA replication and telomere capping, respectively. While RPA binds to ssDNA in a non-sequence-specific manner, POT1 specifically recognizes singlestranded TTAGGG telomeric repeats. Loss of POT1 leads to aberrant accumulation of RPA at telomeres and activation of the ataxia telangiectasia and Rad3-related kinase (ATR)-mediated checkpoint response, suggesting that POT1 antagonizes RPA binding to telomeric ssDNA. The requirement for both POT1 and RPA in telomere maintenance and the antagonism between the two proteins raises the important question of how they function in concert on telomeric ssDNA. Two interesting models were proposed by recent studies to explain the regulation of POT1 and RPA at telomeres. Here, we discuss how these models help unravel the coordination, and also the antagonism, between POT1 and RPA during the cell cycle.

Conflict detection and resolution rely on a combination of common and distinct cognitive control networks.

PubMed

Li, Qi; Yang, Guochun; Li, Zhenghan; Qi, Yanyan; Cole, Michael W; Liu, Xun

2017-12-01

Cognitive control can be activated by stimulus-stimulus (S-S) and stimulus-response (S-R) conflicts. However, whether cognitive control is domain-general or domain-specific remains unclear. To deepen the understanding of the functional organization of cognitive control networks, we conducted activation likelihood estimation (ALE) from 111 neuroimaging studies to examine brain activation in conflict-related tasks. We observed that fronto-parietal and cingulo-opercular networks were commonly engaged by S-S and S-R conflicts, showing a domain-general pattern. In addition, S-S conflicts specifically activated distinct brain regions to a greater degree. These regions were implicated in the processing of the semantic-relevant attribute, including the inferior frontal cortex (IFC), superior parietal cortex (SPC), superior occipital cortex (SOC), and right anterior cingulate cortex (ACC). By contrast, S-R conflicts specifically activated the left thalamus, middle frontal cortex (MFC), and right SPC, which were associated with detecting response conflict and orienting spatial attention. These findings suggest that conflict detection and resolution involve a combination of domain-general and domain-specific cognitive control mechanisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Differential roles of SS18-SSX fusion gene and insulin-like growth factor-1 receptor in synovial sarcoma cell growth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toernkvist, Maria; Natalishvili, Natalia; Xie Yuntao

2008-04-11

Recently we demonstrated that the synovial sarcoma specific fusion gene SS18-SSX is crucial for cyclin D1 expression and is linked to cell proliferation. In this report we explore the role of SS18-SSX and IGF-1R for their potential functions in cellular proliferation and survival in cultured synovial sarcoma cells. We found that targeting of SS18-SSX mRNA by antisense oligonucleotide treatment drastically and rapidly decreased cell proliferation but caused only a slight increase of apoptosis. The synovial sarcoma cells were confirmed to express IGF-1R, and treatment with an IGF-1R inhibitor resulted in substantially reduced cell viability by inducing apoptosis in these cells.more » Conversely, inhibition of the IGF-1R resulted only in a slight to moderate decrease in DNA synthesis. In conclusion, SS18-SSX and IGF-1R seem to play important but different roles in maintaining malignant growth of synovial sarcoma cells. Whereas SS18-SSX maintains cyclin D1 and cell proliferation, IGF-1R protects from apoptosis.« less

Pyrolytic carbon-coated stainless steel felt as a high-performance anode for bioelectrochemical systems.

PubMed

Guo, Kun; Hidalgo, Diana; Tommasi, Tonia; Rabaey, Korneel

2016-07-01

Scale up of bioelectrochemical systems (BESs) requires highly conductive, biocompatible and stable electrodes. Here we present pyrolytic carbon-coated stainless steel felt (C-SS felt) as a high-performance and scalable anode. The electrode is created by generating a carbon layer on stainless steel felt (SS felt) via a multi-step deposition process involving α-d-glucose impregnation, caramelization, and pyrolysis. Physicochemical characterizations of the surface elucidate that a thin (20±5μm) and homogenous layer of polycrystalline graphitic carbon was obtained on SS felt surface after modification. The carbon coating significantly increases the biocompatibility, enabling robust electroactive biofilm formation. The C-SS felt electrodes reach current densities (jmax) of 3.65±0.14mA/cm(2) within 7days of operation, which is 11 times higher than plain SS felt electrodes (0.30±0.04mA/cm(2)). The excellent biocompatibility, high specific surface area, high conductivity, good mechanical strength, and low cost make C-SS felt a promising electrode for BESs. Copyright © 2016 Elsevier Ltd. All rights reserved.

MCM ring hexamerization is a prerequisite for DNA-binding

DOE PAGES

Froelich, Clifford A.; Nourse, Amanda; Enemark, Eric J.

2015-09-13

The hexameric Minichromosome Maintenance (MCM) protein complex forms a ring that unwinds DNA at the replication fork in eukaryotes and archaea. Our recent crystal structure of an archaeal MCM N-terminal domain bound to single-stranded DNA (ssDNA) revealed ssDNA associating across tight subunit interfaces but not at the loose interfaces, indicating that DNA-binding is governed not only by the DNA-binding residues of the subunits (MCM ssDNA-binding motif, MSSB) but also by the relative orientation of the subunits. We now extend these findings to show that DNA-binding by the MCM N-terminal domain of the archaeal organism Pyrococcus furiosus occurs specifically in themore » hexameric oligomeric form. We show that mutants defective for hexamerization are defective in binding ssDNA despite retaining all the residues observed to interact with ssDNA in the crystal structure. One mutation that exhibits severely defective hexamerization and ssDNA-binding is at a conserved phenylalanine that aligns with the mouse Mcm4(Chaos3) mutation associated with chromosomal instability, cancer, and decreased intersubunit association.« less

Development of a communication intervention to assist hospitalized suddenly speechless patients.

PubMed

Rodriguez, Carmen S; Rowe, Meredeth; Koeppel, Brent; Thomas, Loris; Troche, Michelle S; Paguio, Glenna

2012-01-01

Healthcare staff face significant challenges while caring for hospitalized patients experiencing sudden inability to verbalize their needs (sudden speechlessness). Familiar methods of communication such as non-verbal strategies are limited and often fail to assist suddenly speechless patients (SS) communicate their needs. Consequently, strategies tailored to the needs of hospitalized speechless patients are necessary, and must consider factors intrinsic to the patients and the complexities of the acute care environment. The feasibility and usability of a multi-functional prototype communication system (speech-generating device) tailored to the needs of hospitalized SS patients was evaluated in this pilot study. Adult SS patients admitted to the intensive care setting (n=11) demonstrated independent use of a multi-functional communication system that integrated messages and strategies tailored to the needs of the hospitalized SS patient. Participants reported high satisfaction levels and considered the use of the technology of high importance during an SS event. Additional research should focus on evaluating the impact of technology specific communication interventions on enhancing the communication process between SS patients and healthcare staff.

Conversion and storage of somatostatin are established before response to secretagogue stimuli in P19 neurons.

PubMed

Cadet, N; Paquin, J

2000-04-14

In mature neurons, neuropeptides are synthesized via limited proteolysis of propolypeptides by convertases. The bioactive peptides are then stored in secretory granules until they are released extracellularly upon the induction of a fusion between granules and the plasma membrane, in response to secretagogues. We used the mouse P19 embryonic carcinoma cells as a model to determine if the capacities to convert and store neuropeptides and to secrete them in a regulated fashion are established coordinately during neuronal differentiation. We have previously shown that both undifferentiated P19 cells and their neuronal derivatives express the largely distributed furin, PACE4 and PC5 convertases, whereas only neuronal derivatives express the neuroendocrine convertase PC2. In addition, undifferentiated cells displayed furin- rather than PC2-like converting capacities. The present work demonstrates that day 8 P19 neurons mainly convert prosomatostatin (proSS) to somatostatin-14 (SS-14) using HPLC and radioimmunoassay (RIA) analyses, indicating that P19 cells acquire PC2-like converting capacities as a consequence of neuronal differentiation. SS-14 was predominantly intracellular in neuronal cells which were shown to express several granins, markers of granules, by Western blotting. However, cell membrane depolarization with 50 mM K+, a general secretagogue stimulus, evoked the release of SS-14 by day 12, but not by day 8, P19 neurons. The results thus demonstrate that capacities to convert and store neuropeptides can be established before coupling of stimulus-secretion during neuronal differentiation.

Sudbury project (University of Muenster-Ontario Geological Survey): Summary of results - an updated impact model

NASA Technical Reports Server (NTRS)

Avermann, M.; Bischoff, L.; Brockmeyer, P.; Buhl, D.; Deutsch, A.; Dressler, B. O.; Lakomy, R.; Mueller-Mohr, V.; Stoeffler, D.

1992-01-01

In 1984 the Ontario Geological Survey initiated a research project on the Sudbury structure (SS) in cooperation with the University of Muenster. The project included field mapping (1984-1989) and petrographic, chemical, and isotope analyses of the major stratigraphic units of the SS. Four diploma theses and four doctoral theses were performed during the project (1984-1992). Specific results of the various investigations are reported. Selected areas of the SS were mapped and sampled: Footwall rocks; Footwall breccia and parts of the sublayer and lower section of the Sudbury Igneous Complex (SIC); Onaping Formation and the upper section of the SIC; and Sudbury breccia and adjacent Footwall rocks along extended profiles up to 55 km from the SIC. All these stratigraphic units of the SS were studied in substantial detail by previous workers. The most important characteristic of the previous research is that it was based either on a volcanic model or on a mixed volcanic-impact model for the origin of the SS. The present project was clearly directed toward a test of the impact origin of the SS without invoking an endogenic component. In general, our results confirm the most widely accepted stratigraphic division of the SS. However, our interpretation of some of the major stratigraphic units is different from most views expressed. The stratigraphy of the SS and its new interpretation is given as a basis for discussion.

Identification of a novel type III secretion-associated outer membrane-bound protein from Xanthomonas campestris pv. campestris

PubMed Central

Li, Lei; Li, Rui-Fang; Ming, Zhen-Hua; Lu, Guang-Tao; Tang, Ji-Liang

2017-01-01

Many bacterial pathogens employ the type III secretion system (T3SS) to translocate effector proteins into eukaryotic cells to overcome host defenses. To date, most of our knowledge about the T3SS molecular architecture comes from the studies on animal pathogens. In plant pathogens, nine Hrc proteins are believed to be structural components of the T3SS, of which HrcC and HrcJ form the outer and inner rings of the T3SS, respectively. Here, we demonstrated that a novel outer membrane-bound protein (HpaM) of Xanthomonas campestris pv. campestris is critical for the type III secretion and is structurally and functionally conserved in phytopathogenic Xanthomonas spp. We showed that the C-terminus of HpaM extends into the periplasm to interact physically with HrcJ and the middle part of HpaM interacts physically with HrcC. It is clear that the outer and inner rings compose the main basal body of the T3SS apparatus in animal pathogens. Therefore, we presume that HpaM may act as a T3SS structural component, or play a role in assisting assembling or affecting the stability of the T3SS apparatus. HpaM is a highly prevalent and specific protein in Xanthomonas spp., suggesting that the T3SS of Xanthomonas is distinctive in some aspects from other pathogens. PMID:28198457

Renal Tumor Necrosis Factor α Contributes to Hypertension in Dahl Salt-Sensitive Rats

PubMed Central

Huang, Baorui; Cheng, Yuan; Usa, Kristie; Liu, Yong; Baker, Maria Angeles; Mattson, David L.; He, Yongcheng; Wang, Niansong; Liang, Mingyu

2016-01-01

Tumor necrosis factor α (TNFα) is a major proinflammatory cytokine and its level is elevated in hypertensive states. Inflammation occurs in the kidneys during the development of hypertension. We hypothesized that TNFα specifically in the kidney contributes to the development of hypertension and renal injury in Dahl salt-sensitive (SS) rats, a widely used model of human salt-sensitive hypertension and renal injury. SS rats were chronically instrumented for renal interstitial infusion and blood pressure measurement in conscious, freely moving state. Gene expression was measured using real-time PCR and renal injury assessed with histological analysis. The abundance of TNFα in the renal medulla of SS rats, but not the salt-insensitive congenic SS.13BN26 rats, was significantly increased when rats had been fed a high-salt diet for 7 days (n = 6 or 9, p < 0.01). The abundance of TNFα receptors in the renal medulla was significantly higher in SS rats than SS.13BN26 rats. Renal interstitial administration of Etanercept, an inhibitor of TNFα, significantly attenuated the development of hypertension in SS rats on a high-salt diet (n = 7–8, p < 0.05). Glomerulosclerosis and interstitial fibrosis were also significantly ameliorated. These findings indicate intrarenal TNFα contributes to the development of hypertension and renal injury in SS rats. PMID:26916681

Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network.

PubMed

Damle, Nikhil Prakash; Mohanty, Debasisa

2014-06-15

In silico prediction of site-specific kinase-substrate relationships (ssKSRs) is crucial for deciphering phosphorylation networks by linking kinomes to phosphoproteomes. However, currently available predictors for ssKSRs give rise to a large number of false-positive results because they use only a short sequence stretch around phosphosite as determinants of kinase specificity and do not consider the biological context of kinase-substrate recognition. Based on the analysis of domain-specific kinase-substrate relationships, we have constructed a domain-level phosphorylation network that implicitly incorporates various contextual factors. It reveals preferential phosphorylation of specific domains by certain kinases. These novel correlations have been implemented in PhosNetConstruct, an automated program for predicting target kinases for a substrate protein. PhosNetConstruct distinguishes cognate kinase-substrate pairs from a large number of non-cognate combinations. Benchmarking on independent datasets using various statistical measures demonstrates the superior performance of PhosNetConstruct over ssKSR-based predictors. PhosNetConstruct is freely available at http://www.nii.ac.in/phosnetconstruct.html. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Data Service: Distributed Data Capture and Replication

NASA Astrophysics Data System (ADS)

Warner, P. B.; Pietrowicz, S. R.

2007-10-01

Data Service is a critical component of the NOAO Data Management and Science Support (DMaSS) Solutions Platform, which is based on a service-oriented architecture, and is to replace the current NOAO Data Transport System. Its responsibilities include capturing data from NOAO and partner telescopes and instruments and replicating the data across multiple (currently six) storage sites. Java 5 was chosen as the implementation language, and Java EE as the underlying enterprise framework. Application metadata persistence is performed using EJB and Hibernate on the JBoss Application Server, with PostgreSQL as the persistence back-end. Although potentially any underlying mass storage system may be used as the Data Service file persistence technology, DTS deployments and Data Service test deployments currently use the Storage Resource Broker from SDSC. This paper presents an overview and high-level design of the Data Service, including aspects of deployment, e.g., for the LSST Data Challenge at the NCSA computing facilities.

Carbon nanotube-based aptasensor for sensitive electrochemical detection of whole-cell Salmonella.

PubMed

Hasan, Md Rakibul; Pulingam, Thiruchelvi; Appaturi, Jimmy Nelson; Zifruddin, Anis Nadyra; Teh, Swe Jyan; Lim, Teck Wei; Ibrahim, Fatimah; Leo, Bey Fen; Thong, Kwai Lin

2018-08-01

In this study, an amino-modified aptasensor using multi-walled carbon nanotubes (MWCNTs)-deposited ITO electrode was prepared and evaluated for the detection of pathogenic Salmonella bacteria. An amino-modified aptamer (ssDNA) which binds selectively to whole-cell Salmonella was immobilised on the COOH-rich MWCNTs to produce the ssDNA/MWCNT/ITO electrode. The morphology of the MWCNT before and after interaction with the aptamers were observed using scanning electron microscopy (SEM). Cyclic voltammetry and electrochemical impedance spectroscopy techniques were used to investigate the electrochemical properties and conductivity of the aptasensor. The results showed that the impedance measured at the ssDNA/MWCNT/ITO electrode surface increased after exposure to Salmonella cells, which indicated successful binding of Salmonella on the aptamer-functionalised surface. The developed ssDNA/MWCNT/ITO aptasensor was stable and maintained linearity when the scan rate was increased from 10 mV s -1 to 90 mV s -1 . The detection limit of the ssDNA/MWCNT/ITO aptasensor, determined from the sensitivity analysis, was found to be 5.5 × 10 1  cfu mL -1 and 6.7 × 10 1  cfu mL -1 for S. Enteritidis and S. Typhimurium, respectively. The specificity test demonstrated that Salmonella bound specifically to the ssDNA/MWCNT/ITO aptasensor surface, when compared with non-Salmonella spp. The prepared aptasensor was successfully applied for the detection of Salmonella in food samples. Copyright © 2018 Elsevier Inc. All rights reserved.

Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen

PubMed Central

Park, Chin-Ju; Lee, Joon-Hwa; Choi, Byong-Seok

2005-01-01

Replication protein A (RPA) is a three-subunit complex with multiple roles in DNA metabolism. DNA-binding domain A in the large subunit of human RPA (hRPA70A) binds to single-stranded DNA (ssDNA) and is responsible for the species-specific RPA–T antigen (T-ag) interaction required for Simian virus 40 replication. Although Saccharomyces cerevisiae RPA70A (scRPA70A) shares high sequence homology with hRPA70A, the two are not functionally equivalent. To elucidate the similarities and differences between these two homologous proteins, we determined the solution structure of scRPA70A, which closely resembled the structure of hRPA70A. The structure of ssDNA-bound scRPA70A, as simulated by residual dipolar coupling-based homology modeling, suggested that the positioning of the ssDNA is the same for scRPA70A and hRPA70A, although the conformational changes that occur in the two proteins upon ssDNA binding are not identical. NMR titrations of hRPA70A with T-ag showed that the T-ag binding surface is separate from the ssDNA-binding region and is more neutral than the corresponding part of scRPA70A. These differences might account for the species-specific nature of the hRPA70A–T-ag interaction. Our results provide insight into how these two homologous RPA proteins can exhibit functional differences, but still both retain their ability to bind ssDNA. PMID:16043636

Myocarditis in Patients With Antisynthetase Syndrome: Prevalence, Presentation, and Outcomes.

PubMed

Dieval, Céline; Deligny, Christophe; Meyer, Alain; Cluzel, Philippe; Champtiaux, Nicolas; Lefevre, Guillaume; Saadoun, David; Sibilia, Jean; Pellegrin, Jean-Luc; Hachulla, Eric; Benveniste, Olivier; Hervier, Baptiste

2015-07-01

Antisynthetase syndrome (aSS) corresponds to an overlapping inflammatory myopathy identified by various myositis-specific autoantibodies (directed against tRNA-synthetases). Myocardial involvement in this condition is poorly described.From a registry of 352 aSS patients, 12 cases of myocarditis were retrospectively identified on the basis of an unexplained increase in troponin T/I levels associated with either suggestive cardiac magnetic resonance imaging (MRI) findings, nonsignificant coronary artery abnormalities or positive endomyocardial biopsy.The prevalence of myocarditis in aSS is 3.4% and was not linked to any autoantibody specificity: anti-Jo1 (n = 8), anti-PL7 (n = 3), and anti-PL12 (n = 1). Myocarditis was a part of the first aSS manifestations in 42% of the cases and was asymptomatic (n = 2) or revealed by an acute (n = 4) or a subacute (n = 6) cardiac failure. It should be noted that myocarditis was always associated with an active myositis. When performed (n = 11), cardiac MRI revealed a late hypersignal in the T1-images in 73% of the cases (n = 8). Half of the patients required intensive care. Ten patients (83%) received dedicated cardiotropic drugs. Steroids and at least 1 immunosuppressive drug were given in all cases. After a median follow-up of 11 months (range 0-84) 9 (75%) patients recovered whereas 3 (25%) developed a chronic cardiac insufficiency. No patient died.The prevalence of myocarditis in aSS is similar to that of other inflammatory myopathies. Although the prognosis is relatively good, myocarditis is a severe condition and should be carefully considered as a possible manifestation in active aSS patients.

Reduction of T cell receptor diversity in NOD mice prevents development of type 1 diabetes but not Sjögren's syndrome.

PubMed

Kern, Joanna; Drutel, Robert; Leanhart, Silvia; Bogacz, Marek; Pacholczyk, Rafal

2014-01-01

Non-obese diabetic (NOD) mice are well-established models of independently developing spontaneous autoimmune diseases, Sjögren's syndrome (SS) and type 1 diabetes (T1D). The key determining factor for T1D is the strong association with particular MHCII molecule and recognition by diabetogenic T cell receptor (TCR) of an insulin peptide presented in the context of I-Ag7 molecule. For SS the association with MHCII polymorphism is weaker and TCR diversity involved in the onset of the autoimmune phase of SS remains poorly understood. To compare the impact of TCR diversity reduction on the development of both diseases we generated two lines of TCR transgenic NOD mice. One line expresses transgenic TCRβ chain originated from a pathogenically irrelevant TCR, and the second line additionally expresses transgenic TCRαmini locus. Analysis of TCR sequences on NOD background reveals lower TCR diversity on Treg cells not only in the thymus, but also in the periphery. This reduction in diversity does not affect conventional CD4+ T cells, as compared to the TCRmini repertoire on B6 background. Interestingly, neither transgenic TCRβ nor TCRmini mice develop diabetes, which we show is due to lack of insulin B:9-23 specific T cells in the periphery. Conversely SS develops in both lines, with full glandular infiltration, production of autoantibodies and hyposalivation. It shows that SS development is not as sensitive to limited availability of TCR specificities as T1D, which suggests wider range of possible TCR/peptide/MHC interactions driving autoimmunity in SS.

L2 Milestone 5433: Characterization of Dynamic Behavior of AM and Conventionally Processed Stainless Steel (316L and 304L)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gray, George Thompson; Livescu, Veronica; Rigg, P. A.

For additive manufacturing (AM) of metallic materials, the certification and qualification paradigm needs to evolve as there currently exists no broadly accepted “ASTM- or DIN-type” additive manufacturing certified process or AM-material produced specifications. Accordingly, design, manufacture, and thereafter implementation and insertion of AM materials to meet engineering applications requires detailed quantification of the constitutive (strength and damage) properties of these evolving materials, across the spectrum of metallic AM methods, in comparison/contrast to conventionally-manufactured metals and alloys. This report summarizes the 316L SS research results and presents initial results of the follow-on study of 304L SS. For the AM-316L SS investigation,more » cylindrical samples of 316L SS were produced using a LENS MR-7 laser additive manufacturing system from Optomec (Albuquerque, NM) equipped with a 1kW Yb-fiber laser. The microstructure of the AM-316L SS was characterized in both the “as-built” Additively Manufactured state and following a heat-treatment designed to obtain full recrystallization to facilitate comparison with annealed wrought 316L SS. The dynamic shock-loading-induced damage evolution and failure response of all three 316L SS materials was quantified using flyer-plate impact driven spallation experiments at peak stresses of 4.5 and 6.35 GPa. The results of these studies are reported in detail in the first section of the report. Publication of the 316L SS results in an archival journal is planned. Following on from the 316L SS completed work, initial results on a study of AM 304L SS are in progress and presented herein. Preliminary results on the structure/dynamic spallation property behavior of AM-304L SS fabricated using both the directed-energy LENS and an EOS powder-bed AM techniques in comparison to wrought 304L SS is detailed in this Level 2 Milestone report.« less

Validity of diagnoses, procedures, and laboratory data in Japanese administrative data.

PubMed

Yamana, Hayato; Moriwaki, Mutsuko; Horiguchi, Hiromasa; Kodan, Mariko; Fushimi, Kiyohide; Yasunaga, Hideo

2017-10-01

Validation of recorded data is a prerequisite for studies that utilize administrative databases. The present study evaluated the validity of diagnoses and procedure records in the Japanese Diagnosis Procedure Combination (DPC) data, along with laboratory test results in the newly-introduced Standardized Structured Medical Record Information Exchange (SS-MIX) data. Between November 2015 and February 2016, we conducted chart reviews of 315 patients hospitalized between April 2014 and March 2015 in four middle-sized acute-care hospitals in Shizuoka, Kochi, Fukuoka, and Saga Prefectures and used them as reference standards. The sensitivity and specificity of DPC data in identifying 16 diseases and 10 common procedures were identified. The accuracy of SS-MIX data for 13 laboratory test results was also examined. The specificity of diagnoses in the DPC data exceeded 96%, while the sensitivity was below 50% for seven diseases and variable across diseases. When limited to primary diagnoses, the sensitivity and specificity were 78.9% and 93.2%, respectively. The sensitivity of procedure records exceeded 90% for six procedures, and the specificity exceeded 90% for nine procedures. Agreement between the SS-MIX data and the chart reviews was above 95% for all 13 items. The validity of diagnoses and procedure records in the DPC data and laboratory results in the SS-MIX data was high in general, supporting their use in future studies. Copyright © 2017 The Authors. Production and hosting by Elsevier B.V. All rights reserved.

Separation of 1-23-kb complementary DNA strands by urea-agarose gel electrophoresis.

PubMed

Hegedüs, Eva; Kókai, Endre; Kotlyar, Alexander; Dombrádi, Viktor; Szabó, Gábor

2009-09-01

Double-stranded (ds), as well as denatured, single-stranded (ss) DNA samples can be analyzed on urea-agarose gels. Here we report that after denaturation by heat in the presence of 8 M urea, the two strands of the same ds DNA fragment of approximately 1-20-kb size migrate differently in 1 M urea containing agarose gels. The two strands are readily distinguished on Southern blots by ss-specific probes. The different migration of the two strands could be attributed to their different, base composition-dependent conformation impinging on the electrophoretic mobility of the ss molecules. This phenomenon can be exploited for the efficient preparation of strand-specific probes and for the separation of the complementary DNA strands for subsequent analysis, offering a new tool for various cell biological research areas.

Breaching the Phalanx: Developing a More Engineer-Centric Modular BCT

DTIC Science & Technology

2007-06-05

Obersturmbannfuehrer Jaochim Peiper’s Kampfgruppe Peiper (of the I SS Panzer Corps).42 The 1111th Engineer commander visualized a defensive scheme for the...the engineer planner scheduled a planning session with the I MEF engineer staff. This planning session was held at Camp Pendleton in September...covered sleeping /work areas, ammo storage, etc.). As the units did not begin the invasion until 20 March, this meant the BCTs lived in abject squalor

The import of abdominal pain in adults with sickle cell disorder.

PubMed

Akinola, N O; Bolarinwa, R A; Faponle, A F

2009-03-01

The aetiology, clinical correlates and outcome of abdominal pain in Nigerian adults with sickle cell disorder (SCD) have not been extensively reported. To determine the prevalence of abdominal vasoocclusive crisis in sickle cell patients with abdominal pain and their clinical correlates if any. Clinical records of adults with SCD (Hb SS and Hb SC) attending the Haematology Outpatients' Clinic of the Obafemi Awolowo University Teaching Hospitals Complex, Southwest Nigerian, over a ten-year period, were reviewed. Demographic, clinical and laboratory data with respect to abdominal pain were retrieved. Data were analysed using appropriate descriptive and inferential statistics. A total of 154 records (128 Hb SS and 26 Hb SC) were available for assessment. The patients mean ages were 22.5 +/- 7.3 years (Hb SS patients) and 24.2 +/- 9.7 years (Hb SC patients) (p > 0.05). The prevalence of abdominal pain was 39.1% and 30.8% in Hb SS and Hb SC respectively (p > 0.05). Pain was commonly in the epigastrium; dull in 35% Hb SS, but peppery/burning in 37.5% Hb SC. All patients with abdominal vaso-occlusive crisis (VOC) had diffuse/generalised dull abdominal pains. A diagnosis of gastritis/peptic ulcer disease was made in 50% of Hb SC patients and 28% of Hb SS patients. Abdominal VOC was diagnosed in 26% Hb SS, but none in Hb SC patients. The size of the liver or spleen and the haematocrit of Hb SS patients did not correlate with the frequency of abdominal pain generally or abdominal VOC specifically. The prevalence rates and patterns of abdominal pain in Hb SS and Hb SC patients appear similar. Abdominal VOC characterised by diffuse/generalised dull abdominal pain occurred in only Hb SS patients and may be a marker of disease severity in these patients.

Promotion of plant growth by Pseudomonas fluorescens strain SS101 via novel volatile organic compounds.

PubMed

Park, Yong-Soon; Dutta, Swarnalee; Ann, Mina; Raaijmakers, Jos M; Park, Kyungseok

2015-05-29

Volatile organic compounds (VOCs) from plant growth-promoting rhizobacteria (PGPR) play key roles in modulating plant growth and induced systemic resistance (ISR) to pathogens. Despite their significance, the physiological functions of the specific VOCs produced by Pseudomonas fluorescens SS101 (Pf.SS101) have not been precisely elucidated. The effects of Pf.SS101 and its VOCs on augmentation of plant growth promotion were investigated in vitro and in planta. A significant growth promotion was observed in plants exposed Pf.SS101 under both conditions, suggesting that its VOCs play a key role in promoting plant growth. Solid-phase micro-extraction (SPME) and a gas chromatography-mass spectrophotometer (GC-MS) system were used to characterize the VOCs emitted by Pf.SS101 and 11 different compounds were detected in samples inoculated this bacterium, including 13-Tetradecadien-1-ol, 2-butanone and 2-Methyl-n-1-tridecene. Application of these compounds resulted in enhanced plant growth. This study suggests that Pf.SS101 promotes the growth of plants via the release of VOCs including 13-Tetradecadien-1-ol, 2-butanone and 2-Methyl-n-1-tridecene, thus increasing understanding of the role of VOCs in plant-bacterial inter-communication. Copyright © 2015 Elsevier Inc. All rights reserved.

The extracellular matrix of the oleolytic biofilms of Marinobacter hydrocarbonoclasticus comprises cytoplasmic proteins and T2SS effectors that promote growth on hydrocarbons and lipids.

PubMed

Ennouri, Habiba; d'Abzac, Paul; Hakil, Florence; Branchu, Priscilla; Naïtali, Murielle; Lomenech, Anne-Marie; Oueslati, Ridha; Desbrières, Jacques; Sivadon, Pierre; Grimaud, Régis

2017-01-01

The assimilation of the nearly water insoluble substrates hydrocarbons and lipids by bacteria entails specific adaptations such as the formation of oleolytic biofilms. The present article reports that the extracellular matrix of an oleolytic biofilm formed by Marinobacter hydrocarbonoclasticus at n-hexadecane-water interfaces is largely composed of proteins typically cytoplasmic such as translation factors and chaperones, and a lesser amount of proteins of unknown function that are predicted extra-cytoplasmic. Matrix proteins appear to form a structured film on hydrophobic interfaces and were found mandatory for the development of biofilms on lipids, alkanes and polystyrene. Exo-proteins secreted through the type-2 secretion system (T2SS) were shown to be essential for the formation of oleolytic biofilms on both alkanes and triglycerides. The T2SS effector involved in biofilm formation on triglycerides was identified as a lipase. In the case of biofilm formation on n-hexadecane, the T2SS effector is likely involved in the mass transfer, capture or transport of alkanes. We propose that M. hydrocarbonoclasticus uses cytoplasmic proteins released by cell lysis to form a proteinaceous matrix and dedicated proteins secreted through the T2SS to act specifically in the assimilation pathways of hydrophobic substrates. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Enzymatic triggered release of an HIV-1 entry inhibitor from prostate specific antigen degradable microparticles.

PubMed

Clark, Meredith R; Aliyar, Hyder A; Lee, Chang-won; Jay, Julie I; Gupta, Kavita M; Watson, Karen M; Stewart, Russell J; Buckheit, Robert W; Kiser, Patrick F

2011-07-15

This paper describes the design, construction and characterization of the first anti-HIV drug delivery system that is triggered to release its contents in the presence of human semen. Microgel particles were synthesized with a crosslinker containing a peptide substrate for the seminal serine protease prostate specific antigen (PSA) and were loaded with the HIV-1 entry inhibitor sodium poly(styrene-4-sulfonate) (pSS). The particles were composed of N-2-hydroxyproplymethacrylamide and bis-methacrylamide functionalized peptides based on the PSA substrates GISSFYSSK and GISSQYSSK. Exposure to human seminal plasma (HSP) degraded the microgel network and triggered the release of the entrapped antiviral polymer. Particles with the crosslinker composed of the substrate GISSFYSSK showed 17 times faster degradation in seminal plasma than that of the crosslinker composed of GISSQYSSK. The microgel particles containing 1 mol% GISSFYSSK peptide crosslinker showed complete degradation in 30 h in the presence of HSP at 37°C and pSS released from the microgels within 30 min reached a concentration of 10 μg/mL, equivalent to the published IC(90) for pSS. The released pSS inactivated HIV-1 in the presence of HSP. The solid phase synthesis of the crosslinkers, preparation of the particles by inverse microemulsion polymerization, HSP-triggered release of pSS and inactivation of HIV-1 studies are described. Copyright © 2011 Elsevier B.V. All rights reserved.

Efficient CNS targeting in adult mice by intrathecal infusion of single-stranded AAV9-GFP for gene therapy of neurological disorders.

PubMed

Bey, K; Ciron, C; Dubreil, L; Deniaud, J; Ledevin, M; Cristini, J; Blouin, V; Aubourg, P; Colle, M-A

2017-05-01

Adeno-associated virus (AAV) gene therapy constitutes a powerful tool for the treatment of neurodegenerative diseases. While AAVs are generally administered systemically to newborns in preclinical studies of neurological disorders, in adults the maturity of the blood-brain barrier (BBB) must be considered when selecting the route of administration. Delivery of AAVs into the cerebrospinal fluid (CSF) represents an attractive approach to target the central nervous system (CNS) and bypass the BBB. In this study, we investigated the efficacy of intra-CSF delivery of a single-stranded (ss) AAV9-CAG-GFP vector in adult mice via intracisternal (iCist) or intralumbar (it-Lumb) administration. It-Lumb ssAAV9 delivery resulted in greater diffusion throughout the entire spinal cord and green fluorescent protein (GFP) expression mainly in the cerebellum, cortex and olfactory bulb. By contrast, iCist delivery led to strong GFP expression throughout the entire brain. Comparison of the transduction efficiency of ssAAV9-CAG-GFP versus ssAAV9-SYN1-GFP following it-Lumb administration revealed widespread and specific GFP expression in neurons and motoneurons of the spinal cord and brain when the neuron-specific synapsin 1 (SYN1) promoter was used. Our findings demonstrate that it-Lumb ssAAV9 delivery is a safe and highly efficient means of targeting the CNS in adult mice.

rmpM genosensor for detection of human brain bacterial meningitis in cerebrospinal fluid.

PubMed

Dash, Sandip Kumar; Sharma, Minakshi; Khare, Shashi; Kumar, Ashok

2013-09-01

Human brain bacterial meningitis is a life-threatening disease caused mainly by Neisseria meningitidis, lead to damage of the outer membrane covering (meninges) of brain or even death. The usual methods of diagnosis are either time-consuming or have some limitations. The specific rmpM (reduction-modifiable protein M) virulent gene based genosensor is more sensitive, specific, and can detect N. meningitidis directly from the patient cerebrospinal fluid in 30 min including 1-min response time. 5'-Thiol-labeled single-stranded DNA (ssDNA) probe was immobilized onto screen-printed gold electrode (SPGE) and hybridized with denatured (95 °C) single-stranded genomic DNA (ssG-DNA) for 10 min at 25 °C. The electrochemical response was measured by cyclic voltammetry, differential pulse voltammetry (DPV) and electrochemical impedance using redox indicators. The sensitivity of the genosensor was 9.5087 (μA/cm(2))/ng with DPV and limit of detection was 3 ng/6 μL ssG-DNA. The immobilization of the ssDNA probe and hybridization with ssG-DNA from N. meningitidis was characterized by atomic force microscopy and Fourier transform infrared spectroscopy. The rmpM genosensor was stable for 6 months at 4 °C with 10 % loss in initial DPV current. The advantage of rmpM genosensor is to detect bacterial meningitis simultaneously in multiple patients using SPGE array during an outbreak of the disease.

Ethnocentrism and Cultural Relativism in Children's Thinking About Foreign Values and Attitudes.

ERIC Educational Resources Information Center

McKenzie, Gary R.

In the study reported here, 133 subjects (Ss) were selected randomly from one elementary school. Ss were showed photographs of Bushmen performing daily activities and asked to predict whether a Bushman would prefer specific indigenous customs or their American equivalents, and then to justify the prediction. Scores for three types of predictions…

The Security Scale as a measure of attachment: meta-analytic evidence of validity.

PubMed

Brumariu, Laura E; Madigan, Sheri; Giuseppone, Kathryn R; Movahed Abtahi, Mahsa; Kerns, Kathryn A

2018-02-05

This meta-analysis evaluated the psychometric properties of the Security Scale (SS; k = 57 studies), a measure specifically designed to assess attachment in middle childhood, using several criteria: stability over time, associations with other attachment measures, relations with caregiver sensitivity, and associations with theoretically driven outcomes. The SS demonstrated moderate stability and meaningful associations with other attachment measures and caregiver sensitivity. Furthermore, the SS showed significant associations with developmental correlates of attachment: school adaptation, emotional and peer social competence, self-esteem, and behavioral problem. Some effect sizes varied as a function of socioeconomic status (SES; peer social competence and maladjustment) and publication status (emotional competence, peer social competence, and self-esteem). The association between the SS and our constructs of interest were, for the most part, independent of geographical location and child gender or age. Overall, findings suggest that the SS is a robust measure of attachment in middle childhood and early adolescence.

Analysis and evaluation of the rationales for single-sex schooling.

PubMed

Bigler, Rebecca S; Hayes, Amy Roberson; Liben, Lynn S

2014-01-01

Amendments passed as part of the No Child Left Behind Act in 2006 made some forms of single-sex (SS) public education legal in the United States. Proponents offer a host of arguments in favor of such schooling. This chapter identifies and evaluates five broad rationales for SS schooling. We conclude that empirical evidence fails to support proponents' claims but nonetheless suggests ways in which to improve coeducation. Specifically, we (a) show that the purported benefits of SS schooling arise from factors confounded with, but not causally linked to, single-sex composition; (b) challenge claims that biological sex is an effective marker of differences relevant to instruction; (c) argue that sexism on the part of teachers and peers persists in SS contexts; and (d) critique the notion that gender per se "disappears" in SS contexts. We also address societal implications of the use of sex-segregated education and conclude that factors found to be beneficial for students should be implemented within coeducational schools.

Boosting biogas production from sewage sludge by adding small amount of agro-industrial by-products and food waste residues.

PubMed

Maragkaki, A E; Fountoulakis, M; Kyriakou, A; Lasaridi, K; Manios, T

2018-01-01

In Greece, in many cities, wastewater treatment plants (WWTPs) operate their own anaerobic digestion (AD) facility in order to treat sewage sludge rather than achieve optimum biogas production. Nowadays, there is a growing interest regarding the addition of other co-substrates in these existing facilities in order to increase gas yield from the biomass. This practice may be possible by adding small amount of co-substrates which will not affect significantly in the designed hydraulic retention time. Nonetheless, the lack of experimental data regarding this option is a serious obstacle. In this study, the effect of co-digestion sewage sludge, with small amount of agro-industrial by-products and food wastes is examined in lab-scale experiments. Specifically, co-digestion of SS and food waste (FW), grape residues (GR), crude glycerol (CG), cheese whey (CW) and sheep manure (SM), in a small ratio of 5-10% (v/v) was investigated. The effect of agro-industrial by-products and food waste residues on biogas production was investigated using one 1L and three 3L lab-scale reactors under mesophilic conditions at a 24-day hydraulic retention time. The biogas production rate reached 223, 259, 406, 572, 682 and 1751 mlbiogas/lreactor/d for 100% SS, 5% SM & 95% SS, 10% CW & 90% SS, 5% FW & 95% SS, 5% FW & 5% CG & 90% SS and 5% CG & 95% SS respectively. Depending on the co-digestion material, the average removal of total chemical oxygen demand (TCOD) ranged between 20% (5% SM & 95% SS) and 76% (5% FW & 5% CG & 90% SS). Reduction in the volatile solids ranged between 26% (5% SM & 95% SS) and 62% (5% FW & 5% CG & 90% SS) for organic loading rates between 0.8kgVSm -3 d -1 and 2.0kgVSm -3 d -1 . Moreover, co-digestion improved biogas production from 14% (5% SM & 95% SS) to 674% (5% CG & 95% SS). This work suggests that WWTPs in Greece can increase biogas production by adding other wastes to the sewage sludge without affecting the operation of existing digesters and without requiring additional facilities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparison of Swirl Sign and Black Hole Sign in Predicting Early Hematoma Growth in Patients with Spontaneous Intracerebral Hemorrhage.

PubMed

Xiong, Xin; Li, Qi; Yang, Wen-Song; Wei, Xiao; Hu, Xi; Wang, Xing-Chen; Zhu, Dan; Li, Rui; Cao, Du; Xie, Peng

2018-01-29

BACKGROUND Early hematoma growth is associated with poor outcome in patients with spontaneous intracerebral hemorrhage (ICH). The swirl sign (SS) and the black hole sign (BHS) are imaging markers in ICH patients. The aim of this study was to compare the predictive value of these 2 signs for early hematoma growth. MATERIAL AND METHODS ICH patients were screened for the appearance of the 2 signs within 6 h after onset of symptoms. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the 2 signs in predicting early hematoma growth were assessed. The accuracy of the 2 signs in predicting early hematoma growth was analyzed by receiver-operator analysis. RESULTS A total of 200 patients were enrolled in this study. BHS was found in 30 (15%) patients, and SS was found in 70 (35%) patients. Of the 71 patients with early hematoma growth, BHS was found on initial computed tomography scans in 24 (33.8%) and SS in 33 (46.5%). The sensitivity, specificity, PPV, and NPV of BHS for predicting early hematoma growth were 33.8%, 95.3%, 80.0%, and 72.0%, respectively. The sensitivity, specificity, PPV, and NPV of SS were 46.5%, 71.3%, 47.0%, and 71.0%, respectively. The area under the curve was 0.646 for BHS and 0.589 for SS (P=0.08). Multivariate logistic regression showed that presence of BHS is an independent predictor of early hematoma growth. CONCLUSIONS The Black hole sign seems to be good predictor for hematoma growth. The presence of swirl sign on admission CT does not independently predict hematoma growth in patients with ICH.

Impact of non-specific normal databases on perfusion quantification of low-dose myocardial SPECT studies.

PubMed

Scabbio, Camilla; Zoccarato, Orazio; Malaspina, Simona; Lucignani, Giovanni; Del Sole, Angelo; Lecchi, Michela

2017-10-17

To evaluate the impact of non-specific normal databases on the percent summed rest score (SR%) and stress score (SS%) from simulated low-dose SPECT studies by shortening the acquisition time/projection. Forty normal-weight and 40 overweight/obese patients underwent myocardial studies with a conventional gamma-camera (BrightView, Philips) using three different acquisition times/projection: 30, 15, and 8 s (100%-counts, 50%-counts, and 25%-counts scan, respectively) and reconstructed using the iterative algorithm with resolution recovery (IRR) Astonish TM (Philips). Three sets of normal databases were used: (1) full-counts IRR; (2) half-counts IRR; and (3) full-counts traditional reconstruction algorithm database (TRAD). The impact of these databases and the acquired count statistics on the SR% and SS% was assessed by ANOVA analysis and Tukey test (P < 0.05). Significantly higher SR% and SS% values (> 40%) were found for the full-counts TRAD databases respect to the IRR databases. For overweight/obese patients, significantly higher SS% values for 25%-counts scans (+19%) are confirmed compared to those of 50%-counts scan, independently of using the half-counts or the full-counts IRR databases. Astonish TM requires the adoption of the own specific normal databases in order to prevent very high overestimation of both stress and rest perfusion scores. Conversely, the count statistics of the normal databases seems not to influence the quantification scores.

Utility of the American-European Consensus Group and American College of Rheumatology Classification Criteria for Sjögren's syndrome in patients with systemic autoimmune diseases in the clinical setting.

PubMed

Hernández-Molina, Gabriela; Avila-Casado, Carmen; Nuñez-Alvarez, Carlos; Cárdenas-Velázquez, Francisco; Hernández-Hernández, Carlos; Luisa Calderillo, María; Marroquín, Verónica; Recillas-Gispert, Claudia; Romero-Díaz, Juanita; Sánchez-Guerrero, Jorge

2015-03-01

The aim of this study was to evaluate the feasibility and performance of the American-European Consensus Group (AECG) and ACR Classification Criteria for SS in patients with systemic autoimmune diseases. Three hundred and fifty patients with primary SS, SLE, RA or scleroderma were randomly selected from our patient registry. Each patient was clinically diagnosed as probable/definitive SS or non-SS following a standardized evaluation including clinical symptoms and manifestations, confirmatory tests, fluorescein staining test, autoantibodies, lip biopsy and medical chart review. Using the clinical diagnosis as the gold standard, the degree of agreement with each criteria set and between the criteria sets was estimated. One hundred fifty-four (44%) patients were diagnosed with SS. The AECG criteria were incomplete in 36 patients (10.3%) and the ACR criteria in 96 (27.4%; P < 0.001). Nevertheless, their ability to classify patients was almost identical, with a sensitivity of 61.6 vs 62.3 and a specificity of 94.3 vs 91.3, respectively. Either set of criteria was met by 123 patients (80%); 95 (61.7%) met the AECG criteria and 96 (62.3%) met the ACR criteria, but only 68 (44.2%) patients met both sets. The concordance rate between clinical diagnosis and AECG or ACR criteria was moderate (k statistic 0.58 and 0.55, respectively). Among 99 patients with definitive SS sensitivity was 83.3 vs 77.7 and specificity was 90.8 vs 85.6, respectively. A discrepancy between clinical diagnosis and criteria was seen in 59 patients (17%). The feasibility of the SS AECG criteria is superior to that of the ACR criteria, however, their performance was similar among patients with systemic autoimmune diseases. A subset of SS patients is still missed by both criteria sets. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Fluorescent carbon dot-gated multifunctional mesoporous silica nanocarriers for redox/enzyme dual-responsive targeted and controlled drug delivery and real-time bioimaging.

PubMed

Wang, Ying; Cui, Yu; Zhao, Yating; He, Bing; Shi, Xiaoli; Di, Donghua; Zhang, Qiang; Wang, Siling

2017-08-01

A distinctive and personalized nanocarrier is described here for controlled and targeted antitumor drug delivery and real-time bioimaging by combining a redox/enzyme dual-responsive disulfide-conjugated carbon dot with mesoporous silica nanoparticles (MSN-SS-CD HA ). The carbon dot with controlling and targeting abilities was prepared through a polymerizing reaction by applying citric acid and HA as starting materials (named CD HA ). The as-prepared MSN-SS-CD HA exhibited not only superior photostability and excellent biocompatibility, but also the ability to target A549 cells with overexpression of CD44 receptors. Upon loading the antitumor drug, doxorubicin (DOX), into the mesoporous channels of MSN nanoparticles, CD HA with a diameter size of 3nm completely blocked the pore entrance of DOX-encapsulated MSN nanoparticles with a pore size of about 3nm, thus preventing the premature leakage of DOX and increasing the antitumor activity until being triggered by specific stimuli in the tumor environment. The results of the cell imaging and cytotoxicity studies demonstrated that the redox/enzyme dual-responsive DOX-encapsulated MSN-SS-CD HA nanoparticles can selectively deliver and control the release of DOX into tumor cells. Ex vivo fluorescence images showed a much stronger fluorescence of MSN-SS-CD HA -DOX in the tumor site than in normal tissues, greatly facilitating the accumulation of DOX in the target tissue. However, its counterpart, MSN-SH-DOX exhibited no or much lower tumor cytotoxicity and drug accumulation in tumor tissue. In addition, MSN-SS-CD was also used as a control to investigate the ability of MSN-SS-CD HA to target A549 cells. The results obtained indicated that MSN-SS-CD HA possessed a higher cellular uptake through the CD44 receptor-mediated endocytosis compared with MSN-SS-CD in the A549 cells. Such specific redox/enzyme dual-responsive targeted nanocarriers are a useful strategy achieving selective controlled and targeted delivery of therapeutic reagents with real-time bioimaging, and may also facilitate the development of drug delivery systems for a number of clinical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Sonority's Effect as a Surface Cue on Lexical Speech Perception of Children With Cochlear Implants.

PubMed

Hamza, Yasmeen; Okalidou, Areti; Kyriafinis, George; van Wieringen, Astrid

2018-03-06

Sonority is the relative perceptual prominence/loudness of speech sounds of the same length, stress, and pitch. Children with cochlear implants (CIs), with restored audibility and relatively intact temporal processing, are expected to benefit from the perceptual prominence cues of highly sonorous sounds. Sonority also influences lexical access through the sonority-sequencing principle (SSP), a grammatical phonotactic rule, which facilitates the recognition and segmentation of syllables within speech. The more nonsonorous the onset of a syllable is, the larger is the degree of sonority rise to the nucleus, and the more optimal the SSP. Children with CIs may experience hindered or delayed development of the language-learning rule SSP, as a result of their deprived/degraded auditory experience. The purpose of the study was to explore sonority's role in speech perception and lexical access of prelingually deafened children with CIs. A case-control study with 15 children with CIs, 25 normal-hearing children (NHC), and 50 normal-hearing adults was conducted, using a lexical identification task of novel, nonreal CV-CV words taught via fast mapping. The CV-CV words were constructed according to four sonority conditions, entailing syllables with sonorous onsets/less optimal SSP (SS) and nonsonorous onsets/optimal SSP (NS) in all combinations, that is, SS-SS, SS-NS, NS-SS, and NS-NS. Outcome measures were accuracy and reaction times (RTs). A subgroup analysis of 12 children with CIs pair matched to 12 NHC on hearing age aimed to study the effect of oral-language exposure period on the sonority-related performance. The children groups showed similar accuracy performance, overall and across all the sonority conditions. However, within-group comparisons showed that the children with CIs scored more accurately on the SS-SS condition relative to the NS-NS and NS-SS conditions, while the NHC performed equally well across all conditions. Additionally, adult-comparable accuracy performance was achieved by the children with CIs only on the SS-SS condition, as opposed to NS-SS, SS-NS, and SS-SS conditions for NHC. Accuracy analysis of the subgroups of children matched in hearing age showed similar results. Overall longer RTs were recorded by the children with CIs on the sonority-treated lexical task, specifically on the SS-SS condition compared with age-matched controls. However, the subgroup analysis showed that both groups of children did not differ on RTs. Children with CIs performed better in lexical tasks relying on the sonority perceptual prominence cues, as in SS-SS condition, than on SSP initial relying conditions as NS-NS and NS-SS. Template-driven word learning, an early word-learning strategy, appears to play a role in the lexical access of children with CIs whether matched in hearing age or not. The SS-SS condition acts as a preferred word template. The longer RTs brought about by the highly accurate SS-SS condition in children with CIs is possibly because listening becomes more effortful. The lack of RTs difference between the children groups when matched on hearing age points out the importance of oral-language exposure period as a key factor in developing the auditory processing skills.

Protocol for the validation of sensitivity and specificity of the Cow's Milk-related Symptom Score (CoMiSS) against open food challenge in a single-blinded, prospective, multicentre trial in infants.

PubMed

Vandenplas, Yvan; Mukherjee, Rajat; Dupont, Christophe; Eigenmann, Philippe; Høst, Arne; Kuitunen, Mikael; Ribes-Koninkx, Carmen; Shah, Neil; Szajewska, Hania; von Berg, Andrea; Heine, Ralf G; Zhao, Zheng-Yan

2018-05-17

The symptoms of cow's milk protein allergy (CMPA) in infancy can be non-specific which may delay a correct diagnosis and cause adverse clinical outcomes. The diagnosis of non-IgE-mediated CMPA is particularly complex as it involves a 2 to 4 week elimination diet followed by oral food challenge (OFC). The Cow's Milk-related Symptom Score (CoMiSS) is a clinical resource for primary healthcare providers which aims to increase awareness of CMPA symptoms to facilitate an earlier diagnosis. The aim of the present study is to assess if the CoMiSS can be used as a potential diagnostic tool in infants with suspected CMPA. Exclusively formula-fed infants aged 0-6 months presenting with symptoms suggestive of CMPA will be included in this prospective, multicentre trial which will be conducted in 10 centres in China. All infants will commence a 2-week trial of an amino acid-based formula (AAF) while eliminating all cow milk protein from their diets. After the AAF treatment period, infants will undergo an open OFC in hospital with standard cow's milk formula, followed by an open home challenge for another 2 weeks. Clinical symptoms will be documented on standardised symptom scorecards. The CoMiSS will be determined at study entry (CoMiSS 1, before the start of the AAF), after 2 weeks (CoMiSS 2, before the OFC) and after a further period of 2 weeks or when symptoms suggestive of CMPA reappear (CoMiSS 3). Weight and length will be measured at each visit. The difference between CoMiSS 1 and 2 as a predictor of the OFC outcome will also be assessed. The diagnostic accuracy of the baseline CoMiSS will be calculated. The study was approved by the Hunan Children's Hospital Medical Ethics Committee, Hunan, China. The findings of this trial will be submitted for publication in a peer-reviewed journal in paediatric nutrition or gastroenterology. Abstracts will be submitted to the relevant national and international conferences. NCT03004729; Pre-results. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolates.

PubMed

Chen, Chen; Tang, Jiaqi; Dong, Wei; Wang, Changjun; Feng, Youjun; Wang, Jing; Zheng, Feng; Pan, Xiuzhen; Liu, Di; Li, Ming; Song, Yajun; Zhu, Xinxing; Sun, Haibo; Feng, Tao; Guo, Zhaobiao; Ju, Aiping; Ge, Junchao; Dong, Yaqing; Sun, Wen; Jiang, Yongqiang; Wang, Jun; Yan, Jinghua; Yang, Huanming; Wang, Xiaoning; Gao, George F; Yang, Ruifu; Wang, Jian; Yu, Jun

2007-03-21

Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen, causing more than 200 cases of severe human infection worldwide, with the hallmarks of meningitis, septicemia, arthritis, etc. Very recently, SS2 has been recognized as an etiological agent for streptococcal toxic shock syndrome (STSS), which was originally associated with Streptococcus pyogenes (GAS) in Streptococci. However, the molecular mechanisms underlying STSS are poorly understood. To elucidate the genetic determinants of STSS caused by SS2, whole genome sequencing of 3 different Chinese SS2 strains was undertaken. Comparative genomics accompanied by several lines of experiments, including experimental animal infection, PCR assay, and expression analysis, were utilized to further dissect a candidate pathogenicity island (PAI). Here we show, for the first time, a novel molecular insight into Chinese isolates of highly invasive SS2, which caused two large-scale human STSS outbreaks in China. A candidate PAI of approximately 89 kb in length, which is designated 89K and specific for Chinese SS2 virulent isolates, was investigated at the genomic level. It shares the universal properties of PAIs such as distinct GC content, consistent with its pivotal role in STSS and high virulence. To our knowledge, this is the first PAI candidate from S. suis worldwide. Our finding thus sheds light on STSS triggered by SS2 at the genomic level, facilitates further understanding of its pathogenesis and points to directions of development on some effective strategies to combat highly pathogenic SS2 infections.

Solar Simulated Ultraviolet Radiation Induces Global Histone Hypoacetylation in Human Keratinocytes.

PubMed

Zhang, Xiaoru; Kluz, Thomas; Gesumaria, Lisa; Matsui, Mary S; Costa, Max; Sun, Hong

2016-01-01

Ultraviolet radiation (UVR) from sunlight is the primary effector of skin DNA damage. Chromatin remodeling and histone post-translational modification (PTM) are critical factors in repairing DNA damage and maintaining genomic integrity, however, the dynamic changes of histone marks in response to solar UVR are not well characterized. Here we report global changes in histone PTMs induced by solar simulated UVR (ssUVR). A decrease in lysine acetylation of histones H3 and H4, particularly at positions of H3 lysine 9, lysine 56, H4 lysine 5, and lysine 16, was found in human keratinocytes exposed to ssUVR. These acetylation changes were highly associated with ssUVR in a dose-dependent and time-specific manner. Interestingly, H4K16ac, a mark that is crucial for higher order chromatin structure, exhibited a persistent reduction by ssUVR that was transmitted through multiple cell divisions. In addition, the enzymatic activities of histone acetyltransferases were significantly reduced in irradiated cells, which may account for decreased global acetylation. Moreover, depletion of histone deacetylase SIRT1 in keratinocytes rescued ssUVR-induced H4K16 hypoacetylation. These results indicate that ssUVR affects both HDAC and HAT activities, leading to reduced histone acetylation.

Functional cloning of Vibrio parahaemolyticus type III secretion system 1 in Escherichia coli K-12 strain as a molecular syringe.

PubMed

Akeda, Yukihiro; Kimura, Tomomi; Yamasaki, Aiko; Kodama, Toshio; Iida, Tetsuya; Honda, Takeshi; Oishi, Kazunori

2012-10-19

The type III secretion system (T3SS) of gram-negative bacteria involves dedicated protein translocation machinery that directly injects proteins into target cells. Pathogenic bacteria already benefit from this unique system. The successful functional cloning of this useful tool into non-pathogenic bacteria would help establish novel clinical and basic biotechnology strategies in areas such as vaccine administration, the development of screening systems for anti-T3SS drugs and the target-specific delivery of bioactive compounds. In this study, we successfully cloned the Vibrio parahaemolyticus T3SS1 genetic locus into a non-pathogenic Escherichia coli K-12 strain. Assays performed here revealed that the T3SS1 cloned into the E. coli K-12 strain has the ability to translocate V. parahaemolyticus T3SS1 secreted proteins. Importantly, we also observed this system to allow the E. coli K-12 strain to inject foreign protein, as well as the V. parahaemolyticus T3SS effector, into cultured cells. These results demonstrate a prospective useful tool with experimental and therapeutic applications. Copyright © 2012 Elsevier Inc. All rights reserved.

An immunoassay for the study of DNA-binding activities of herpes simplex virus protein ICP8.

PubMed

Lee, C K; Knipe, D M

1985-06-01

An immunoassay was used to examine the interaction between a herpes simplex virus protein, ICP8, and various types of DNA. The advantage of this assay is that the protein is not subjected to harsh purification procedures. We characterized the binding of ICP8 to both single-stranded (ss) and double-stranded (ds) DNA. ICP8 bound ss DNA fivefold more efficiently than ds DNA, and both binding activities were most efficient in 150 mM NaCl. Two lines of evidence indicate that the binding activities were not identical: (i) ds DNA failed to complete with ss DNA binding even with a large excess of ds DNA; (ii) Scatchard plots of DNA binding with various amounts of DNA were fundamentally different for ss DNA and ds DNA. However, the two activities were related in that ss DNA efficiently competed with the binding of ds DNA. We conclude that the ds DNA-binding activity of ICP8 is probably distinct from the ss DNA-binding activity. No evidence for sequence-specific ds DNA binding was obtained for either the entire herpes simplex virus genome or cloned viral sequences.

Down-regulation of delayed rectifier K+ channels in the hippocampus of seizure sensitive gerbils.

PubMed

Lee, Sang-Moo; Kim, Ji-Eun; Sohn, Jong-Hee; Choi, Hui-Chul; Lee, Ju-Sang; Kim, Sung-Hun; Kim, Min-Ju; Choi, Ihn-Geun; Kang, Tae-Cheon

2009-12-16

In order to confirm the species-specific distribution of voltage-gated K(+) (Kv) channels and the definitive relationship between their immunoreactivities and seizure activity, we investigated Kv2.x, Kv3.x and Kv4.x channel immunoreactivities in the hippocampi of seizure-resistant (SR) and seizure-sensitive (SS) gerbils. There was no difference in Kv2.1, Kv3.4, Kv4.2 and Kv4.3 immunoreactivity in the hippocampus between SR and SS gerbils. In comparison to SR gerbils, Kv3.1b immunoreactivity in neurons was significantly lower in SS gerbils instead Kv3.1b-immunoreactive astrocytes were clearly observed in SS gerbils (p<0.05). Kv3.2 immunoreactivity was also significantly lower in neurons of SS gerbils than in those of SR gerbils (p<0.05). Considering the findings of our previous study, these findings suggest that delayed rectifier K(+) channels (Kv1.1, Kv1.2, Kv1.5, Kv1.6, Kv2.1 and Kv3.1-2), not A-type K(+) channels (Kv1.4, Kv3.4 and Kv4.x), may be down-regulated in the SS gerbil hippocampus, as compared to SR gerbils.

Swallowing Disorders in Sjögren's Syndrome: Prevalence, Risk Factors, and Effects on Quality of Life.

PubMed

Pierce, Jenny L; Tanner, Kristine; Merrill, Ray M; Miller, Karla L; Kendall, Katherine A; Roy, Nelson

2016-02-01

This epidemiological investigation examined the prevalence, risk factors, and quality-of-life effects of swallowing disorders in Sjögren's syndrome (SS). One hundred and one individuals with primary or secondary SS (94 females, 7 males; mean age 59.4, SD = 14.1) were interviewed regarding the presence, nature, and impact of swallowing disorders and symptoms. Associations among swallowing disorders and symptoms, select medical and social history factors, SS disease severity, and the M.D. Anderson Dysphagia Inventory (MDADI) and Short Form 36 Health Survey (SF-36) were examined. The prevalence of a current self-reported swallowing disorder was 64.4 %. SS disease severity was the strongest predictor of swallowing disorders, including significant associations with the following swallow symptoms: taking smaller bites, thick mucus in the throat, difficulty placing food in the mouth, and wheezing while eating (p < .05). Additional swallowing disorder risk factors included the presence of a self-reported voice disorder, esophageal reflux, current exposure to secondary tobacco smoke, frequent neck or throat tension, frequent throat clearing, chronic post-nasal drip, and stomach or duodenal ulcers. Swallowing disorders did not differ on the basis of primary or secondary SS. Swallowing disorders and specific swallowing symptoms were uniquely associated with reduced quality of life. Among those with swallowing disorders, 42 % sought treatment, with approximately half reporting improvement. Patient-perceived swallowing disorders are relatively common in SS and increase with disease severity. Specific swallowing symptoms uniquely and significantly reduce swallow and health-related quality of life, indicating the need for increased identification and management of dysphagia in this population.

Use of Operational Criteria in an Office Practice for Diagnosis of Children Referred for Evaluation of Learning or Behavior Disorders.

ERIC Educational Resources Information Center

Brumback, Roger A.

1979-01-01

Operational criteria for childhood depression, specific learning disability, developmental hyperactivity, and Gilles de la Tourette syndrome were used to establish the correct diagnosis in 55 of 100 school age Ss. Forty-five Ss were diagnosed as having one of three classical neurological syndromes (epilepsy, sensorineural deafness, and childhood…

Functions for fission yeast splicing factors SpSlu7 and SpPrp18 in alternative splice-site choice and stress-specific regulated splicing.

PubMed

Melangath, Geetha; Sen, Titash; Kumar, Rakesh; Bawa, Pushpinder; Srinivasan, Subha; Vijayraghavan, Usha

2017-01-01

Budding yeast spliceosomal factors ScSlu7 and ScPrp18 interact and mediate intron 3'ss choice during second step pre-mRNA splicing. The fission yeast genome with abundant multi-intronic transcripts, degenerate splice signals and SR proteins is an apt unicellular fungal model to deduce roles for core spliceosomal factors in alternative splice-site choice, intron retention and to study the cellular implications of regulated splicing. From our custom microarray data we deduce a stringent reproducible subset of S. pombe alternative events. We examined the role of factors SpSlu7 or SpPrp18 for these splice events and investigated the relationship to growth phase and stress. Wild-type log and stationary phase cells showed ats1+ exon 3 skipped and intron 3 retained transcripts. Interestingly the non-consensus 5'ss in ats1+ intron 3 caused SpSlu7 and SpPrp18 dependent intron retention. We validated the use of an alternative 5'ss in dtd1+ intron 1 and of an upstream alternative 3'ss in DUF3074 intron 1. The dtd1+ intron 1 non-canonical 5'ss yielded an alternative mRNA whose levels increased in stationary phase. Utilization of dtd1+ intron 1 sub-optimal 5' ss required functional SpPrp18 and SpSlu7 while compromise in SpSlu7 function alone hampered the selection of the DUF3074 intron 1 non canonical 3'ss. We analysed the relative abundance of these splice isoforms during mild thermal, oxidative and heavy metal stress and found stress-specific splice patterns for ats1+ and DUF3074 intron 1 some of which were SpSlu7 and SpPrp18 dependent. By studying ats1+ splice isoforms during compromised transcription elongation rates in wild-type, spslu7-2 and spprp18-5 mutant cells we found dynamic and intron context-specific effects in splice-site choice. Our work thus shows the combinatorial effects of splice site strength, core splicing factor functions and transcription elongation kinetics to dictate alternative splice patterns which in turn serve as an additional recourse of gene regulation in fission yeast.

Functions for fission yeast splicing factors SpSlu7 and SpPrp18 in alternative splice-site choice and stress-specific regulated splicing

PubMed Central

Kumar, Rakesh; Bawa, Pushpinder; Srinivasan, Subha

2017-01-01

Budding yeast spliceosomal factors ScSlu7 and ScPrp18 interact and mediate intron 3’ss choice during second step pre-mRNA splicing. The fission yeast genome with abundant multi-intronic transcripts, degenerate splice signals and SR proteins is an apt unicellular fungal model to deduce roles for core spliceosomal factors in alternative splice-site choice, intron retention and to study the cellular implications of regulated splicing. From our custom microarray data we deduce a stringent reproducible subset of S. pombe alternative events. We examined the role of factors SpSlu7 or SpPrp18 for these splice events and investigated the relationship to growth phase and stress. Wild-type log and stationary phase cells showed ats1+ exon 3 skipped and intron 3 retained transcripts. Interestingly the non-consensus 5’ss in ats1+ intron 3 caused SpSlu7 and SpPrp18 dependent intron retention. We validated the use of an alternative 5’ss in dtd1+ intron 1 and of an upstream alternative 3’ss in DUF3074 intron 1. The dtd1+ intron 1 non-canonical 5’ss yielded an alternative mRNA whose levels increased in stationary phase. Utilization of dtd1+ intron 1 sub-optimal 5’ ss required functional SpPrp18 and SpSlu7 while compromise in SpSlu7 function alone hampered the selection of the DUF3074 intron 1 non canonical 3’ss. We analysed the relative abundance of these splice isoforms during mild thermal, oxidative and heavy metal stress and found stress-specific splice patterns for ats1+ and DUF3074 intron 1 some of which were SpSlu7 and SpPrp18 dependent. By studying ats1+ splice isoforms during compromised transcription elongation rates in wild-type, spslu7-2 and spprp18-5 mutant cells we found dynamic and intron context-specific effects in splice-site choice. Our work thus shows the combinatorial effects of splice site strength, core splicing factor functions and transcription elongation kinetics to dictate alternative splice patterns which in turn serve as an additional recourse of gene regulation in fission yeast. PMID:29236736

Enantiomers of Single-Wall Carbon Nanotubes Show Distinct Coating Displacement Kinetics.

PubMed

Zheng, Yu; Bachilo, Sergei M; Weisman, R Bruce

2018-06-27

It is known that specific oligomers of single-stranded DNA (ssDNA) can show remarkable selectivity when coating different structural species of single-wall carbon nanotubes (SWCNTs). We report that (ATT) 4 ssDNA coatings strongly distinguish between the two optical isomers of (7,5) SWCNTs. This causes resolvable shifts in their fluorescence spectra and differences of 2 orders of magnitude in the room temperature rates of coating displacement, as monitored through changes in nanotube fluorescence wavelength and intensity on exposure to sodium deoxycholate. During coating displacement, the enantiomer with high affinity for the ssDNA oligomer is deduced to form an intermediate hybrid that is not observed for the low affinity enantiomer. These results reveal that enantiomeric differences in SWCNTs complexed with ssDNA are more diverse and dramatic than previously recognized.

The influence of technological parameters on the dynamic behavior of "liquid wood" samples obtained by injection molding

NASA Astrophysics Data System (ADS)

Plavanescu Mazurchevici, Simona; Carausu, Constantin; Comaneci, Radu; Nedelcu, Dumitru

2017-10-01

The plastic products contribute to environmental pollution. Replacing the plastic materials with biodegradable materials with superior properties is an absolute necessity and important research direction for the near future. The first steps in this regard were the creation of composite materials containing natural fibers with positive effects on the environment that have penetrated in different fields. The bioplastics and biocomposites made from natural fibers is a topical solution. The next step was made towards obtaining biodegradable and recyclable materials based on cellulose, lignin and no carcinogens. In this category fall the "liquid wood" with a use up to five times without affecting the mechanical properties. "Liquid wood" is a high quality thermoplastic biocomposite. "Liquid wood" is a biopolymer composite divided in three categories, ARBOFORM®, ARBOBLEND® and ARBOFILL®, which have differed composition in terms of lignin percentage, being delivered by Tecnaro, as granules, [1]. The paper's research was focus on Arboform L V3 Nature and Arboform L V3 Nature reinforced with aramid fiber. In the experimental plan were taken into account six parameters (Dinj - direction of injection [°]; Ttop - melting temperature [°C]; Pinj - injection pressure [MPa] Ss - speed [m/min]; tinj - injection time [s] and tc - cooling time [s]) each with two levels, research carried on by Taguchi methodology. Processing Taguchi method allowed both Taguchi setting work parameters influence on storage modulus and damping as the size and influence their ranking. Experimental research concerning the influence technological parameters on storage modulus of samples obtained by injection from Arboform L V3 Nature yielded an average of 6055MPa and descending order as follows: Trac, Ss, Pinj, Dinj and Ttop. The average of model for reinforced material was 6419MPa and descending order of parameters influence such as: Dinj, Trac, Ttop, tinj, Ss and Pinj.

Occurrence and molecular characterisation of Vibrio parahaemolyticus in crustaceans commercialised in Venice area, Italy.

PubMed

Caburlotto, Greta; Suffredini, Elisabetta; Toson, Marica; Fasolato, Luca; Antonetti, Paolo; Zambon, Michela; Manfrin, Amedeo

2016-03-02

Infections due to the pathogenic human vibrios, Vibrio parahaemolyticus, Vibrio cholerae and Vibrio vulnificus, are mainly associated with consumption of raw or partially cooked bivalve molluscs. At present, little is known about the presence of Vibrio species in crustaceans and the risk of vibriosis associated with the consumption of these products. The aim of the present study was to evaluate the prevalence and concentration of the main pathogenic Vibrio spp. in samples of crustaceans (n=143) commonly eaten in Italy, taking into account the effects of different variables such as crustacean species, storage conditions and geographic origin. Subsequently, the potential pathogenicity of V. parahaemolyticus strains isolated from crustaceans (n=88) was investigated, considering the classic virulence factors (tdh and trh genes) and four genes coding for relevant proteins of the type III secretion systems 2 (T3SS2α and T3SS2β). In this study, the presence of V. cholerae and V. vulnificus was never detected, whereas 40 samples (28%) were positive for V. parahaemolyticus with an overall prevalence of 41% in refrigerated products and 8% in frozen products. The highest prevalence and average contamination levels were detected in Crangon crangon (prevalence 58% and median value 3400 MPN/g) and in products from the northern Adriatic Sea (35%), with the samples from the northern Venetian Lagoon reaching a median value of 1375 MPN/g. While genetic analysis confirmed absence of the tdh gene, three of the isolates contained the trh gene and, simultaneously, the T3SS2β genes. Moreover three possibly clonal tdh-negative/trh-negative isolates carried the T3SS2α apparatus. The detection of both T3SS2α and T3SS2β apparatuses in V. parahaemolyticus strains isolated from crustaceans emphasised the importance of considering new genetic markers associated with virulence besides the classical factors. Moreover this study represents the first report dealing with Vibrio spp. in crustaceans in Italy, and it may provide useful information for the development of sanitary surveillance plans to prevent the risk of vibriosis in seafood consumers. Copyright © 2016 Elsevier B.V. All rights reserved.

pH salivary analysis of subjects suffering from Sjögren's syndrome and laryngopharyngeal reflux.

PubMed

Corvo, Marco Antonio Dos Anjos; Eckley, Claudia Alessandra; Liquidato, Bianca Maria; Castilho, Gustavo Leão; Arruda, Cibelle Nunes de

2012-02-01

Saliva is one of the components for the digestive homeostasis. Recent studies have shown that patients with laryngopharyngeal reflux (LPR) present a drop in salivary pH. Patients with Sjögren's syndrome (SS) are a potential clinical research model for xerostomia and its laryngeal and pharyngeal consequences. The aim was to evaluate the characteristics of saliva of patients with SS and LPR. 19 patients with SS plus LPR, and 12 healthy controls had their saliva studied prospectively for volume and pH. Two salivary samples were obtained from each participant: whole unstimulated saliva(WUS) and whole stimulated saliva(WSS) while chewing parafilm M®. All the participants were females. Mean age was 60 years (study group) and 44 years (control). LPR was diagnosed on all 19 subjects. The mean pH of WUS was 7.53 (SS) and 7.57 (controls), raising to 7.87 and 7.83 respectively after stimulation. The mean salivary volume of patients with SS was 1.27 mL (WUS) and 3.78 mL (WSS), whereas controls had a significantly higher salivary volume both before and after stimuli. A very high prevalence of LPR was found in patients with SS, which is probably caused by a uniform drop in salivary volume and all its contents, rather than a specific deficiency in its components, as shown previously in patients without SS.

Novel Immunocytokine IL12-SS1 (Fv) Inhibits Mesothelioma Tumor Growth in Nude Mice

PubMed Central

Kim, Heungnam; Gao, Wei; Ho, Mitchell

2013-01-01

Mesothelin is a glycosylphosphatidylinositol-anchored glycoprotein that is highly expressed on the cell surface of malignant mesothelioma. Monoclonal antibodies against mesothelin are being evaluated for the treatment of mesothelioma. Immunocytokines represent a novel class of armed antibodies. To provide an alternative approach to current mesothelin-targeted antibody therapies, we have developed a novel immunocytokine based on interleukin-12 (IL12) and the SS1 Fv specific for mesothelin. IL12 possesses potent anti-tumor activity in a wide variety of solid tumors. The newly-developed recombinant immunocytokine, IL12-SS1 (Fv), was produced in insect cells using a baculovirus-insect cell expression system. The SS1 single-chain Fv was fused to the C terminus of the p35 subunit of IL12 through a short linker (GSADGG). The single-chain IL12-SS1 (Fv) immunocytokine bound native mesothelin proteins on malignant mesothelioma (NCI-H226) and ovarian (OVCAR-3) cells as well as recombinant mesothelin on A431/H9 cells. The immunocytokine retained sufficient bioactivity of IL12 and significantly inhibited human malignant mesothelioma (NCI-H226) grown in the peritoneal cavity of nude mice and showed comparable anti-tumor activity to that of the SS1P immunotoxin. IL12-SS1 (Fv) is the first reported immunocytokine to mesothelin-positive tumors and may be an attractive addition to mesothelin-targeted cancer therapies. PMID:24260587

Ferulic Acid, But Not All Hydroxycinnamic Acids, Is a Novel T3SS Inducer of Ralstonia solanacearum and Promotes Its Infection Process in Host Plants under Hydroponic Condition.

PubMed

Zhang, Yong; Li, Jing; Zhang, Weiqi; Wang, Rongsheng; Qiu, Qiaoqing; Luo, Feng; Hikichi, Yasufumi; Ohnishi, Kouhei; Ding, Wei

2017-01-01

Hydroxycinnamic acids (HCAs) are typical monocyclic phenylpropanoids, including cinnamic acid (Cin), coumaric acid (Cou), caffeic acid (Caf), ferulic acid (FA) and their isomers, and involved in the interactions between pathogens and host plants. Here, we focused on the impact of HCAs on expression of type III secretion system (T3SS) in Ralstonia solanacearum . FA significantly induced the expression of the T3SS and some type III effectors (T3Es) genes in hrp -inducing medium, while did not the other HCAs. However, exogenously supplemented FA did not affect the T3SS expression in planta and the elicitation of the hypersensitive response (HR) in tobacco leaves. Consistent with its central roles in pathogenicity, the FA-induced expression of the T3SS led to significant promotion on infection process of R. solanacearum in tomato plants under hydroponics cultivation. Moreover, the FA-induced expression of the T3SS was specifically mediated by the well-characterized signaling cascade PrhA-prhI/R-PrhJ-HrpG-HrpB, independent of the other known regulatory pathways. In summary, our results demonstrated that FA, a novel inducer of the T3SS in R. solanacearum , was able to promote its infection process in host plants under hydroponics condition.

Diagnostic Ability of Wide-field Retinal Nerve Fiber Layer Maps Using Swept-Source Optical Coherence Tomography for Detection of Preperimetric and Early Perimetric Glaucoma.

PubMed

Lee, Won June; Na, Kyeong Ik; Kim, Young Kook; Jeoung, Jin Wook; Park, Ki Ho

2017-06-01

To evaluate the diagnostic ability of wide-field retinal nerve fiber layer (RNFL) maps with swept-source optical coherence tomography (SS-OCT) for detection of preperimetric (PPG) and early perimetric glaucoma (EG). One hundred eighty-four eyes, including 67 healthy eyes, 43 eyes with PPG, and 74 eyes with EG, were analyzed. Patients underwent a comprehensive ocular examination including red-free RNFL photography, visual field testing and wide-field SS-OCT scanning (DRI-OCT-1 Atlantis; Topcon, Tokyo, Japan). SS-OCT provides a wide-field RNFL thickness map and a SuperPixel map, which are composed of the RNFL deviation map of the peripapillary area and the deviation map of the composition of the ganglion cell layer with the inner plexiform layer and RNFL (GC-IPL+RNFL) in the macular area. The ability to discriminate PPG and EG from healthy eyes was assessed using sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) for all parameters and criteria provided by the wide-field SS-OCT scan. The wide-field RNFL thickness map using SS-OCT showed the highest sensitivity of PPG-diagnostic and EG-diagnostic performance compared with the other SS-OCT criteria based on the internal normative base (93.0 and 97.3%, respectively). Among the SS-OCT continuous parameters, the RFNL thickness of the 7 clock-hour, inferior and inferotemporal macular ganglion cell analyses showed the largest AUC of PPG-diagnostic and EG-diagnostic performance (AUC=0.809 to 0.865). The wide-field RNFL thickness map using SS-OCT performed well in distinguishing eyes with PPG and EG from healthy eyes. In the clinical setting, wide-field RNFL maps of SS-OCT can be useful tools for detection of early-stage glaucoma.

Risk of Sjögren's syndrome in Taiwanese female adults with irregular menstrual cycles: a population-based case-control study.

PubMed

Lu, Ming-Chi; Hsieh, Min-Chih; Koo, Malcolm; Lai, Ning-Sheng

2016-01-01

Primary Sjögren's syndrome (pSS) is a progressive systemic autoimmune disorder with a strong female predominance. Hormonal influences are thought to play a role in the development of pSS. However, no studies have specifically evaluated the association between irregular menstrual cycles and pSS. Therefore, using a health claims database, this study investigated the risk of pSS in women with irregular menstrual cycles. We conducted a case-control study using the Taiwan's National Health Insurance Research Database. A total of 360 patients diagnosed with pSS (International Classification of Diseases, ninth revision, clinical modification, ICD-9-CM code 710.2) between 2001 and 2012 were identified. Controls were frequency-matched at a rate of 5:1 to the cases by five-year age interval and index year. Both cases and controls were retrospectively traced back until 2001 for the diagnosis of irregular menstrual cycles (ICD-9-CM code 626.4). The risk of pSS was assessed using multivariate logistic regression analyses. Irregular menstrual cycles were significantly associated with pSS [adjusted odds ratio, (AOR) = 1.38, p = 0.027], after adjusted for insured amount, urbanization level, and thyroid disorder. In addition, when the data were stratified by three age categories, only the patients in the age category of 45-55 years showed significant association between irregular menstrual cycles and pSS (AOR = 1.74, p = 0.005). In this nationwide, population-based case-control study, we found a significant increased risk of pSS in female patients with irregular menstrual cycles, particularly those in their mid-forties to mid-fifties.

Associations between salivary gland histopathologic diagnoses and phenotypic features of Sjögren’s Syndrome (SS) among 1726 registry participants

PubMed Central

Daniels, Troy E.; Cox, Darren; Shiboski, Caroline H.; Schiødt, Morten; Wu, Ava; Lanfranchi, Hector; Umehara, Hisanori; Zhao, Yan; Challacombe, Stephen; Lam, Mi Y.; DeSouza, Yvonne; Schiødt, Julie; Holm, Helena; Bisio, Patricia A. M.; Gandolfo, Mariana S.; Sawaki, Toshioki; Li, Mengtao; Zhang, Wen; Varghese-Jacob, Beni; Ibsen, Per; Keszler, Alicia; Kurose, Nozomu; Nojima, Takayuki; Odell, Edward; Criswell, Lindsey A.; Jordan, Richard; Greenspan, John S.

2011-01-01

Objectives The Sjögren’s International Collaborative Clinical Alliance (SICCA) is an ongoing NIH-funded registry whose cohort ranges from those with symptoms of possible Sjögren’s syndrome (SS) to those with obvious disease. Using this database we examined associations between labial salivary gland (LSG) histopathology and other phenotypic features of SS. Methods LSG biopsy specimens from SICCA participants underwent protocol-directed histopathological assessments. Among 1726 LSG specimens exhibiting any pattern of sialadenitis, we compared biopsy diagnoses against concurrent salivary, ocular and serological assessments. Results LSG specimens included 61% with focal lymphocytic sialadenitis, (FLS; 66% of which had focus scores [FS] ≥ 1 per 4 mm2) and 38% with non-specific or sclerosing chronic sialadenitis (NS/SCS). FS ≥ 1 was strongly associated with positive serum anti-SS-A/-B, rheumatoid factor and the ocular component of SS, but not with symptoms of dry mouth or eyes. Those with positive anti-SS-A/-B were 9 times more likely to have a FS ≥ 1 (95% CI: 7.4; 11.9) than FS<1 or another pattern, while those with unstimulated whole salivary flow < 0.1 ml/min were only 2 times more likely to have a FS ≥ 1 (95% CI:1.7; 2.8) than FS<1 or another pattern, while controlling for other phenotypic features of SS. Conclusions Distinguishing FLS from NS/SCS is essential in assessing LSG biopsies, before determining FS. A diagnosis of FLS with FS ≥ 1 per 4 mm2, as compared to FLS with FS< 1 or with NS/SCS, was strongly associated with the ocular and serological components of SS and reflects SS autoimmunity. PMID:21480190

Applying Fourier Transform Mid Infrared Spectroscopy to Detect the Adulteration of Salmo salar with Oncorhynchus mykiss

PubMed Central

Moreira, Maria João

2018-01-01

The aim of this study was to evaluate the potential of Fourier transform infrared (FTIR) spectroscopy coupled with chemometric methods to detect fish adulteration. Muscles of Atlantic salmon (Salmo salar) (SS) and Salmon trout (Onconrhynchus mykiss) (OM) muscles were mixed in different percentages and transformed into mini-burgers. These were stored at 3 °C, then examined at 0, 72, 160, and 240 h for deteriorative microorganisms. Mini-burgers was submitted to Soxhlet extraction, following which lipid extracts were analyzed by FTIR. The principal component analysis (PCA) described the studied adulteration using four principal components with an explained variance of 95.60%. PCA showed that the absorbance in the spectral region from 721, 1097, 1370, 1464, 1655, 2805, to 2935, 3009 cm−1 may be attributed to biochemical fingerprints related to differences between SS and OM. The partial least squares regression (PLS-R) predicted the presence/absence of adulteration in fish samples of an external set with high accuracy. The proposed methods have the advantage of allowing quick measurements, despite the storage time of the adulterated fish. FTIR combined with chemometrics showed that a methodology to identify the adulteration of SS with OM can be established, even when stored for different periods of time. PMID:29621135

Biocompatible Nanoemulsions for Improved Aceclofenac Skin Delivery: Formulation Approach Using Combined Mixture-Process Experimental Design.

PubMed

Isailović, Tanja; Ðorđević, Sanela; Marković, Bojan; Ranđelović, Danijela; Cekić, Nebojša; Lukić, Milica; Pantelić, Ivana; Daniels, Rolf; Savić, Snežana

2016-01-01

We aimed to develop lecithin-based nanoemulsions intended for effective aceclofenac (ACF) skin delivery utilizing sucrose esters [sucrose palmitate (SP) and sucrose stearate (SS)] as additional stabilizers and penetration enhancers. To find the suitable surfactant mixtures and levels of process variables (homogenization pressure and number of cycles - high pressure homogenization manufacturing method) that result in drug-loaded nanoemulsions with minimal droplet size and narrow size distribution, a combined mixture-process experimental design was employed. Based on optimization data, selected nanoemulsions were evaluated regarding morphology, surface charge, drug-excipient interactions, physical stability, and in vivo skin performances (skin penetration and irritation potential). The predicted physicochemical properties and storage stability were proved satisfying for ACF-loaded nanoemulsions containing 2% of SP in the blend with 0%-1% of SS and 1%-2% of egg lecithin (produced at 50°C/20 cycles/800 bar). Additionally, the in vivo tape stripping demonstrated superior ACF skin absorption from these nanoemulsions, particularly from those containing 2% of SP, 0.5% of SS, and 1.5% of egg lecithin, when comparing with the sample costabilized by conventional surfactant - polysorbate 80. In summary, the combined mixture-process experimental design was shown as a feasible tool for formulation development of multisurfactant-based nanosized delivery systems with potentially improved overall product performances.

Extraordinary GU-rich single-strand RNA identified from SARS coronavirus contributes an excessive innate immune response.

PubMed

Li, Yan; Chen, Ming; Cao, Hongwei; Zhu, Yuanfeng; Zheng, Jiang; Zhou, Hong

2013-02-01

A dangerous cytokine storm occurs in the SARS involving in immune disorder, but many aspects of the pathogenetic mechanism remain obscure since its outbreak. To deeply reveal the interaction of host and SARS-CoV, based on the basic structural feature of pathogen-associated molecular pattern, we created a new bioinformatics method for searching potential pathogenic molecules and identified a set of SARS-CoV specific GU-rich ssRNA fragments with a high-density distribution in the genome. In vitro experiments, the result showed the representative SARS-CoV ssRNAs had powerful immunostimulatory activities to induce considerable level of pro-inflammatory cytokine TNF-a, IL-6 and IL-12 release via the TLR7 and TLR8, almost 2-fold higher than the strong stimulatory ssRNA40 that was found previously from other virus. Moreover, SARS-CoV ssRNA was able to cause acute lung injury in mice with a high mortality rate in vivo experiment. It suggests that SARS-CoV specific GU-rich ssRNA plays a very important role in the cytokine storm associated with a dysregulation of the innate immunity. This study not only presents new evidence about the immunopathologic damage caused by overactive inflammation during the SARS-CoV infection, but also provides a useful clue for a new therapeutic strategy. Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Designing a Pediatric Severe Sepsis Screening Tool

PubMed Central

Sepanski, Robert J.; Godambe, Sandip A.; Mangum, Christopher D.; Bovat, Christine S.; Zaritsky, Arno L.; Shah, Samir H.

2014-01-01

We sought to create a screening tool with improved predictive value for pediatric severe sepsis (SS) and septic shock that can be incorporated into the electronic medical record and actively screen all patients arriving at a pediatric emergency department (ED). “Gold standard” SS cases were identified using a combination of coded discharge diagnosis and physician chart review from 7,402 children who visited a pediatric ED over 2 months. The tool’s identification of SS was initially based on International Consensus Conference on Pediatric Sepsis (ICCPS) parameters that were refined by an iterative, virtual process that allowed us to propose successive changes in sepsis detection parameters in order to optimize the tool’s predictive value based on receiver operating characteristics (ROC). Age-specific normal and abnormal values for heart rate (HR) and respiratory rate (RR) were empirically derived from 143,603 children seen in a second pediatric ED over 3 years. Univariate analyses were performed for each measure in the tool to assess its association with SS and to characterize it as an “early” or “late” indicator of SS. A split-sample was used to validate the final, optimized tool. The final tool incorporated age-specific thresholds for abnormal HR and RR and employed a linear temperature correction for each category. The final tool’s positive predictive value was 48.7%, a significant, nearly threefold improvement over the original ICCPS tool. False positive systemic inflammatory response syndrome identifications were nearly sixfold lower. PMID:24982852

Ion-channel genosensor for the detection of specific DNA sequences derived from Plum Pox Virus in plant extracts.

PubMed

Malecka, Kamila; Michalczuk, Lech; Radecka, Hanna; Radecki, Jerzy

2014-10-09

A DNA biosensor for detection of specific oligonucleotides sequences of Plum Pox Virus (PPV) in plant extracts and buffer is proposed. The working principles of a genosensor are based on the ion-channel mechanism. The NH2-ssDNA probe was deposited onto a glassy carbon electrode surface to form an amide bond between the carboxyl group of oxidized electrode surface and amino group from ssDNA probe. The analytical signals generated as a result of hybridization were registered in Osteryoung square wave voltammetry in the presence of [Fe(CN)6]3-/4- as a redox marker. The 22-mer and 42-mer complementary ssDNA sequences derived from PPV and DNA samples from plants infected with PPV were used as targets. Similar detection limits of 2.4 pM (31.0 pg/mL) and 2.3 pM (29.5 pg/mL) in the concentration range 1-8 pM were observed in the presence of the 22-mer ssDNA and 42-mer complementary ssDNA sequences of PPV, respectively. The genosensor was capable of discriminating between samples consisting of extracts from healthy plants and leaf extracts from infected plants in the concentration range 10-50 pg/mL. The detection limit was 12.8 pg/mL. The genosensor displayed good selectivity and sensitivity. The 20-mer partially complementary DNA sequences with four complementary bases and DNA samples from healthy plants used as negative controls generated low signal.

Application of optical coherence tomography attenuation imaging for quantification of optical properties in medulloblastoma

NASA Astrophysics Data System (ADS)

Vuong, Barry; Skowron, Patryk; Kiehl, Tim-Rasmus; Kyan, Matthew; Garzia, Livia; Genis, Helen; Sun, Cuiru; Taylor, Michael D.; Yang, Victor X. D.

2015-03-01

The hemodynamic environment is known to play a crucial role in the progression, rupture, and treatment of intracranial aneurysms. Currently there is difficulty assessing and measuring blood flow profiles in vivo. An emerging high resolution imaging modality known as split spectrum Doppler optical coherence tomography (ssDOCT) has demonstrated the capability to quantify hemodynamic patterns as well as arterial microstructural changes. In this study, we present a novel in vitro method to acquire precise blood flow patterns within a patient- specific aneurysm silicone flow models using ssDOCT imaging. Computational fluid dynamics (CFD) models were generated to verify ssDOCT results.

The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes

PubMed Central

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph

2010-01-01

Bacterial pathogens typically infect only a limited range of hosts; however, the genetic mechanisms governing host-specificity are poorly understood. The α-proteobacterial genus Bartonella comprises 21 species that cause host-specific intraerythrocytic bacteremia as hallmark of infection in their respective mammalian reservoirs, including the human-specific pathogens Bartonella quintana and Bartonella bacilliformis that cause trench fever and Oroya fever, respectively. Here, we have identified bacterial factors that mediate host-specific erythrocyte colonization in the mammalian reservoirs. Using mouse-specific Bartonella birtlesii, human-specific Bartonella quintana, cat-specific Bartonella henselae and rat-specific Bartonella tribocorum, we established in vitro adhesion and invasion assays with isolated erythrocytes that fully reproduce the host-specificity of erythrocyte infection as observed in vivo. By signature-tagged mutagenesis of B. birtlesii and mutant selection in a mouse infection model we identified mutants impaired in establishing intraerythrocytic bacteremia. Among 45 abacteremic mutants, five failed to adhere to and invade mouse erythrocytes in vitro. The corresponding genes encode components of the type IV secretion system (T4SS) Trw, demonstrating that this virulence factor laterally acquired by the Bartonella lineage is directly involved in adherence to erythrocytes. Strikingly, ectopic expression of Trw of rat-specific B. tribocorum in cat-specific B. henselae or human-specific B. quintana expanded their host range for erythrocyte infection to rat, demonstrating that Trw mediates host-specific erythrocyte infection. A molecular evolutionary analysis of the trw locus further indicated that the variable, surface-located TrwL and TrwJ might represent the T4SS components that determine host-specificity of erythrocyte parasitism. In conclusion, we show that the laterally acquired Trw T4SS diversified in the Bartonella lineage to facilitate host-restricted adhesion to erythrocytes in a wide range of mammals. PMID:20548954

Serodiagnosis of sporotrichosis infection in cats by enzyme-linked immunosorbent assay using a specific antigen, SsCBF, and crude exoantigens.

PubMed

Fernandes, Geisa Ferreira; Lopes-Bezerra, Leila Maria; Bernardes-Engemann, Andréa Reis; Schubach, Tânia Maria Pacheco; Dias, Maria Adelaide Galvão; Pereira, Sandro Antonio; de Camargo, Zoilo Pires

2011-01-27

The main objective of this study is to standardize an ELISA for the diagnosis of feline sporotrichosis. Sporothrix schenckii is the etiological agent of human and animal sporotrichosis. Cats may act as reservoirs for S. schenckii and can transmit the infection to humans by a bite or scratch. There are few methods for the serological diagnosis of fungal diseases in animals. In this paper, an ELISA test for the diagnosis of cat sporotrichosis is proposed, which detects S. schenckii-specific antibodies in feline sera. Two different kinds of antigens were used: "SsCBF", a specific molecule from S. schenckii that consists of a Con A-binding fraction derived from a peptido-rhamnomannan component of the cell wall, and a S. schenckii crude exoantigen preparation. The ELISA was developed, optimized, and evaluated using sera from 30 cats with proven sporotrichosis (by culture isolation); 22 sera from healthy feral cats from a zoonosis center were used as negative controls. SsCBF showed 90% sensitivity and 96% specificity in ELISA; while crude exoantigens demonstrated 96% sensitivity and 98% specificity. The ELISA assay described here would be a valuable screening tool for the detection of specific S. schenckii antibodies in cats with sporotrichosis. The assay is inexpensive, quick to perform, easy to interpret, and permits the diagnosis of feline sporotrichosis. Copyright © 2010 Elsevier B.V. All rights reserved.

The Role of Self-Efficacy and Referent Specific Social Support in Promoting Rural Adolescent Girls' Physical Activity

ERIC Educational Resources Information Center

Beets, Michael W.; Pitetti, Kenneth H.; Forlaw, Loretta

2007-01-01

Objective: To examine the role of social support (SS) and self-efficacy (SE) for physical activity (PA) in rural high school girls (N = 259, 15.5+1.2yrs). Methods: Using structural equation modeling, the relationships among PA, SS for PA from mother, father, and peers, and SE for overcoming barriers, seeking support, and resisting competing…

Investigation of L-leucine in reducing the moisture-induced deterioration of spray-dried salbutamol sulfate power for inhalation.

PubMed

Li, Liang; Leung, Sharon Shui Yee; Gengenbach, Thomas; Yu, Jiaqi; Gao, Ge Fiona; Tang, Patricia; Zhou, Qi Tony; Chan, Hak-Kim

2017-09-15

The aim of this study was to investigate the ability of L-leucine (LL) in preventing moisture-induced deterioration in the in vitro aerosolization performance of spray-dried (SD) salbutamol sulfate (SS). Increasing mass fraction of LL (5-80%) were co-spray dried with SS, and the physicochemical properties of the powders were characterized by laser diffraction, X-ray powder diffraction (XRD) and dynamic vapour sorption (DVS). Furthermore, the surface morphology and chemistry of fine particles was analyzed by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). The in vitro aerosolization performance of powders stored at different relative humidity (RH) was evaluated by a next generation impactor (NGI). The SD SS powders were moderately hygroscopic and amorphous, of which the uptake of moisture upon storage caused a drop in the aerosolization performance. The results showed that 40% (w/w) LL was sufficient to eliminate the effect of moisture on the aerosolization performance at 60% RH. The formulation containing 40% (w/w) LL also maximized the aerosolization performance of SD SS powders (stored in desiccator) with the emitted fraction being 90.0±1.8%, and the fine particle fraction based on the recovered dose (FPF recovered ) and emitted dose (FPF emitted ) being 78.0±3.7% and 86.6±2.9%, respectively. The underlying mechanisms were that the crystalline LL increased the degree of particle surface corrugation, and reduced particle fusion and cohesiveness to facilitate dispersion. However, there is still a great challenge to prevent the moisture-induced deterioration in the aerosolization performance at 75% RH due to the recrystallization of SD SS. In conclusion, LL is a potential excipient for reducing moisture-induced deterioration in the aerosolization performance of SD amorphous powders, but still has drawbacks in preventing the recrystallization-induced deterioration. Copyright © 2017 Elsevier B.V. All rights reserved.

Manganese scavenging and oxidative stress response mediated by type VI secretion system in Burkholderia thailandensis

PubMed Central

Si, Meiru; Zhao, Chao; Burkinshaw, Brianne; Zhang, Bing; Wei, Dawei; Wang, Yao; Dong, Tao G.; Shen, Xihui

2017-01-01

Type VI secretion system (T6SS) is a versatile protein export machinery widely distributed in Gram-negative bacteria. Known to translocate protein substrates to eukaryotic and prokaryotic target cells to cause cellular damage, the T6SS has been primarily recognized as a contact-dependent bacterial weapon for microbe–host and microbial interspecies competition. Here we report contact-independent functions of the T6SS for metal acquisition, bacteria competition, and resistance to oxidative stress. We demonstrate that the T6SS-4 in Burkholderia thailandensis is critical for survival under oxidative stress and is regulated by OxyR, a conserved oxidative stress regulator. The T6SS-4 is important for intracellular accumulation of manganese (Mn2+) under oxidative stress. Next, we identified a T6SS-4–dependent Mn2+-binding effector TseM, and its interacting partner MnoT, a Mn2+-specific TonB-dependent outer membrane transporter. Similar to the T6SS-4 genes, expression of mnoT is regulated by OxyR and is induced under oxidative stress and low Mn2+ conditions. Both TseM and MnoT are required for efficient uptake of Mn2+ across the outer membrane under Mn2+-limited and -oxidative stress conditions. The TseM–MnoT-mediated active Mn2+ transport system is also involved in contact-independent bacteria–bacteria competition and bacterial virulence. This finding provides a perspective for understanding the mechanisms of metal ion uptake and the roles of T6SS in bacteria–bacteria competition. PMID:28242693

Acquired Type III Secretion System Determines Environmental Fitness of Epidemic Vibrio parahaemolyticus in the Interaction with Bacterivorous Protists

PubMed Central

Matz, Carsten; Nouri, Bianka; McCarter, Linda; Martinez-Urtaza, Jaime

2011-01-01

Genome analyses of marine microbial communities have revealed the widespread occurrence of genomic islands (GIs), many of which encode for protein secretion machineries described in the context of bacteria-eukaryote interactions. Yet experimental support for the specific roles of such GIs in aquatic community interactions remains scarce. Here, we test for the contribution of type III secretion systems (T3SS) to the environmental fitness of epidemic Vibrio parahaemolyticus. Comparisons of V. parahaemolyticus wild types and T3SS-defective mutants demonstrate that the T3SS encoded on genome island VPaI-7 (T3SS-2) promotes survival of V. parahaemolyticus in the interaction with diverse protist taxa. Enhanced persistence was found to be due to T3SS-2 mediated cytotoxicity and facultative parasitism of V. parahaemolyticus on coexisting protists. Growth in the presence of bacterivorous protists and the T3SS-2 genotype showed a strong correlation across environmental and clinical isolates of V. parahaemolyticus. Short-term microcosm experiments provide evidence that protistan hosts facilitate the invasion of T3SS-2 positive V. parahaemolyticus into a coastal plankton community, and that water temperature and productivity further promote enhanced survival of T3SS-2 positive V. parahaemolyticus. This study is the first to describe the fitness advantage of GI-encoded functions in a microbial food web, which may provide a mechanistic explanation for the global spread and the seasonal dynamics of V. parahaemolyticus pathotypes, including the pandemic serotype cluster O3:K6, in aquatic environments. PMID:21629787

Tremor–genic slow slip regions may be deeper and warmer and may slip slower than non–tremor–genic regions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Montgomery-Brown, E. K.; Syracuse, E. M.

The slow slip events (SSEs) are observed worldwide and often coincide with tectonic tremor. Notable examples of SSEs lacking observed tectonic tremor, however, occur beneath Kilauea Volcano, Hawaii, the Boso Peninsula, Japan, {near San Juan Bautista on the San Andreas Fault, California, and recently in Central Ecuador. These SSEs are similar to other worldwide SSEs in many ways (e.g., size or duration), but lack the concurrent tectonic tremor observed elsewhere; instead they trigger swarms of regular earthquakes. We investigate the physical conditions that may distinguish these non-tremor-genic SSEs from those associated with tectonic tremor including: slip velocity, pressure, temperature, fluidsmore » and fault asperities, although we cannot eliminate the possibility that tectonic tremor may be obscured in highly attenuating regions. Slip velocities of SSEs at Kilauea Volcano (~10⁻⁶ m/s) and Boso Peninsula (~10⁻⁷ m/s) are among the fastest SSEs worldwide. Kilauea Volcano, the Boso Peninsula and Central Ecuador are also among the shallowest SSEs worldwide, and thus have lower confining pressures and cooler temperatures in their respective slow slip zones. {Fluids also likely contribute to tremor generation, and no corresponding zone of high v p/v s has been noted at Kilauea or Boso. We suggest that the relatively faster slip velocities at Kilauea Volcano and the Boso Peninsula result from specific physical conditions that may also be responsible for triggering swarms of regular earthquakes adjacent to the slow slip, while different conditions produce slower SSE velocities elsewhere and trigger tectonic tremor.« less

Manganese scavenging and oxidative stress response mediated by type VI secretion system in Burkholderia thailandensis.

PubMed

Si, Meiru; Zhao, Chao; Burkinshaw, Brianne; Zhang, Bing; Wei, Dawei; Wang, Yao; Dong, Tao G; Shen, Xihui

2017-03-14

Type VI secretion system (T6SS) is a versatile protein export machinery widely distributed in Gram-negative bacteria. Known to translocate protein substrates to eukaryotic and prokaryotic target cells to cause cellular damage, the T6SS has been primarily recognized as a contact-dependent bacterial weapon for microbe-host and microbial interspecies competition. Here we report contact-independent functions of the T6SS for metal acquisition, bacteria competition, and resistance to oxidative stress. We demonstrate that the T6SS-4 in Burkholderia thailandensis is critical for survival under oxidative stress and is regulated by OxyR, a conserved oxidative stress regulator. The T6SS-4 is important for intracellular accumulation of manganese (Mn 2+ ) under oxidative stress. Next, we identified a T6SS-4-dependent Mn 2+ -binding effector TseM, and its interacting partner MnoT, a Mn 2+ -specific TonB-dependent outer membrane transporter. Similar to the T6SS-4 genes, expression of mnoT is regulated by OxyR and is induced under oxidative stress and low Mn 2+ conditions. Both TseM and MnoT are required for efficient uptake of Mn 2+ across the outer membrane under Mn 2+ -limited and -oxidative stress conditions. The TseM-MnoT-mediated active Mn 2+ transport system is also involved in contact-independent bacteria-bacteria competition and bacterial virulence. This finding provides a perspective for understanding the mechanisms of metal ion uptake and the roles of T6SS in bacteria-bacteria competition.

Epigenetic Regulation of Tumor Necrosis Factor α (TNFα) Release in Human Macrophages by HIV-1 Single-stranded RNA (ssRNA) Is Dependent on TLR8 Signaling*

PubMed Central

Han, Xinbing; Li, Xin; Yue, Simon C.; Anandaiah, Asha; Hashem, Falah; Reinach, Peter S.; Koziel, Henry; Tachado, Souvenir D.

2012-01-01

Human macrophages at mucosal sites are essential targets for acute HIV infection. During the chronic phase of infection, they are persistent reservoirs for the AIDS virus. HIV virions gain entry into macrophages following ligation of surface CD4-CCR5 co-receptors, which leads to the release of two copies of HIV ssRNA. These events lead to reverse transcription and viral replication initiation. Toll-like receptors TLR7 and TLR8 recognize specific intracellular viral ssRNA sequences, but in human alveolar macrophages, their individual roles in TLR-mediated HIV ssRNA recognition are unclear. In the current study, HIV-1 ssRNA induced TNFα release in a dose-dependent manner in adherent human macrophages expressing both intracellular TLR7 and TLR8. This response was reduced by inhibiting either endocytosis (50 μm dynasore) or endosomal acidification (1 μg/ml chloroquine). Either MYD88 or TLR8 gene knockdown with relevant siRNA reduced HIV-1 ssRNA-mediated TNFα release, but silencing TLR7 had no effect on this response. Furthermore, HIV-1 ssRNA induced histone 4 acetylation at the TNFα promoter as well as trimethylation of histone 3 at lysine 4, whereas TLR8 gene knockdown reduced these effects. Taken together in human macrophages, TLR8 binds and internalizes HIV ssRNA, leading to endosomal acidification, chromatin remodeling, and increases in TNFα release. Drugs targeting macrophage TLR8-linked signaling pathways may modulate the innate immune response to acute HIV infection by reducing viral replication. PMID:22393042

Tremor-genic slow slip regions may be deeper and warmer and may slip slower than non-tremor-genic regions

USGS Publications Warehouse

Montgomery-Brown, Emily; Syracuse, Ellen M.

2015-01-01

Slow slip events (SSEs) are observed worldwide and often coincide with tectonic tremor. Notable examples of SSEs lacking observed tectonic tremor, however, occur beneath Kīlauea Volcano, Hawaii, the Boso Peninsula, Japan, near San Juan Bautista on the San Andreas Fault, California, and recently in Central Ecuador. These SSEs are similar to other worldwide SSEs in many ways (e.g., size or duration), but lack the concurrent tectonic tremor observed elsewhere; instead, they trigger swarms of regular earthquakes. We investigate the physical conditions that may distinguish these non-tremor-genic SSEs from those associated with tectonic tremor, including slip velocity, pressure, temperature, fluids, and fault asperities, although we cannot eliminate the possibility that tectonic tremor may be obscured in highly attenuating regions. Slip velocities of SSEs at Kīlauea Volcano (∼10−6 m/s) and Boso Peninsula (∼10−7 m/s) are among the fastest SSEs worldwide. Kīlauea Volcano, the Boso Peninsula, and Central Ecuador are also among the shallowest SSEs worldwide, and thus have lower confining pressures and cooler temperatures in their respective slow slip zones. Fluids also likely contribute to tremor generation, and no corresponding zone of high vp/vs has been noted at Kīlauea or Boso. We suggest that the relatively faster slip velocities at Kīlauea Volcano and the Boso Peninsula result from specific physical conditions that may also be responsible for triggering swarms of regular earthquakes adjacent to the slow slip, while different conditions produce slower SSE velocities elsewhere and trigger tectonic tremor.

Tremor–genic slow slip regions may be deeper and warmer and may slip slower than non–tremor–genic regions

DOE PAGES

Montgomery-Brown, E. K.; Syracuse, E. M.

2015-09-17

The slow slip events (SSEs) are observed worldwide and often coincide with tectonic tremor. Notable examples of SSEs lacking observed tectonic tremor, however, occur beneath Kilauea Volcano, Hawaii, the Boso Peninsula, Japan, {near San Juan Bautista on the San Andreas Fault, California, and recently in Central Ecuador. These SSEs are similar to other worldwide SSEs in many ways (e.g., size or duration), but lack the concurrent tectonic tremor observed elsewhere; instead they trigger swarms of regular earthquakes. We investigate the physical conditions that may distinguish these non-tremor-genic SSEs from those associated with tectonic tremor including: slip velocity, pressure, temperature, fluidsmore » and fault asperities, although we cannot eliminate the possibility that tectonic tremor may be obscured in highly attenuating regions. Slip velocities of SSEs at Kilauea Volcano (~10⁻⁶ m/s) and Boso Peninsula (~10⁻⁷ m/s) are among the fastest SSEs worldwide. Kilauea Volcano, the Boso Peninsula and Central Ecuador are also among the shallowest SSEs worldwide, and thus have lower confining pressures and cooler temperatures in their respective slow slip zones. {Fluids also likely contribute to tremor generation, and no corresponding zone of high v p/v s has been noted at Kilauea or Boso. We suggest that the relatively faster slip velocities at Kilauea Volcano and the Boso Peninsula result from specific physical conditions that may also be responsible for triggering swarms of regular earthquakes adjacent to the slow slip, while different conditions produce slower SSE velocities elsewhere and trigger tectonic tremor.« less

A silencing-mediated enhancement of osteogenic differentiation by supramolecular ternary siRNA polyplexes comprising biocleavable cationic polyrotaxanes and anionic fusogenic peptides.

PubMed

Inada, Takasuke; Tamura, Atsushi; Terauchi, Masahiko; Yamaguchi, Satoshi; Yui, Nobuhiko

2018-01-30

Gene silencing of noggin by small interfering RNA (siRNA) is a promising approach for the treatment of bone defects, because noggin deactivates bone morphogenetic protein-2 (BMP-2) and suppresses osteogenic differentiation. Here, we demonstrated the silencing of the noggin gene by siRNA polyplexes composed of noggin-targeted siRNA and biocleavable cationic polyrotaxanes (DMAE-SS-PRX). To improve the endosomal escape efficiencies of the DMAE-SS-PRX/siRNA polyplexes, anionic and fusogenic GALA peptides were integrated onto the DMAE-SS-PRX/siRNA polyplexes via simple electrostatic interactions. The formation of ternary complexes was confirmed by gel electrophoresis, dynamic light scattering, and zeta-potential measurements. Although the association of GALA peptides with the DMAE-SS-PRX/siRNA polyplexes did not remarkably affect the cellular uptake efficiency of siRNA, the endosomal escape efficiency was remarkably increased for GALA/DMAE-SS-PRX/siRNA ternary polyplexes because of the endosomal and lysosomal membrane destabilization by GALA peptides. Consequently, GALA/DMAE-SS-PRX/siRNA ternary polyplexes showed significantly higher gene silencing efficiency against noggin and enhanced the BMP-2-mediated osteogenic differentiation efficiency. Therefore, we concluded that GALA/DMAE-SS-PRX/siRNA ternary polyplexes can be effective siRNA carriers for suppressing the expression of specific endogenous genes. Consequently, we believe that a more practical approach in vivo will be the combined use of BMP-2 and GALA/DMAE-SS-PRX/siRNA ternary polyplexes, because it will improve the efficacy of bone regeneration therapy.

The Type VI Secretion System Encoded in Salmonella Pathogenicity Island 19 Is Required for Salmonella enterica Serotype Gallinarum Survival within Infected Macrophages

PubMed Central

Blondel, Carlos J.; Jiménez, Juan C.; Leiva, Lorenzo E.; Álvarez, Sergio A.; Pinto, Bernardo I.; Contreras, Francisca; Pezoa, David; Santiviago, Carlos A.

2013-01-01

Salmonella enterica serotype Gallinarum is the causative agent of fowl typhoid, a disease characterized by high morbidity and mortality that causes major economic losses in poultry production. We have reported that S. Gallinarum harbors a type VI secretion system (T6SS) encoded in Salmonella pathogenicity island 19 (SPI-19) that is required for efficient colonization of chicks. In the present study, we aimed to characterize the SPI-19 T6SS functionality and to investigate the mechanisms behind the phenotypes previously observed in vivo. Expression analyses revealed that SPI-19 T6SS core components are expressed and produced under in vitro bacterial growth conditions. However, secretion of the structural/secreted components Hcp1, Hcp2, and VgrG to the culture medium could not be determined, suggesting that additional signals are required for T6SS-dependent secretion of these proteins. In vitro bacterial competition assays failed to demonstrate a role for SPI-19 T6SS in interbacterial killing. In contrast, cell culture experiments with murine and avian macrophages (RAW264.7 and HD11, respectively) revealed production of a green fluorescent protein-tagged version of VgrG soon after Salmonella uptake. Furthermore, infection of RAW264.7 and HD11 macrophages with deletion mutants of SPI-19 or strains with genes encoding specific T6SS core components (clpV and vgrG) revealed that SPI-19 T6SS contributes to S. Gallinarum survival within macrophages at 20 h postuptake. SPI-19 T6SS function was not linked to Salmonella-induced cytotoxicity or cell death of infected macrophages, as has been described for other T6SS. Our data indicate that SPI-19 T6SS corresponds to a novel tool used by Salmonella to survive within host cells. PMID:23357385

Ecotoxicological and microbiological assessment of sewage sludge associated with sugarcane bagasse.

PubMed

Sommaggio, Lais Roberta Deroldo; Mazzeo, Dânia Elisa Christofoletti; Sant' Anna, Débora de Andrade E Silva; Levy, Carlos Emílio; Marin-Morales, Maria Aparecida

2018-01-01

Sewage sludge (SS) obtained after sewage treatment process may contain several toxic substances. Bioremediation can decrease the toxicity of the sludge, mainly when it is associated with stimulant agents, such as sugarcane bagasse (B). Samples of pure SS (SSP); SS+B; SS+Soil; and SS+B+Soil were bioremediated for 1, 3, and 6 months (T1, T2, and T3, respectively). After each period, the cytotoxic, genotoxic, and mutagenic potentials of the solid samples and their respective aqueous extracts (aqueous eluate and percolate water) were evaluated by the Allium cepa test. A microbiological analysis of the samples was also performed after each period tested. All solid samples of SS+B (in T1, T2, and T3) and the solid sample of SSP (treatment T3) showed a significant decrease of cell division (cytotoxic effects). The aqueous eluate extracts of SS+B (T1 and T3) and SSP (T2 and T3) induced cytotoxic effect. The solid sample of SS+B (T2 and T3) and aqueous extracts of SSP (T1) were genotoxic, indicating a harmful effect of SS on A. cepa, even after 6 months of bioremediation. There was an alternation in the microbial community both in diversity and in abundance, with the predominance of nonfermenting gram-negative bacilli. The tested bioremediation periods were not sufficient for the complete detoxification of SS, and the use of B did not seem to contribute to the degradation of the pollutants to inert compounds. These data emphasize that a specific relationship should exist between the sludge characteristic and the biostimulating agent used to promote a more efficient bioremediation. These results suggest the necessity to study longer periods of biodegradation and the use of other decomposing agents for greater safety and sustainability for the agricultural use of this residue. Copyright © 2017 Elsevier Inc. All rights reserved.

Proteomic Identification of Novel Secreted Antibacterial Toxins of the Serratia marcescens Type VI Secretion System*

PubMed Central

Fritsch, Maximilian J.; Trunk, Katharina; Diniz, Juliana Alcoforado; Guo, Manman; Trost, Matthias; Coulthurst, Sarah J.

2013-01-01

It has recently become apparent that the Type VI secretion system (T6SS) is a complex macromolecular machine used by many bacterial species to inject effector proteins into eukaryotic or bacterial cells, with significant implications for virulence and interbacterial competition. “Antibacterial” T6SSs, such as the one elaborated by the opportunistic human pathogen, Serratia marcescens, confer on the secreting bacterium the ability to rapidly and efficiently kill rival bacteria. Identification of secreted substrates of the T6SS is critical to understanding its role and ability to kill other cells, but only a limited number of effectors have been reported so far. Here we report the successful use of label-free quantitative mass spectrometry to identify at least eleven substrates of the S. marcescens T6SS, including four novel effector proteins which are distinct from other T6SS-secreted proteins reported to date. These new effectors were confirmed as antibacterial toxins and self-protecting immunity proteins able to neutralize their cognate toxins were identified. The global secretomic study also unexpectedly revealed that protein phosphorylation-based post-translational regulation of the S. marcescens T6SS differs from that of the paradigm, H1-T6SS of Pseudomonas aeruginosa. Combined phosphoproteomic and genetic analyses demonstrated that conserved PpkA-dependent threonine phosphorylation of the T6SS structural component Fha is required for T6SS activation in S. marcescens and that the phosphatase PppA can reverse this modification. However, the signal and mechanism of PpkA activation is distinct from that observed previously and does not appear to require cell–cell contact. Hence this study has not only demonstrated that new and species-specific portfolios of antibacterial effectors are secreted by the T6SS, but also shown for the first time that PpkA-dependent post-translational regulation of the T6SS is tailored to fit the needs of different bacterial species. PMID:23842002

In vivo fate of 125I SS-B (La) injected into mice.

PubMed Central

Schrieber, L; Erhardt, C C; Melsom, R D; Venables, P J; McCarthy, D A; Mumford, P A; Horsfall, A C; Maini, R N

1983-01-01

The fate of the radiolabelled soluble cellular antigen SS-B (La) was compared with that of other 125I-labelled proteins of known molecular weight (MW) and electrostatic charge, following i.v. injection into BALB/c mice. The plasma half-life of 125I-SS-B was 3 min, while that of 125I-bovine serum albumin (similar MW and electrostatic charge) was 270 min. 125I-heat-aggregated IgG (MW greater than 1 x 10(6)) and 125I-7S human IgG (MW 168,000) had plasma half-lives of 40 min and greater than 300 min, respectively. Liver and kidney showed preferential uptake of 125I-SS-B, followed by a rapid decrease in radioactivity. During this time low MW, trichloroacetic acid (TCA) soluble, material appeared in urine. This suggests a specific uptake mechanism followed by a catabolic phase. These studies demonstrate that normal mice remove 125I-SS-B rapidly from the circulation and then degrade it. This rapid antigen elimination may protect against the induction of potentially harmful autoantibody responses. PMID:6832805

Age and adolescent social stress effects on fear extinction in female rats.

PubMed

McCormick, C M; Mongillo, D L; Simone, J J

2013-11-01

We previously observed that social instability stress (SS: daily 1 h isolation and change of cage partners for 16 days) in adolescence, but not in adulthood, decreased context and cue memory after fear conditioning in male rats. Effects of stress are typically sex-specific, and so here we investigated adolescent and adult SS effects in females on the strength of acquired contextual and cued fear conditioning, as well as extinction learning, beginning either the day after the stress procedure or four weeks later. For SS in adolescence, SS females spent more time freezing (fear measure) during extinction than did controls, whereas SS in adulthood had no effect on any measure of fear conditioning. The results also indicated an effect of age: females in late adolescence show more rapid extinction of cue and better memory of extinction of context compared to adult females, which may indicate resilience to acute footshock in adolescence. Thus fear circuitry continues to mature into late adolescence, which may underlie the heightened plasticity in response to chronic stressors of adolescents compared to adults.

MiniSODAR(TradeMark) Evaluation

NASA Technical Reports Server (NTRS)

Short, David A.; Wheeler, Mark M.

2003-01-01

This report describes results of the AMU's Instrumentation and Measurement task for evaluation of the Doppler miniSODAR(TradeMark) System (DmSS). The DmSS is an acoustic wind profiler providing high resolution data to a height of approx. 410 ft. The Boeing Company installed a DmSS near Space Launch Complex 37 in mid-2002 as a substitute for a tall wind tower and plans to use DmSS data for the analysis and forecasting of winds during ground and launch operations. Peak wind speed data are of particular importance to Launch Weather Officers of the 45th Weather Squadron for evaluating user Launch Commit Criteria. The AMU performed a comparative analysis of wind data between the DmSS and nearby wind towers from August 2002 to July 2003. The DmSS vertical profile of average wind speed showed good agreement with the wind towers. However, the DMSS peak wind speeds were higher, on average, than the wind tower peak wind speeds by about 25%. A statistical model of an idealized Doppler profiler was developed and it predicted that average wind speeds would be well determined but peak wind speeds would be over-estimated due to an under-specification of vertical velocity variations in the atmosphere over the Profiler.

Copper and nickel hexacyanoferrate nanostructures with graphene-coated stainless steel sheets for electrochemical supercapacitors

NASA Astrophysics Data System (ADS)

Wu, Mao-Sung; Lyu, Li-Jyun; Syu, Jhih-Hao

2015-11-01

Copper and nickel hexacyanoferrate (CuHCF and NiHCF) nanostructures featuring three-dimensional open-framework tunnels are prepared using a solution-based coprecipitation process. CuHCF shows superior supercapacitive behavior than the NiHCF, due to the presence of numerous macropores in CuHCF particles for facilitating the transport of electrolyte. Both CuHCF and NiHCF electrodes with stainless steel (SS) substrate tend to lose their electroactivity towards intercalation/deintercalation of hydrated potassium ions owing to the partial corrosion of SS. Formation of a protective and conductive carbon layer in between SS and CuHCF (NiHCF) film is of paramount importance for improving the irreversible loss of electroactivity. Thin and compact graphene (GN) layer without observable holes in its normal plane is the most effective way to suppress the corrosion of SS compared with porous carbon nanotube and activated carbon layers. Specific capacitance of CuHCF electrode with GN layer (CuHCF/GN/SS) reaches 570 F g-1, which is even better than that of CuHCF with Pt substrate (500 F g-1) at 1 A g-1. The CuHCF/GN/SS exhibits high stability with 96% capacitance retention over 1000 cycles, greater than the CuHCF with Pt (75%).

The impact of base stacking on the conformations and electrostatics of single-stranded DNA.

PubMed

Plumridge, Alex; Meisburger, Steve P; Andresen, Kurt; Pollack, Lois

2017-04-20

Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy are employed to determine the composition of the ion atmosphere at physiological ionic strength. Applying this combined approach to poly dA and poly dT, we find that the global properties of these sequences are very similar, despite having vastly different propensities for single-stranded helical stacking. These results suggest that a relatively simple mechanism for the binding of ssDNA to non-specific SSBs may be at play, which explains the disparity in binding affinities observed for these systems. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Solar Simulated Ultraviolet Radiation Induces Global Histone Hypoacetylation in Human Keratinocytes

PubMed Central

Zhang, Xiaoru; Kluz, Thomas; Gesumaria, Lisa; Matsui, Mary S.; Costa, Max; Sun, Hong

2016-01-01

Ultraviolet radiation (UVR) from sunlight is the primary effector of skin DNA damage. Chromatin remodeling and histone post-translational modification (PTM) are critical factors in repairing DNA damage and maintaining genomic integrity, however, the dynamic changes of histone marks in response to solar UVR are not well characterized. Here we report global changes in histone PTMs induced by solar simulated UVR (ssUVR). A decrease in lysine acetylation of histones H3 and H4, particularly at positions of H3 lysine 9, lysine 56, H4 lysine 5, and lysine 16, was found in human keratinocytes exposed to ssUVR. These acetylation changes were highly associated with ssUVR in a dose-dependent and time-specific manner. Interestingly, H4K16ac, a mark that is crucial for higher order chromatin structure, exhibited a persistent reduction by ssUVR that was transmitted through multiple cell divisions. In addition, the enzymatic activities of histone acetyltransferases were significantly reduced in irradiated cells, which may account for decreased global acetylation. Moreover, depletion of histone deacetylase SIRT1 in keratinocytes rescued ssUVR-induced H4K16 hypoacetylation. These results indicate that ssUVR affects both HDAC and HAT activities, leading to reduced histone acetylation. PMID:26918332

Structure of a Bacterial ABC Transporter Involved in the Import of an Acidic Polysaccharide Alginate.

PubMed

Maruyama, Yukie; Itoh, Takafumi; Kaneko, Ai; Nishitani, Yu; Mikami, Bunzo; Hashimoto, Wataru; Murata, Kousaku

2015-09-01

The acidic polysaccharide alginate represents a promising marine biomass for the microbial production of biofuels, although the molecular and structural characteristics of alginate transporters remain to be clarified. In Sphingomonas sp. A1, the ATP-binding cassette transporter AlgM1M2SS is responsible for the import of alginate across the cytoplasmic membrane. Here, we present the substrate-transport characteristics and quaternary structure of AlgM1M2SS. The addition of poly- or oligoalginate enhanced the ATPase activity of reconstituted AlgM1M2SS coupled with one of the periplasmic solute-binding proteins, AlgQ1 or AlgQ2. External fluorescence-labeled oligoalginates were specifically imported into AlgM1M2SS-containing proteoliposomes in the presence of AlgQ2, ATP, and Mg(2+). The crystal structure of AlgQ2-bound AlgM1M2SS adopts an inward-facing conformation. The interaction between AlgQ2 and AlgM1M2SS induces the formation of an alginate-binding tunnel-like structure accessible to the solvent. The translocation route inside the transmembrane domains contains charged residues suitable for the import of acidic saccharides. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structure/property (constitutive and dynamic strength/damage) characterization of additively manufactured 316L SS

NASA Astrophysics Data System (ADS)

Gray, G. T., III; Livescu, V.; Rigg, P. A.; Trujillo, C. P.; Cady, C. M.; Chen, S. R.; Carpenter, J. S.; Lienert, T. J.; Fensin, S.

2015-09-01

For additive manufacturing (AM), the certification and qualification paradigm needs to evolve as there exists no "ASTM-type" additive manufacturing certified process or AM-material produced specifications. Accordingly, utilization of AM materials to meet engineering applications requires quantification of the constitutive properties of these evolving materials in comparison to conventionally-manufactured metals and alloys. Cylinders of 316L SS were produced using a LENS MR-7 laser additive manufacturing system from Optomec (Albuquerque, NM) equipped with a 1kW Yb-fiber laser. The microstructure of the AM-316L SS is detailed in both the as-built condition and following heat-treatments designed to obtain full recrystallization. The constitutive behavior as a function of strain rate and temperature is presented and compared to that of nominal annealed wrought 316L SS plate. The dynamic damage evolution and failure response of all three materials was probed using flyer-plate impact driven spallation experiments at a peak stress of 4.5 GPa to examine incipient spallation response. The spall strength of AM-produced 316L SS was found to be very similar for the peak shock stress studied to that of annealed wrought or AM-316L SS following recrystallization. The damage evolution as a function of microstructure was characterized using optical metallography.

A type IV translocated Legionella cysteine phytase counteracts intracellular growth restriction by phytate.

PubMed

Weber, Stephen; Stirnimann, Christian U; Wieser, Mara; Frey, Daniel; Meier, Roger; Engelhardt, Sabrina; Li, Xiaodan; Capitani, Guido; Kammerer, Richard A; Hilbi, Hubert

2014-12-05

The causative agent of Legionnaires' pneumonia, Legionella pneumophila, colonizes diverse environmental niches, including biofilms, plant material, and protozoa. In these habitats, myo-inositol hexakisphosphate (phytate) is prevalent and used as a phosphate storage compound or as a siderophore. L. pneumophila replicates in protozoa and mammalian phagocytes within a unique "Legionella-containing vacuole." The bacteria govern host cell interactions through the Icm/Dot type IV secretion system (T4SS) and ∼300 different "effector" proteins. Here we characterize a hitherto unrecognized Icm/Dot substrate, LppA, as a phytate phosphatase (phytase). Phytase activity of recombinant LppA required catalytically essential cysteine (Cys(231)) and arginine (Arg(237)) residues. The structure of LppA at 1.4 Å resolution revealed a mainly α-helical globular protein stabilized by four antiparallel β-sheets that binds two phosphate moieties. The phosphates localize to a P-loop active site characteristic of dual specificity phosphatases or to a non-catalytic site, respectively. Phytate reversibly abolished growth of L. pneumophila in broth, and growth inhibition was relieved by overproduction of LppA or by metal ion titration. L. pneumophila lacking lppA replicated less efficiently in phytate-loaded Acanthamoeba castellanii or Dictyostelium discoideum, and the intracellular growth defect was complemented by the phytase gene. These findings identify the chelator phytate as an intracellular bacteriostatic component of cell-autonomous host immunity and reveal a T4SS-translocated L. pneumophila phytase that counteracts intracellular bacterial growth restriction by phytate. Thus, bacterial phytases might represent therapeutic targets to combat intracellular pathogens. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Land-use effects on fluxes of suspended sediment, nitrogen and phosphorus from a river catchment of the Great Barrier Reef, Australia

NASA Astrophysics Data System (ADS)

Hunter, Heather M.; Walton, Richard S.

2008-07-01

SummaryA 6-year study was conducted in the Johnstone River system in the wet tropics of north-eastern Australia, to address concerns that the Great Barrier Reef is at risk from elevated levels of suspended sediment (SS) and nutrients discharged from its river catchments. Aims were to quantify: (i) fluxes of SS, phosphorus (P) and nitrogen (N) exported annually from the catchment and (ii) the influence of rural land uses on these fluxes. Around 55% of the 1602 km2 catchment was native rainforest, with the reminder developed mainly for livestock and crop production. Water quality and stream flow were monitored at 16 sites, with the emphasis on sampling major runoff events. Monitoring data were used to calibrate a water quality model for the catchment (HSPF), which was run with 39 years of historical precipitation and evaporation data. Modelled specific fluxes from the catchment of 1.2 ± 1.1 t SS ha-1 y-1, 2.2 ± 1.8 kg P ha-1 y-1 and 11.4 ± 7.3 kg N ha-1y-1 were highly variable between and within years. Fluxes of SS and P were strongly dominated by major events, with 91% of SS and 84% of P exported during the highest 10% of daily flows. On average, sediment P comprised 81% of the total P flux. The N flux was less strongly dominated by major events and sediment N comprised 46% of total N exports. Specific fluxes of SS, N and P from areas receiving precipitation of 3545 mm y-1 were around 3-4 times those from areas receiving 1673 mm y-1. For a given mean annual precipitation, specific fluxes of SS and P from beef pastures, dairy pastures and unsewered residential areas were similar to those from rainforest, while fluxes from areas of sugar cane and bananas were 3-4 times higher. Specific fluxes of N from areas with an annual precipitation of 3545 mm ranged from 8.9 ± 6.5 kg N ha-1 y-1 (rainforest) to 72 ± 50 kg N ha-1 y-1 (unsewered residential). Aggregated across the entire catchment, disproportionately large fluxes of SS, total P and total N were derived from areas of sugar cane and banana production. Fluxes of nitrate N comprised 32% of mean annual total N flux and were disproportionately high from unsewered residential areas and from areas used for sugar cane and banana production. Notably, 60% of the total catchment flux of nitrate came from areas of sugar cane, which comprised only 12% of the total land area. Modelled scenarios suggest contemporary nitrate fluxes were nearly six times those under natural conditions (pre-development), a much greater increase than estimated for SS, total P and total N. These elevated nitrate fluxes are of particular concern for the protection of aquatic ecosystems, since nitrate is a readily bio-available form of N. Results of the study suggest management practices associated with certain land uses may need further investigation and improvement. To reduce nitrate fluxes, this includes a need to address fertiliser management in the sugar cane and banana industries and wastewater disposal practices in unsewered residential areas.

Deoxygenation permeabilizes sickle cell anaemia red cells to magnesium and reverses its gradient in the dense cells.

PubMed

Ortiz, O E; Lew, V L; Bookchin, R M

1990-08-01

1. Our findings of a low total magnesium content in the dense fraction (over 1.118 g ml-1) of sickle cell anaemia (SS) red cells seemed inconsistent with the low Mg2+ permeability and outward Mg2+ gradient seen in normal red cells, and prompted studies of the Mg2+ permeability and equilibria in the SS cells. 2. Deoxygenation and sickling induced Mg2+ permeabilization in SS cells, supporting non-specificity of the sickling-induced cation permeabilization, previously described for Na+, K+ and Ca2+. The extent of Mg2+ permeabilization was comparable in SS cells with normal or high density. 3. Compared with normal-density SS cells and normal red cells, the dense SS cells showed a much larger increase in the fraction of ionized magnesium ([Mg2+]i) on deoxygenation, resulting in [Mg2+]i levels sufficient to reverse the normal inward direction of the transmembrane Mg2+ gradient. 4. The molar ratio of 2,3-diphosphoglycerate (2,3-DPG) to haemoglobin was markedly reduced in the dense SS cells. Since 2,3-DPG and ATP are the main cytoplasmic Mg2+ buffers, their further reduction upon binding to deoxyhaemoglobin accounts for the high [Mg2+]i in the deoxygenated dense SS cells; the resulting outward electrochemical Mg2+ gradient, together with sickling-induced Mg2+ permeabilization, could explain the decreased total magnesium content of these cells. 5. The above findings suggested that the documented low sodium pump fluxes in dense SS cells may result from an increased Mg2+:ATP ratio, which is known to inhibit Na(+)-K+ exchange fluxes through the sodium pump. If so, deoxygenation, by increasing the Mg2+:ATP ratio, should inhibit the pump further, whereas increasing ATP should relieve the inhibition. Experiments designed to test this possibility showed that in these dense SS cells, the ouabain-sensitive K(86Rb) influx was low in oxygenated cells, was reduced further by deoxygenation, but was substantially increased after treatment with inosine, pyruvate and phosphate to increase their organic phosphate pool. These results were thus consistent with such a mechanism for Na+ pump inhibition in the dense SS cells.

Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function.

PubMed

Ohto, Tatsuhiko; Usui, Kota; Hasegawa, Taisuke; Bonn, Mischa; Nagata, Yuki

2015-09-28

Interfacial water structures have been studied intensively by probing the O-H stretch mode of water molecules using sum-frequency generation (SFG) spectroscopy. This surface-specific technique is finding increasingly widespread use, and accordingly, computational approaches to calculate SFG spectra using molecular dynamics (MD) trajectories of interfacial water molecules have been developed and employed to correlate specific spectral signatures with distinct interfacial water structures. Such simulations typically require relatively long (several nanoseconds) MD trajectories to allow reliable calculation of the SFG response functions through the dipole moment-polarizability time correlation function. These long trajectories limit the use of computationally expensive MD techniques such as ab initio MD and centroid MD simulations. Here, we present an efficient algorithm determining the SFG response from the surface-specific velocity-velocity correlation function (ssVVCF). This ssVVCF formalism allows us to calculate SFG spectra using a MD trajectory of only ∼100 ps, resulting in the substantial reduction of the computational costs, by almost an order of magnitude. We demonstrate that the O-H stretch SFG spectra at the water-air interface calculated by using the ssVVCF formalism well reproduce those calculated by using the dipole moment-polarizability time correlation function. Furthermore, we applied this ssVVCF technique for computing the SFG spectra from the ab initio MD trajectories with various density functionals. We report that the SFG responses computed from both ab initio MD simulations and MD simulations with an ab initio based force field model do not show a positive feature in its imaginary component at 3100 cm(-1).

Secondary Signs May Improve the Diagnostic Accuracy of Equivocal Ultrasounds for Suspected Appendicitis in Children

PubMed Central

Partain, Kristin N.; Patel, Adarsh; Travers, Curtis; McCracken, Courtney; Loewen, Jonathan; Braithwaite, Kiery; Heiss, Kurt F.; Raval, Mehul V.

2016-01-01

Introduction Ultrasound (US) is the preferred imaging modality for evaluating appendicitis. Our purpose was to determine if including secondary signs (SS) improves diagnostic accuracy in equivocal US studies. Methods Retrospective review identified 825 children presenting with concern for appendicitis and with a right lower quadrant (RLQ) US. Regression models identified which SS were associated with appendicitis. Test characteristics were demonstrated. Results 530 patients (64%) had equivocal US reports. Of 114 (22%) patients with equivocal US undergoing CT, those with SS were more likely to have appendicitis (48.6% vs 14.6%, p<0.001). Of 172 (32%) patients with equivocal US admitted for observation, those with SS were more likely to have appendicitis (61.0% vs 33.6%, p<0.001). SS associated with appendicitis included fluid collection (adjusted odds ratio (OR) 13.3, 95% Confidence Interval (CI) 2.1–82.8), hyperemia (OR=2.0, 95%CI 1.5–95.5), free fluid (OR=9.8, 95%CI 3.8–25.4), and appendicolith (OR=7.9, 95%CI 1.7–37.2). Wall thickness, bowel peristalsis, and echogenic fat were not associated with appendicitis. Equivocal US that included hyperemia, a fluid collection, or an appendicolith had 96% specificity and 88% accuracy. Conclusion Use of SS in RLQ US assists in the diagnostic accuracy of appendicitis. SS may guide clinicians and reduce unnecessary CT and admissions. PMID:27039121

NASA Controller Acceptability Study 1(CAS-1) Experiment Description and Initial Observations

NASA Technical Reports Server (NTRS)

Chamberlain, James P.; Consiglio, Maria C.; Comstock, James R., Jr.; Ghatas, Rania W.; Munoz, Cesar

2015-01-01

This paper describes the Controller Acceptability Study 1 (CAS-1) experiment that was conducted by NASA Langley Research Center personnel from January through March 2014 and presents partial CAS-1 results. CAS-1 employed 14 air traffic controller volunteers as research subjects to assess the viability of simulated future unmanned aircraft systems (UAS) operating alongside manned aircraft in moderate-density, moderate-complexity Class E airspace. These simulated UAS were equipped with a prototype pilot-in-the-loop (PITL) Detect and Avoid (DAA) system, specifically the Self-Separation (SS) function of such a system based on Stratway+ software to replace the see-and-avoid capabilities of manned aircraft pilots. A quantitative CAS-1 objective was to determine horizontal miss distance (HMD) values for SS encounters that were most acceptable to air traffic controllers, specifically HMD values that were assessed as neither unsafely small nor disruptively large. HMD values between 0.5 and 3.0 nautical miles (nmi) were assessed for a wide array of encounter geometries between UAS and manned aircraft. The paper includes brief introductory material about DAA systems and their SS functions, followed by descriptions of the CAS-1 simulation environment, prototype PITL SS capability, and experiment design, and concludes with presentation and discussion of partial CAS-1 data and results.

Selection of DNA aptamers against Human Cardiac Troponin I for colorimetric sensor based dot blot application.

PubMed

Dorraj, Ghamar Soltan; Rassaee, Mohammad Javad; Latifi, Ali Mohammad; Pishgoo, Bahram; Tavallaei, Mahmood

2015-08-20

Troponin T and I are ideal markers which are highly sensitive and specific for myocardial injury and have shown better efficacy than earlier markers. Since aptamers are ssDNA or RNA that bind to a wide variety of target molecules, the purpose of this research was to select an aptamer from a 79bp single-stranded DNA (ssDNA) random library that was used to bind the Human Cardiac Troponin I from a synthetic nucleic acids library by systematic evolution of ligands exponential enrichment (Selex) based on several selection and amplification steps. Human Cardiac Troponin I protein was coated onto the surface of streptavidin magnetic beads to extract specific aptamer from a large and diverse random ssDNA initial oligonucleotide library. As a result, several aptamers were selected and further examined for binding affinity and specificity. Finally TnIApt 23 showed beast affinity in nanomolar range (2.69nM) toward the target protein. A simple and rapid colorimetric detection assay for Human Cardiac Troponin I using the novel and specific aptamer-AuNPs conjugates based on dot blot assay was developed. The detection limit for this protein using aptamer-AuNPs-based assay was found to be 5ng/ml. Copyright © 2015 Elsevier B.V. All rights reserved.

Study on organic matter fractions in the surface microlayer in the Baltic Sea by spectrophotometric and spectrofluorometric methods

NASA Astrophysics Data System (ADS)

Drozdowska, Violetta; Wrobel, Iwona; Markuszewski, Piotr; Makuch, Przemysław; Raczkowska, Anna; Kowalczuk, Piotr

2017-08-01

The fluorescence and absorption measurements of the samples collected from a surface microlayer (SML) and a subsurface layer (SS), at a depth of 1 m, were studied during three research cruises in the Baltic Sea along with hydrophysical studies and meteorological observations. Several absorption (E2 : E3, S, SR) and fluorescence (fluorescence intensities at Coble classified peaks: A, C, M, T the ratio M + T/A + C, HIX (humification index)) indices of colored and fluorescent dissolved organic matter (CDOM and FDOM) helped to describe the changes in molecular size and weight as well as in composition of organic matter. The investigation allowed the assessment of a decrease in the contribution of two terrestrial components (A and C) with increasing salinity ( ˜ 1.64 and ˜ 1.89 % in the SML and ˜ 0.78 and ˜ 0.71 % in the SS, respectively) and an increase in components produced in situ (M and T) with salinity ( ˜ 0.52 and ˜ 2.83 % in the SML and ˜ 0.98 and ˜ 1.87 % in the SS, respectively). Hence, a component T reveals the biggest relative changes along the transect from the Vistula River outlet to Gdansk Deep, in both the SML and SS, although an increase was higher in the SML than in the SS ( ˜ 18.5 and ˜ 12.3 %, respectively). The ratio E2 : E3 points to greater changes in the molecular weight of CDOM affected by a higher rate of photobleaching in the SML. The HIX index reflects a more advanced stage of humification and condensation processes in the SS. Finally, the results reveal a higher rate of degradation processes occurring in the SML than in the SS. Thus, the specific physical properties of surface active organic molecules (surfactants) may modify, in a specific way, the solar light spectrum entering the sea and a penetration depth of the solar radiation. Research on the influence of surfactants on the physical processes linked to the sea surface becomes an important task, especially in coastal waters and in the vicinity of the river mouths.

MeSS: A novel prognostic scale specific for pediatric well-differentiated thyroid cancer: a population-based, SEER outcomes study.

PubMed

Shayota, Brian J; Pawar, Shonali C; Chamberlain, Ronald S

2013-09-01

High-risk prognostic factors for adults with well-differentiated thyroid cancer (WDTC) have been well established, but the same is not true for pediatric patients. This study sought to determine whether validated adult prognostic systems are applicable to pediatric patients and to develop a novel prognostic scale that may better reflect outcomes in pediatric subgroups. We queried 62,007 cases of WDTC from the Surveillance, Epidemiology, and End Results (SEER) database (1973-2009) to identify 895 patients <20 years of age with WDTC. Data abstracted included age, gender, race, histology type, primary tumor size, cancer stage, and mortality. Odds ratio and 95% confidence intervals were set and data were analyzed with SAS version 9.2. Among 895 pediatric WDTC patients, the overall cause-specific mortality was 0.8%. The presence of distant metastasis was associated with the worst prognosis (P = .0045) followed by larger primary tumor size (P = .0135) and male gender (P = .0162). When classified into low-, moderate-, and high-risk categories according to the distant metastasis (Me), larger primary tumor size (S), and male sex (S) (MeSS) algorithm, mortality rates were 0%, 2.7%, and 23%, respectively. Commonly used prognostic indices for WDTC in adults do not reliably predict poor outcomes among pediatric patients. Rather, a system based on MeSS is more applicable to pediatric patients. Patients who exhibit a high MeSS score have a significantly worse overall survival than those who do not express any MeSS characteristics. Copyright © 2013 Mosby, Inc. All rights reserved.

Regulation of Gene Editing Activity Directed by Single-Stranded Oligonucleotides and CRISPR/Cas9 Systems

PubMed Central

Bialk, Pawel; Rivera-Torres, Natalia; Strouse, Bryan; Kmiec, Eric B.

2015-01-01

Single-stranded DNA oligonucleotides (ssODNs) can direct the repair of a single base mutation in human genes. While the regulation of this gene editing reaction has been partially elucidated, the low frequency with which repair occurs has hampered development toward clinical application. In this work a CRISPR/Cas9 complex is employed to induce double strand DNA breakage at specific sites surrounding the nucleotide designated for exchange. The result is a significant elevation in ssODN-directed gene repair, validated by a phenotypic readout. By analysing reaction parameters, we have uncovered restrictions on gene editing activity involving CRISPR/Cas9 complexes. First, ssODNs that hybridize to the non-transcribed strand direct a higher level of gene repair than those that hybridize to the transcribed strand. Second, cleavage must be proximal to the targeted mutant base to enable higher levels of gene editing. Third, DNA cleavage enables a higher level of gene editing activity as compared to single-stranded DNA nicks, created by modified Cas9 (Nickases). Fourth, we calculated the hybridization potential and free energy levels of ssODNs that are complementary to the guide RNA sequences of CRISPRs used in this study. We find a correlation between free energy potential and the capacity of single-stranded oligonucleotides to inhibit specific DNA cleavage activity, thereby indirectly reducing gene editing activity. Our data provide novel information that might be taken into consideration in the design and usage of CRISPR/Cas9 systems with ssODNs for gene editing. PMID:26053390

Regulation of Gene Editing Activity Directed by Single-Stranded Oligonucleotides and CRISPR/Cas9 Systems.

PubMed

Bialk, Pawel; Rivera-Torres, Natalia; Strouse, Bryan; Kmiec, Eric B

2015-01-01

Single-stranded DNA oligonucleotides (ssODNs) can direct the repair of a single base mutation in human genes. While the regulation of this gene editing reaction has been partially elucidated, the low frequency with which repair occurs has hampered development toward clinical application. In this work a CRISPR/Cas9 complex is employed to induce double strand DNA breakage at specific sites surrounding the nucleotide designated for exchange. The result is a significant elevation in ssODN-directed gene repair, validated by a phenotypic readout. By analysing reaction parameters, we have uncovered restrictions on gene editing activity involving CRISPR/Cas9 complexes. First, ssODNs that hybridize to the non-transcribed strand direct a higher level of gene repair than those that hybridize to the transcribed strand. Second, cleavage must be proximal to the targeted mutant base to enable higher levels of gene editing. Third, DNA cleavage enables a higher level of gene editing activity as compared to single-stranded DNA nicks, created by modified Cas9 (Nickases). Fourth, we calculated the hybridization potential and free energy levels of ssODNs that are complementary to the guide RNA sequences of CRISPRs used in this study. We find a correlation between free energy potential and the capacity of single-stranded oligonucleotides to inhibit specific DNA cleavage activity, thereby indirectly reducing gene editing activity. Our data provide novel information that might be taken into consideration in the design and usage of CRISPR/Cas9 systems with ssODNs for gene editing.

Electrical DNA biosensor using aluminium interdigitated electrode for E.Coli O157:H7 detection

NASA Astrophysics Data System (ADS)

Natasha, N. Z.; Rajapaksha, R. D. A. A.; Uda, M. N. A.; Hashim, U.

2017-09-01

Escherichia Coli (E.Coli) O157:H7 is the one of the most dangerous foodborne pathogens based diseases that presence in our daily life that causes illness and death increase every year. Aluminum Interdigitated Electrode (Al IDE) biosensor was introduced to detect E.Coli O157:H7 in earlier stage. In this paper we investigated ssDNA of E.Coli O157:H7 bacteria detection through electrical behavior of Al IDE sensor. The physical properties of Al IDE biosensor has been characterized using Low Power Microscope (LPM), High Power Microscope (HPM), Scanning Electron Microscope (SEM) and 3D Nano Profiler. The bare Al IDE was electrical characterized by using I-V measurement. The surface modification was accomplished by salinization using APTES and immobilization using Carboxylic Probe E.Coli which was the first step in preparing Al IDE biosensor. Geared up prepared biosensor was hybridized with complementary, non-complementary and single based mismatch ssDNA to confirmed specificity detection of E Coli O157:H7 ssDNA target. The Current - Voltage was performed for each step such as bare Al IDE, surface modification, immobilization and hybridization. Sensitivity measurement was accomplished using different concentration of complementary ssDNA target from 1 fM - 10 µM. Selectivity measurements was achieved using same concentration which was 10 µM concentration for complement, non-complement and mismatch E.Coli O157:H7 ssDNA target. It's totally proved that the Al IDE able to detect specific and small current down to Femtomolar concentration.

MnO2-x nanosheets on stainless steel felt as a carbon- and binder-free cathode for non-aqueous lithium-oxygen batteries

NASA Astrophysics Data System (ADS)

Wei, Z. H.; Zhao, T. S.; Zhu, X. B.; Tan, P.

2016-02-01

Manganese dioxide (MnO2) has been recognized as an effective catalyst for the oxygen reduction and oxygen evolution reactions in non-aqueous lithium-oxygen batteries. However, a further improvement in battery performance with the MnO2 catalyst is limited by its low electronic conductivity and catalytic activity, which strongly depend on the morphology and composition. In this work, we develop a carbon- and binder-free MnO2-x nanosheets/stainless steel (SS) cathode via a simple and effective electrodeposition-solvothermal route. The created Mn(III) and oxygen vacancy in MnO2-x nanosheets allows an significant increase in the electronic conductivity and catalytic activity. It is experimentally shown that the use of the present nanostructure MnO2-x/SS cathode in a non-aqueous lithium-oxygen battery results in a rechargeable specific capacity of 7300 mAh g-1 at a current density of 200 mA g-1, which is 39% higher than that with the MnO2/SS cathode. In addition, the specific capacities at 400 mA g-1 and 800 mA g-1 reach 5249 mAh g-1 and 2813 mAh g-1, respectively, which are over 30% higher than that with the MnO2/SS cathode. Furthermore, the discharge/charge cycle test shows no degradation for 120 cycles. All the results show that the present nanostructure MnO2-x/SS cathode is a promising candidate for high-performance lithium-oxygen batteries.

Mucolipin 1 positively regulates TLR7 responses in dendritic cells by facilitating RNA transportation to lysosomes.

PubMed

Li, Xiaobing; Saitoh, Shin-Ichiroh; Shibata, Takuma; Tanimura, Natsuko; Fukui, Ryutaro; Miyake, Kensuke

2015-02-01

Toll-like receptor 7 (TLR7) and TLR9 sense microbial single-stranded RNA (ssRNA) and ssDNA in endolysosomes. Nucleic acid (NA)-sensing in endolysosomes is thought to be important for avoiding TLR7/9 responses to self-derived NAs. Aberrant self-derived NA transportation to endolysosomes predisposes to autoimmune diseases. To restrict NA-sensing in endolysosomes, TLR7/9 trafficking is tightly controlled by a multiple transmembrane protein Unc93B1. In contrast to TLR7/9 trafficking, little is known about a mechanism underlying NA transportation. We here show that Mucolipin 1 (Mcoln1), a member of the transient receptor potential (TRP) cation channel gene family, has an important role in ssRNA trafficking into lysosomes. Mcoln1(-/-) dendritic cells (DCs) showed impaired TLR7 responses to ssRNA. A mucolipin agonist specifically enhanced TLR7 responses to ssRNAs. The channel activity of Mcoln1 is activated by a phospholipid phosphatidylinositol (3,5) bisphosphate (PtdIns(3,5)P2), which is generated by a class III lipid kinase PIKfyve. A PIKfyve inhibitor completely inhibited TLR7 responses to ssRNA in DCs. Confocal analyses showed that ssRNA transportation to lysosomes in DCs was impaired by PIKfyve inhibitor as well as by the lack of Mcoln1. Transportation of TLR9 ligands was also impaired by the PIKfyve inhibitor. These results demonstrate that the PtdIns(3,5)P2-Mcoln1 axis has an important role in ssRNA transportation into lysosomes in DCs. © The Japanese Society for Immunology. 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Opportunistic Pathogen Serratia marcescens Utilizes Type VI Secretion To Target Bacterial Competitors ▿†

PubMed Central

Murdoch, Sarah L.; Trunk, Katharina; English, Grant; Fritsch, Maximilian J.; Pourkarimi, Ehsan; Coulthurst, Sarah J.

2011-01-01

The type VI secretion system (T6SS) is the most recently described and least understood of the protein secretion systems of Gram-negative bacteria. It is widely distributed and has been implicated in the virulence of various pathogens, but its mechanism and exact mode of action remain to be defined. Additionally there have been several very recent reports that some T6SSs can target bacteria rather than eukaryotic cells. Serratia marcescens is an opportunistic enteric pathogen, a class of bacteria responsible for a significant proportion of hospital-acquired infections. We describe the identification of a functional T6SS in S. marcescens strain Db10, the first report of type VI secretion by an opportunist enteric bacterium. The T6SS of S. marcescens Db10 is active, with secretion of Hcp to the culture medium readily detected, and is expressed constitutively under normal growth conditions from a large transcriptional unit. Expression of the T6SS genes did not appear to be dependent on the integrity of the T6SS. The S. marcescens Db10 T6SS is not required for virulence in three nonmammalian virulence models. It does, however, exhibit dramatic antibacterial killing activity against several other bacterial species and is required for S. marcescens to persist in a mixed culture with another opportunist pathogen, Enterobacter cloacae. Importantly, this antibacterial killing activity is highly strain specific, with the S. marcescens Db10 T6SS being highly effective against another strain of S. marcescens with a very similar and active T6SS. We conclude that type VI secretion plays a crucial role in the competitiveness, and thus indirectly the virulence, of S. marcescens and other opportunistic bacterial pathogens. PMID:21890705

[Anti-M3 muscarinic acetylcholine receptor antibodies and Sjögren's syndrome].

PubMed

Tsuboi, Hiroto; Iizuka, Mana; Asashima, Hiromitsu; Sumida, Takayuki

2013-01-01

Sjögren's syndrome (SS) is an autoimmune disease that affects exocrine glands including salivary and lacrimal glands. It is characterized by lymphocytic infiltration into exocrine glands, leading to dry mouth and eyes. A number of auto-antibodies are detected in patients with SS. However, no SS-specific pathologic auto-antibodies have yet been found in this condition. M3 muscarinic acetylcholine receptor (M3R) plays a crucial role in the secretion of saliva. It is reported that some patients with SS carried inhibitory auto-antibodies against M3R. To clarify the epitopes and function of anti-M3R antibodies in SS, we examined antibodies to the extracellular domains (N terminal region, the first, second, and third extracellular loop) of M3R by ELISA using synthesized peptide antigens encoding these domains in 42 SS and 42 healthy controls (HC). Titers and positivity of anti-M3R antibodies to every extracellular domain of M3R were significantly higher in SS than in HC. Our results indicated the presence of several B cell epitopes on M3R in SS. Moreover, we analyzed the functions of anti-M3R antibodies by Ca(2+)-influx assays using a human salivary gland (HSG) cell line. The functional analysis indicated that the influence of such anti-M3R antibodies on Ca(2+)-influx in HSG cells might differ based on the epitopes to which they bind. Interestingly, both IgG from anti-M3R antibodies to the second extracellular loop positive SS and anti-M3R monoclonal antibodies against the second extracellular loop of M3R, which we generated, suppressed Ca(2+)-influx in the HSG cells induced by cevimeline stimulation. These observations suggested that auto-antibodies against the second extracellular loop of M3R could be involved in salivary dysfunction in patients with SS. These results indicated the presence of several B cell epitopes on M3R in SS and the influence of anti-M3R antibodies on salivary secretion might differ based on these epitopes. Thus, anti-M3R antibodies could be not only potential pathologic auto-antibodies, but also new diagnostic makers and therapeutic targets for SS.

A Small Secreted Virulence-Related Protein Is Essential for the Necrotrophic Interactions of Sclerotinia sclerotiorum with Its Host Plants

PubMed Central

Lyu, Xueliang; Shen, Cuicui; Fu, Yanping; Xie, Jiatao; Jiang, Daohong; Li, Guoqing; Cheng, Jiasen

2016-01-01

Small, secreted proteins have been found to play crucial roles in interactions between biotrophic/hemi-biotrophic pathogens and plants. However, little is known about the roles of these proteins produced by broad host-range necrotrophic phytopathogens during infection. Here, we report that a cysteine-rich, small protein SsSSVP1 in the necrotrophic phytopathogen Sclerotinia sclerotiorum was experimentally confirmed to be a secreted protein, and the secretion of SsSSVP1 from hyphae was followed by internalization and cell-to-cell movement independent of a pathogen in host cells. SsSSVP1∆SP could induce significant plant cell death and targeted silencing of SsSSVP1 resulted in a significant reduction in virulence. Through yeast two-hybrid (Y2H), coimmunoprecipitation (co-IP) and bimolecular fluorescence complementation (BiFC) assays, we demonstrated that SsSSVP1∆SP interacted with QCR8, a subunit of the cytochrome b-c1 complex of mitochondrial respiratory chain in plants. Double site-directed mutagenesis of two cysteine residues (C38 and C44) in SsSSVP1∆SP had significant effects on its homo-dimer formation, SsSSVP1∆SP-QCR8 interaction and plant cell death induction, indicating that partial cysteine residues surely play crucial roles in maintaining the structure and function of SsSSVP1. Co-localization and BiFC assays showed that SsSSVP1∆SP might hijack QCR8 to cytoplasm before QCR8 targeting into mitochondria, thereby disturbing its subcellular localization in plant cells. Furthermore, virus induced gene silencing (VIGS) of QCR8 in tobacco caused plant abnormal development and cell death, indicating the cell death induced by SsSSVP1∆SP might be caused by the SsSSVP1∆SP-QCR8 interaction, which had disturbed the QCR8 subcellular localization and hence disabled its biological functions. These results suggest that SsSSVP1 is a potential effector which may manipulate plant energy metabolism to facilitate the infection of S. sclerotiorum. Our findings indicate novel roles of small secreted proteins in the interactions between host-non-specific necrotrophic fungi and plants, and highlight the significance to illuminate the pathogenic mechanisms of this type of interaction. PMID:26828434

Impact of adhesive and photoactivation method on sealant integrity and polymer network formation.

PubMed

Borges, Boniek Castillo Dutra; Pereira, Fabrício Lopes da Rocha; Alonso, Roberta Caroline Bruschi; Braz, Rodivan; Montes, Marcos Antônio Japiassú Resende; Pinheiro, Isauremi Vieira de Assunção; Santos, Alex José Souza dos

2012-01-01

We evaluated the influence of photoactivation method and hydrophobic resin (HR) application on the marginal and internal adaptation, hardness (KHN), and crosslink density (CLD) of a resin-based fissure sealant. Model fissures were created in bovine enamel fragments (n = 10) and sealed using one of the following protocols: no adhesive system + photoactivation of the sealant using continuous light (CL), no adhesive system + photoactivation of the sealant using the soft-start method (SS), HR + CL, or HR + SS. Marginal and internal gaps and KHN were assessed after storage in water for 24 h. The CLD was indirectly assessed by repeating the KHN measurement after 24 h of immersion in 100% ethanol. There was no difference among the samples with regard to marginal or internal adaptation. The KHN and CLD were similar for samples cured using either photoactivation method. Use of a hydrophobic resin prior to placement of fissure sealants and curing the sealant using the soft-start method may not provide any positive influence on integrity or crosslink density.

A bio-artificial renal epithelial cell system conveys survival advantage in a porcine model of septic shock.

PubMed

Westover, Angela J; Buffington, Deborah A; Johnston, Kimberly A; Smith, Peter L; Pino, Christopher J; Humes, H David

2017-03-01

Renal cell therapy using the hollow fiber based renal assist device (RAD) improved survival time in an animal model of septic shock (SS) through the amelioration of cardiac and vascular dysfunction. Safety and ability of the RAD to improve clinical outcomes was demonstrated in a Phase II clinical trial, in which patients had high prevalence of sepsis. Even with these promising results, clinical delivery of cell therapy is hampered by manufacturing hurdles, including cell sourcing, large-scale device manufacture, storage and delivery. To address these limitations, the bioartificial renal epithelial cell system (BRECS) was developed. The BRECS contains human renal tubule epithelial cells derived from adult progenitor cells using enhanced propagation techniques. Cells were seeded onto trabeculated disks of niobium-coated carbon, held within cryopreservable, perfusable, injection-moulded polycarbonate housing. The study objective was to evaluate the BRECS in a porcine model of SS to establish conservation of efficacy after necessary cell sourcing and design modifications; a pre-clinical requirement to move back into clinical trials. SS was incited by peritoneal injection of E. coli simultaneous to insertion of BRECS (n=10) or control (n=15), into the ultrafiltrate biofeedback component of an extracorporeal circuit. Comparable to RAD, prolonged survival of the BRECS cohort was conveyed through stabilization of cardiac output and vascular leak. In conclusion, the demonstration of conserved efficacy with BRECS therapy in a porcine SS model represents a crucial step toward returning renal cell therapy to the clinical setting, initially targeting ICU patients with acute kidney injury requiring continuous renal replacement therapy. Copyright © 2014 John Wiley & Sons, Ltd. Copyright © 2014 John Wiley & Sons, Ltd.

[Coexistence of sarcoidosis and primary Sjögren syndrome: a clinical analysis and literature review].

PubMed

Song, X Y; Huang, H; Liu, Y Z; Zhao, Y Y; Li, S; Xu, Z J

2017-05-01

Four patients with coexistence of sarcoidosis and primary Sjögren syndrome (pSS) were retrospectively analyzed.All patients were female, who were referred to our department mainly because of respiratory symptoms.Positive antinuclear antibody(ANA) was detected in 2 patients and anti-Sjögrens syndrome A (SSA) antibody positive in 1 patient.All patients presented specific histologic patterns of both sarcoidosis and pSS.Publications related to coexistence of these two diseases were reviewed.Forty-one patients were finally included in the analysis, among whom 37 confirmed patients were from literature search.There were 37 women and 4 men.The main clinical features presentation were xerophthalmia in 40, xerostomia in 38, hilaradenopathies in 28, interstitial lung disease in 15, respiratory symptoms in 13.The main immunologic data were positive ANA in 23, SSA antibody in 19, anti-Sjögrens syndrome B antibody in 10 and rheumatoid factor in 12.All patients presented specific histologic patterns of both diseases.Patients with both sarcoidosis and pSS of ten represent multisystemic involvement and positive immunologic parameters, as well as the dual expression of specific histologic characteristics.

Label-free detection of DNA using a light-addressable potentiometric sensor modified with a positively charged polyelectrolyte layer

NASA Astrophysics Data System (ADS)

Wu, Chunsheng; Bronder, Thomas; Poghossian, Arshak; Werner, Carl Frederik; Schöning, Michael J.

2015-03-01

A multi-spot (16 spots) light-addressable potentiometric sensor (MLAPS) consisting of an Al-p-Si-SiO2 structure modified with a weak polyelectrolyte layer of PAH (poly(allylamine hydrochloride)) was applied for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization by the intrinsic molecular charge for the first time. To achieve a preferentially flat orientation of DNA strands and thus, to reduce the distance between the DNA charge and MLAPS surface, the negatively charged probe single-stranded DNAs (ssDNA) were electrostatically adsorbed onto the positively charged PAH layer using a simple layer-by-layer (LbL) technique. In this way, more DNA charge can be positioned within the Debye length, yielding a higher sensor signal. The surface potential changes in each spot induced due to the surface modification steps (PAH adsorption, probe ssDNA immobilization, hybridization with complementary target DNA (cDNA), non-specific adsorption of mismatched ssDNA) were determined from the shifts of photocurrent-voltage curves along the voltage axis. A high sensor signal of 83 mV was registered after immobilization of probe ssDNA onto the PAH layer. The hybridization signal increases from 5 mV to 32 mV with increasing the concentration of cDNA from 0.1 nM to 5 μM. In contrast, a small signal of 5 mV was recorded in the case of non-specific adsorption of fully mismatched ssDNA (5 μM). The obtained results demonstrate the potential of the MLAPS in combination with the simple and rapid LbL immobilization technique as a promising platform for the future development of multi-spot light-addressable label-free DNA chips with direct electrical readout.A multi-spot (16 spots) light-addressable potentiometric sensor (MLAPS) consisting of an Al-p-Si-SiO2 structure modified with a weak polyelectrolyte layer of PAH (poly(allylamine hydrochloride)) was applied for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization by the intrinsic molecular charge for the first time. To achieve a preferentially flat orientation of DNA strands and thus, to reduce the distance between the DNA charge and MLAPS surface, the negatively charged probe single-stranded DNAs (ssDNA) were electrostatically adsorbed onto the positively charged PAH layer using a simple layer-by-layer (LbL) technique. In this way, more DNA charge can be positioned within the Debye length, yielding a higher sensor signal. The surface potential changes in each spot induced due to the surface modification steps (PAH adsorption, probe ssDNA immobilization, hybridization with complementary target DNA (cDNA), non-specific adsorption of mismatched ssDNA) were determined from the shifts of photocurrent-voltage curves along the voltage axis. A high sensor signal of 83 mV was registered after immobilization of probe ssDNA onto the PAH layer. The hybridization signal increases from 5 mV to 32 mV with increasing the concentration of cDNA from 0.1 nM to 5 μM. In contrast, a small signal of 5 mV was recorded in the case of non-specific adsorption of fully mismatched ssDNA (5 μM). The obtained results demonstrate the potential of the MLAPS in combination with the simple and rapid LbL immobilization technique as a promising platform for the future development of multi-spot light-addressable label-free DNA chips with direct electrical readout. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07225a

Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

PubMed Central

Zook, Justin M.; Samarov, Daniel; McDaniel, Jennifer; Sen, Shurjo K.; Salit, Marc

2012-01-01

While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cause base quality scores to underestimate the probability of error at certain genomic positions, resulting in false positive variant calls, particularly in mixtures such as samples with RNA editing, tumors, circulating tumor cells, bacteria, mitochondrial heteroplasmy, or pooled DNA. Most algorithms proposed for correction of SSEs require a data set used to calculate association of SSEs with various features in the reads and sequence context. This data set is typically either from a part of the data set being “recalibrated” (Genome Analysis ToolKit, or GATK) or from a separate data set with special characteristics (SysCall). Here, we combine the advantages of these approaches by adding synthetic RNA spike-in standards to human RNA, and use GATK to recalibrate base quality scores with reads mapped to the spike-in standards. Compared to conventional GATK recalibration that uses reads mapped to the genome, spike-ins improve the accuracy of Illumina base quality scores by a mean of 5 Phred-scaled quality score units, and by as much as 13 units at CpG sites. In addition, since the spike-in data used for recalibration are independent of the genome being sequenced, our method allows run-specific recalibration even for the many species without a comprehensive and accurate SNP database. We also use GATK with the spike-in standards to demonstrate that the Illumina RNA sequencing runs overestimate quality scores for AC, CC, GC, GG, and TC dinucleotides, while SOLiD has less dinucleotide SSEs but more SSEs for certain cycles. We conclude that using these DNA and RNA spike-in standards with GATK improves base quality score recalibration. PMID:22859977

Genome-wide identification and characterization of WRKY gene family in Salix suchowensis.

PubMed

Bi, Changwei; Xu, Yiqing; Ye, Qiaolin; Yin, Tongming; Ye, Ning

2016-01-01

WRKY proteins are the zinc finger transcription factors that were first identified in plants. They can specifically interact with the W-box, which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to this study, a plenty of WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow. With the whole genome sequencing of Salix suchowensis, we have the opportunity to conduct the genome-wide research for willow WRKY gene family. In this study, we identified 85 WRKY genes in the willow genome and renamed them from SsWRKY1 to SsWRKY85 on the basis of their specific distributions on chromosomes. Due to their diverse structural features, the 85 willow WRKY genes could be further classified into three main groups (group I-III), with five subgroups (IIa-IIe) in group II. With the multiple sequence alignment and the manual search, we found three variations of the WRKYGQK heptapeptide: WRKYGRK, WKKYGQK and WRKYGKK, and four variations of the normal zinc finger motif, which might execute some new biological functions. In addition, the SsWRKY genes from the same subgroup share the similar exon-intron structures and conserved motif domains. Further studies of SsWRKY genes revealed that segmental duplication events (SDs) played a more prominent role in the expansion of SsWRKY genes. Distinct expression profiles of SsWRKY genes with RNA sequencing data revealed that diverse expression patterns among five tissues, including tender roots, young leaves, vegetative buds, non-lignified stems and barks. With the analyses of WRKY gene family in willow, it is not only beneficial to complete the functional and annotation information of WRKY genes family in woody plants, but also provide important references to investigate the expansion and evolution of this gene family in flowering plants.

Genome-wide identification and characterization of WRKY gene family in Salix suchowensis

PubMed Central

Ye, Qiaolin; Yin, Tongming

2016-01-01

WRKY proteins are the zinc finger transcription factors that were first identified in plants. They can specifically interact with the W-box, which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to this study, a plenty of WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow. With the whole genome sequencing of Salix suchowensis, we have the opportunity to conduct the genome-wide research for willow WRKY gene family. In this study, we identified 85 WRKY genes in the willow genome and renamed them from SsWRKY1 to SsWRKY85 on the basis of their specific distributions on chromosomes. Due to their diverse structural features, the 85 willow WRKY genes could be further classified into three main groups (group I–III), with five subgroups (IIa–IIe) in group II. With the multiple sequence alignment and the manual search, we found three variations of the WRKYGQK heptapeptide: WRKYGRK, WKKYGQK and WRKYGKK, and four variations of the normal zinc finger motif, which might execute some new biological functions. In addition, the SsWRKY genes from the same subgroup share the similar exon–intron structures and conserved motif domains. Further studies of SsWRKY genes revealed that segmental duplication events (SDs) played a more prominent role in the expansion of SsWRKY genes. Distinct expression profiles of SsWRKY genes with RNA sequencing data revealed that diverse expression patterns among five tissues, including tender roots, young leaves, vegetative buds, non-lignified stems and barks. With the analyses of WRKY gene family in willow, it is not only beneficial to complete the functional and annotation information of WRKY genes family in woody plants, but also provide important references to investigate the expansion and evolution of this gene family in flowering plants. PMID:27651997

PG1058 Is a Novel Multidomain Protein Component of the Bacterial Type IX Secretion System

PubMed Central

Veith, Paul D.; Butler, Catherine A.; Nor Muhammad, Nor A.; Chen, Yu-Yen; Slakeski, Nada; Peng, Benjamin; Zhang, Lianyi; Dashper, Stuart G.; Cross, Keith J.; Cleal, Steven M.; Moore, Caroline; Reynolds, Eric C.

2016-01-01

Porphyromonas gingivalis utilises the Bacteroidetes-specific type IX secretion system (T9SS) to export proteins across the outer membrane (OM), including virulence factors such as the gingipains. The secreted proteins have a conserved carboxy-terminal domain essential for type IX secretion that is cleaved upon export. In P. gingivalis the T9SS substrates undergo glycosylation with anionic lipopolysaccharide (A-LPS) and are attached to the OM. In this study, comparative analyses of 24 Bacteroidetes genomes identified ten putative novel components of the T9SS in P. gingivalis, one of which was PG1058. Computer modelling of the PG1058 structure predicted a novel N- to C-terminal architecture comprising a tetratricopeptide repeat (TPR) domain, a β-propeller domain, a carboxypeptidase regulatory domain-like fold (CRD) and an OmpA_C-like putative peptidoglycan binding domain. Inactivation of pg1058 in P. gingivalis resulted in loss of both colonial pigmentation and surface-associated proteolytic activity; a phenotype common to T9SS mutants. Immunoblot and LC-MS/MS analyses of subcellular fractions revealed T9SS substrates accumulated within the pg1058 mutant periplasm whilst whole-cell ELISA showed the Kgp gingipain was absent from the cell surface, confirming perturbed T9SS function. Immunoblot, TEM and whole-cell ELISA analyses indicated A-LPS was produced and present on the pg1058 mutant cell surface although it was not linked to T9SS substrate proteins. This indicated that PG1058 is crucial for export of T9SS substrates but not for the translocation of A-LPS. PG1058 is a predicted lipoprotein and was localised to the periplasmic side of the OM using whole-cell ELISA, immunoblot and LC-MS/MS analyses of subcellular fractions. The structural prediction and localisation of PG1058 suggests that it may have a role as an essential scaffold linking the periplasmic and OM components of the T9SS. PMID:27711252

Annular erythema in primary Sjogren's syndrome: description of 43 non-Asian cases.

PubMed

Brito-Zerón, P; Retamozo, S; Akasbi, M; Gandía, M; Perez-De-Lis, M; Soto-Cardenas, M-J; Diaz-Lagares, C; Kostov, B; Bove, A; Bosch, X; Perez-Alvarez, R; Siso, A; Ramos-Casals, M

2014-02-01

The objective of this paper is to evaluate the prevalence and characterize the main epidemiological, clinical and immunological features of annular erythema (AE) in non-Asian patients with primary Sjögren's syndrome (SS). We carried out a retrospective study searching for AE in 377 Spanish patients with primary SS fulfilling the 2002 American-European criteria. In addition, we searched PubMed (1994-2012) using the MeSH terms "annular erythema" and "primary Sjögren's syndrome" for additional cases. All cases with AE reported in patients with SS associated with systemic lupus erythematosus were excluded. In our Spanish cohort, we found 35 (9%) patients diagnosed with AE. All were white females, with a mean age of 47 years at diagnosis of AE. AE preceded diagnosis of SS in 27 (77%) patients. Cutaneous AE lesions involved principally the face and upper extremities. All patients reported photosensitivity, with cutaneous flares being reported during the warmest months in 93% of patients. Immunological markers consisted of anti-Ro/La antibodies in 31 (89%) patients. In the literature search, we identified eight additional non-Asian patients with primary SS diagnosed with AE. In comparison with 52 Asian patients, the 43 non-Asian patients with AE related to primary SS were more frequently women (100% vs 78%, p=0.008), and cutaneous lesions were less frequently reported in the face (55% vs 81%, p=0.045) and more frequently in the neck (40% vs 14%, p=0.041). Immunologically, non-Asian patients had a lower frequency of anti-Ro antibodies and a higher frequency of negative Ro/La antibodies, although the differences were not statistically significant. AE is not an exclusive cutaneous feature of Asian patients with primary SS. In addition to the characteristic cutaneous expression, AE has a very specific clinical and immunological profile: often presenting before the fulfillment of SS criteria, overwhelmingly associated with anti-Ro antibodies but weakly associated with other immunological markers and the main systemic SS-related features.

Two Functional Type VI Secretion Systems in Avian Pathogenic Escherichia coli Are Involved in Different Pathogenic Pathways

PubMed Central

Ma, Jiale; Bao, Yinli; Sun, Min; Dong, Wenyang; Pan, Zihao; Zhang, Wei; Lu, Chengping

2014-01-01

Type VI secretion systems (T6SSs) are involved in the pathogenicity of several Gram-negative bacteria. The VgrG protein, a core component and effector of T6SS, has been demonstrated to perform diverse functions. The N-terminal domain of VgrG protein is a homologue of tail fiber protein gp27 of phage T4, which performs a receptor binding function and determines the host specificity. Based on sequence analysis, we found that two putative T6SS loci exist in the genome of the avian pathogenic Escherichia coli (APEC) strain TW-XM. To assess the contribution of these two T6SSs to TW-XM pathogenesis, the crucial clpV clusters of these two T6SS loci and their vgrG genes were deleted to generate a series of mutants. Consequently, T6SS1-associated mutants presented diminished adherence to and invasion of several host cell lines cultured in vitro, decreased pathogenicity in duck and mouse infection models in vivo, and decreased biofilm formation and bacterial competitive advantage. In contrast, T6SS2-associated mutants presented a significant decrease only in the adherence to and invasion of mouse brain microvascular endothelial cell (BMEC) line bEnd.3 and brain tissue of the duck infection model. These results suggested that T6SS1 was involved in the proliferation of APEC in systemic infection, whereas VgrG-T6SS2 was responsible only for cerebral infection. Further study demonstrated that VgrG-T6SS2 was able to bind to the surface of bEnd.3 cells, whereas it did not bind to DF-1 (chicken embryo fibroblast) cells, which further proved the interaction of VgrG-T6SS2 with the surface of BMECs. PMID:24980972

Prevalence of lactose intolerance in Chile: a double-blind placebo study.

PubMed

Latorre, Gonzalo; Besa, Pablo; Parodi, Carmen G; Ferrer, Verónica; Azocar, Lorena; Quirola, Marife; Villarroel, Luis; Miquel, Juan F; Agosin, Eduardo; Chianale, José

2014-01-01

Lactase non-persistence (LNP), or primary hypolactasia, is a genetic condition that mediates lactose malabsorption and can cause lactose intolerance. Here we report the prevalence of lactose intolerance in a double-blind placebo study. The LCT C>T-13910 variant was genotyped by RT-PCR in 121 volunteers and lactose malabsorption was assessed using the hydrogen breath test (HBT) after consuming 25 g of lactose. Lactose intolerance was assessed by scoring symptoms (SS) using a standardized questionnaire following challenge with a lactose solution or saccharose placebo. The LNP genotype was observed in 57% of the volunteers, among whom 87% were HBT⁺. In the HBT⁺ group the median SS was 9 and in the HBT⁻ group the median SS was 3 (p < 0.001). No difference was observed in the SS when both groups were challenged with the placebo. The most common symptoms included audible bowel sounds, abdominal pain and meteorism. In the ROC curve analysis, an SS ≥ 6 demonstrated 72% sensitivity and 81% specificity for predicting a positive HBT. To estimate prevalence, lactose intolerance was defined as the presence of an SS ≥ 6 points after subtracting the placebo effect and 34% of the study population met this definition. The LNP genotype was present in more than half of subjects evaluated and the observed prevalence of lactose intolerance was 34%. © 2014 S. Karger AG, Basel.

Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach.

PubMed

Domenyuk, Valeriy; Zhong, Zhenyu; Stark, Adam; Xiao, Nianqing; O'Neill, Heather A; Wei, Xixi; Wang, Jie; Tinder, Teresa T; Tonapi, Sonal; Duncan, Janet; Hornung, Tassilo; Hunter, Andrew; Miglarese, Mark R; Schorr, Joachim; Halbert, David D; Quackenbush, John; Poste, George; Berry, Donald A; Mayer, Günter; Famulok, Michael; Spetzler, David

2017-02-20

Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood. To develop ADAPT, we enriched a library of ~10 11 ssODNs for those associating with exosomes from breast cancer patients or controls. The resulting 10 6 enriched ssODNs were then profiled against plasma from independent groups of healthy and breast cancer-positive women. ssODN-mediated affinity purification and mass spectrometry identified low-abundance exosome-associated proteins and protein complexes, some with known significance in both normal homeostasis and disease. Sequencing of the recovered ssODNs provided quantitative measures that were used to build highly accurate multi-analyte signatures for patient classification. Probing plasma from 500 subjects with a smaller subset of 2000 resynthesized ssODNs stratified healthy, breast biopsy-negative, and -positive women. An AUC of 0.73 was obtained when comparing healthy donors with biopsy-positive patients.

Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach

PubMed Central

Domenyuk, Valeriy; Zhong, Zhenyu; Stark, Adam; Xiao, Nianqing; O’Neill, Heather A.; Wei, Xixi; Wang, Jie; Tinder, Teresa T.; Tonapi, Sonal; Duncan, Janet; Hornung, Tassilo; Hunter, Andrew; Miglarese, Mark R.; Schorr, Joachim; Halbert, David D.; Quackenbush, John; Poste, George; Berry, Donald A.; Mayer, Günter; Famulok, Michael; Spetzler, David

2017-01-01

Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood. To develop ADAPT, we enriched a library of ~1011 ssODNs for those associating with exosomes from breast cancer patients or controls. The resulting 106 enriched ssODNs were then profiled against plasma from independent groups of healthy and breast cancer-positive women. ssODN-mediated affinity purification and mass spectrometry identified low-abundance exosome-associated proteins and protein complexes, some with known significance in both normal homeostasis and disease. Sequencing of the recovered ssODNs provided quantitative measures that were used to build highly accurate multi-analyte signatures for patient classification. Probing plasma from 500 subjects with a smaller subset of 2000 resynthesized ssODNs stratified healthy, breast biopsy-negative, and -positive women. An AUC of 0.73 was obtained when comparing healthy donors with biopsy-positive patients. PMID:28218293

Structural plasticity in hippocampal cells related to the facilitative effect of intracranial self-stimulation on a spatial memory task.

PubMed

Chamorro-López, Jacobo; Miguéns, Miguel; Morgado-Bernal, Ignacio; Kastanauskaite, Asta; Selvas, Abraham; Cabané-Cucurella, Alberto; Aldavert-Vera, Laura; DeFelipe, Javier; Segura-Torres, Pilar

2015-12-01

Posttraining intracranial self-stimulation (SS) in the lateral hypothalamus facilitates the acquisition and retention of several implicit and explicit memory tasks. Here, intracellular injections of Lucifer yellow were used to assess morphological changes in hippocampal neurons that might be specifically related to the facilitative posttraining SS effect upon the acquisition and retention of a distributed spatial task in the Morris water maze. We examined the structure, size and branching complexity of cornus ammonis 1 (CA1) cells, and the spine density of CA1 pyramidal neurons and granular cells of the dentate gyrus (DG). Animals that received SS after each acquisition session performed faster and better than Sham ones--an improvement that was also evident in a probe trial 3 days after the last training session. The neuromorphological analysis revealed an increment in the size and branching complexity in apical CA1 dendritic arborization in SS-treated subjects as compared with Sham animals. Furthermore, increased spine density was observed in the CA1 field in SS animals, whereas no effects were observed in DG cells. Our results support the hypothesis that the facilitating effect of SS on the acquisition and retention of a spatial memory task could be related to structural plasticity in CA1 hippocampal cells. (c) 2015 APA, all rights reserved).

Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: polynucleotide binding and cooperativity

PubMed Central

Jose, Davis; Weitzel, Steven E.; Baase, Walter A.; Michael, Miya M.; von Hippel, Peter H.

2015-01-01

We here use our site-specific base analog mapping approach to study the interactions and binding equilibria of cooperatively-bound clusters of the single-stranded DNA binding protein (gp32) of the T4 DNA replication complex with longer ssDNA (and dsDNA) lattices. We show that in cooperatively bound clusters the binding free energy appears to be equi-partitioned between the gp32 monomers of the cluster, so that all bind to the ssDNA lattice with comparable affinity, but also that the outer domains of the gp32 monomers at the ends of the cluster can fluctuate on and off the lattice and that the clusters of gp32 monomers can slide along the ssDNA. We also show that at very low binding densities gp32 monomers bind to the ssDNA lattice at random, but that cooperatively bound gp32 clusters bind preferentially at the 5′-end of the ssDNA lattice. We use these results and the gp32 monomer-binding results of the companion paper to propose a detailed model for how gp32 might bind to and interact with ssDNA lattices in its various binding modes, and also consider how these clusters might interact with other components of the T4 DNA replication complex. PMID:26275774

A pilot randomized controlled trial of mindfulness-based stress reduction for caregivers of family members with dementia.

PubMed

Brown, Kirk Warren; Coogle, Constance L; Wegelin, Jacob

2016-11-01

The majority of care for those with Alzheimer's disease and other age-related dementias is provided in the home by family members. To date, there is no consistently effective intervention for reducing the significant stress burden of many family caregivers. The present pilot randomized controlled trial tested the efficacy of an adapted, eight-week mindfulness-based stress reduction (MBSR) program, relative to a near structurally equivalent, standard social support (SS) control condition for reducing caregiver stress and enhancing the care giver-recipient relationship. Thirty-eight family caregivers were randomized to MBSR or SS, with measures of diurnal salivary cortisol, and perceived stress, mental health, experiential avoidance, caregiver burden, and relationship quality collected pre- and post-intervention and at three-month follow-up. MBSR participants reported significantly lower levels of perceived stress and mood disturbance at post-intervention relative to SS participants. At three-month follow-up, participants in both treatment conditions reported improvements on several psychosocial outcomes. At follow-up, there were no condition differences on these outcomes, nor did MBSR and SS participants differ in diurnal cortisol response change over the course of the study. Both MBSR and SS showed stress reduction effects, and MBSR showed no sustained neuroendocrine and psychosocial advantages over SS. The lack of treatment condition differences could be attributable to active ingredients in both interventions, and to population-specific and design factors.

Structure of the heterotrimeric complex that regulates type III secretion needle formation

PubMed Central

Quinaud, Manuelle; Plé, Sophie; Job, Viviana; Contreras-Martel, Carlos; Simorre, Jean-Pierre; Attree, Ina; Dessen, Andréa

2007-01-01

Type III secretion systems (T3SS), found in several Gram-negative pathogens, are nanomachines involved in the transport of virulence effectors directly into the cytoplasm of target cells. T3SS are essentially composed of basal membrane-embedded ring-like structures and a hollow needle formed by a single polymerized protein. Within the bacterial cytoplasm, the T3SS needle protein requires two distinct chaperones for stabilization before its secretion, without which the entire T3SS is nonfunctional. The 2.0-Å x-ray crystal structure of the PscE-PscF55–85-PscG heterotrimeric complex from Pseudomonas aeruginosa reveals that the C terminus of the needle protein PscF is engulfed within the hydrophobic groove of the tetratricopeptide-like molecule PscG, indicating that the macromolecular scaffold necessary to stabilize the T3SS needle is totally distinct from chaperoned complexes between pilus- or flagellum-forming molecules. Disruption of specific PscG–PscF interactions leads to impairment of bacterial cytotoxicity toward macrophages, indicating that this essential heterotrimer, which possesses homologs in a wide variety of pathogens, is a unique attractive target for the development of novel antibacterials. PMID:17470796

Phagocyte-specific S100A8/A9 is upregulated in primary Sjögren's syndrome and triggers the secretion of pro-inflammatory cytokines in vitro.

PubMed

Nicaise, Charles; Weichselbaum, Laura; Schandene, Liliane; Gangji, Valérie; Dehavay, Florence; Bouchat, Joanna; Balau, Benoît; Vogl, Thomas; Soyfoo, Muhammad S

2017-01-01

To determine the role of S100A8/A9 in the pathogenesis of primary Sjögren's syndrome (pSS). The serum levels of S100A8/A9 were determined in pSS patients and healthy controls by ELISA. The expression of S100A8/A9 in salivary glands was assessed by immunohistochemistry. The phenotype of S100A8+ and S100A9+ cells was identified using double immunofluorescence. The effects of S100A8/A9 on cytokine production by peripheral blood mononuclear cells (PBMCs) from pSS patients were determined in vitro by flow cytometry. The effects of pro-inflammatory cytokines on S100A8/A9 secretion were additionally investigated in vitro by ELISA in PBMCs from pSS patients and control subjects. Serum levels of S100A8/A9 were significantly increased in pSS patients compared to healthy controls. The tissular expression of S100A8 and S100A9, identified in professional phagocytes (neutrophils, monocytes and plasmacytoid dendritic cells), was increased in the salivary glands of pSS patients and correlated with focus score. In vitro, recombinant S100A8/A9 increased the production of IL-1β, IL-6, TNF-α, IFN-γ, IL-10, IL-17A and IL-22 by PBMCs. The S100A8/A9-induced increase in TNF-α production in pSS patients was significant relative to controls. Furthermore, IL-1β, TNF-α, IL-6, and IL-17A stimulated release of S100A8/A9 from PBMCs in pSS patients. S100A8/A9 is increased in pSS patients contributing to the in vitro increased production of pro-inflammatory cytokines. As such, S100A8/A9 in concert with other cytokines might contribute to the pathogenesis of pSS.

The Chromobacterium violaceum type III effector CopE, a guanine nucleotide exchange factor for Rac1 and Cdc42, is involved in bacterial invasion of epithelial cells and pathogenesis.

PubMed

Miki, Tsuyoshi; Akiba, Kinari; Iguchi, Mirei; Danbara, Hirofumi; Okada, Nobuhiko

2011-06-01

The type III secretion system (T3SS) encoded by Chromobacterium pathogenicity islands 1 and 1a (Cpi-1/-1a) is critical for Chromobacterium violaceum pathogenesis. T3SS-dependent virulence is commonly characterized by type III effector virulence function, but the full repertoire of the effector proteins of Cpi-1/-1a T3SS is unknown. In this study, we showed that expression of Cpi-1/-1a T3SS is controlled by the master regulator CilA. We used transcriptional profiling with DNA microarrays to define CilA regulon and identified genes encoding T3SS effectors whose translocation into host cells was dependent on Cpi-1/-1a T3SS. From these effectors, we found that CopE (CV0296) has similarities to a guanine nucleotide exchange factor (GEF) for Rho GTPases in its C-terminal portion. The N-terminal portions (1-81 amino acids) of CopE and a CivB as a putative chaperone were required for its translocation. CopE specifically activates Rac1 and Cdc42 followed by the induction of actin cytoskeletal rearrangement. Interestingly, C. violaceum invades human epithelial HeLa cells in a Cpi-1/-1a-encoded T3SS- and CopE-dependent manner. Finally, C. violaceum strains lacking copE and expressing a CopE-G168V deficient in GEF activity were attenuated for virulence in mice, suggesting that CopE contributes to the virulence of this pathogen. © 2011 Blackwell Publishing Ltd.

TERRA and hnRNPA1 orchestrate an RPA-to-POT1 switch on telomeric single-stranded DNA.

PubMed

Flynn, Rachel Litman; Centore, Richard C; O'Sullivan, Roderick J; Rai, Rekha; Tse, Alice; Songyang, Zhou; Chang, Sandy; Karlseder, Jan; Zou, Lee

2011-03-24

Maintenance of telomeres requires both DNA replication and telomere 'capping' by shelterin. These two processes use two single-stranded DNA (ssDNA)-binding proteins, replication protein A (RPA) and protection of telomeres 1 (POT1). Although RPA and POT1 each have a critical role at telomeres, how they function in concert is not clear. POT1 ablation leads to activation of the ataxia telangiectasia and Rad3-related (ATR) checkpoint kinase at telomeres, suggesting that POT1 antagonizes RPA binding to telomeric ssDNA. Unexpectedly, we found that purified POT1 and its functional partner TPP1 are unable to prevent RPA binding to telomeric ssDNA efficiently. In cell extracts, we identified a novel activity that specifically displaces RPA, but not POT1, from telomeric ssDNA. Using purified protein, here we show that the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) recapitulates the RPA displacing activity. The RPA displacing activity is inhibited by the telomeric repeat-containing RNA (TERRA) in early S phase, but is then unleashed in late S phase when TERRA levels decline at telomeres. Interestingly, TERRA also promotes POT1 binding to telomeric ssDNA by removing hnRNPA1, suggesting that the re-accumulation of TERRA after S phase helps to complete the RPA-to-POT1 switch on telomeric ssDNA. Together, our data suggest that hnRNPA1, TERRA and POT1 act in concert to displace RPA from telomeric ssDNA after DNA replication, and promote telomere capping to preserve genomic integrity.

Molecular cloning and promoter analysis of squalene synthase and squalene epoxidase genes from Betula platyphylla.

PubMed

Zhang, Mengyan; Wang, Siyao; Yin, Jing; Li, Chunxiao; Zhan, Yaguang; Xiao, Jialei; Liang, Tian; Li, Xin

2016-09-01

Betula platyphylla is a rich repository of pharmacologically active secondary metabolites known as birch triterpenoids (TBP). Here, we cloned the squalene synthase (SS) and squalene epoxidase genetic (SE) sequences from B. platyphylla that encode the key enzymes that are involved in triterpenoid biosynthesis and analyzed the conserved domains and phylogenetics of their corresponding proteins. The full-length sequence of BpSS is 1588 bp with a poly-A tail, which contained an open reading frame (ORF) of 1241 bp that encoded a protein of 413 amino acids. Additionally, the BpSE full-length sequence of 2040 bp with a poly-A tail was also obtained, which contained an ORF of 1581 bp encoding a protein of 526 amino acids. Their organ-specific expression patterns in 4-week-old tissue culture seedlings of B. platyphylla were detected by real-time PCR and showed that they were all highly expressed in leaves, as compared to stem and root tissues. Additionaly, both BpSS and BpSE were enhanced following stimulation with ethephon and MeJA. The expression of BpSS was enhanced by ABA, whereas BpSE was not. The SA treatment did not affect the BpSS and BpSE transcripts notably. Using a genome walking approach, promoter sequences of 965 and 1193 bp, respectively, for BpSS and BpSE were isolated, and they revealed several key cis-regulatory elements known to be involved in the response to phytohormone and abiotic plant stress. We also found that the BpSS protein is localized in the cytoplasm. Opening reading frames of BpSS and BpSE were ligated into yeast expression plasmid pYES2 under control of GAL1 promoter and introduced into the yeast INVScl1 strain. The transformants were cultured for 12 h, the squalene content of galactose-induced BpSS expression yeast cells was 13.2 times of control (empty vector control yeast cells) by high-performance liquid chromatography (HPLC) test method. And, the squalene epoxidase activity of induced BpSE expression yeast cell was about 11.8 times of control. These indicated that we cloned birch BpSS and BpSE that were indeed involved in the synthesis of triteropenoids. This is the first report wherein SS and SE from B. platyphylla were cloned and may be of significant interest to understand the regulatory role of SS and SE in the triterpenoids biosynthesis of B. platyphylla. This is the first report wherein SS and SE from B. platyphylla were cloned and may be of significant interest to understand the regulatory role of SS and SE in the biosynthesis of birch triterpenoids.

Lee-Carter state space modeling: Application to the Malaysia mortality data

NASA Astrophysics Data System (ADS)

Zakiyatussariroh, W. H. Wan; Said, Z. Mohammad; Norazan, M. R.

2014-06-01

This article presents an approach that formalizes the Lee-Carter (LC) model as a state space model. Maximum likelihood through Expectation-Maximum (EM) algorithm was used to estimate the model. The methodology is applied to Malaysia's total population mortality data. Malaysia's mortality data was modeled based on age specific death rates (ASDR) data from 1971-2009. The fitted ASDR are compared to the actual observed values. However, results from the comparison of the fitted and actual values between LC-SS model and the original LC model shows that the fitted values from the LC-SS model and original LC model are quite close. In addition, there is not much difference between the value of root mean squared error (RMSE) and Akaike information criteria (AIC) from both models. The LC-SS model estimated for this study can be extended for forecasting ASDR in Malaysia. Then, accuracy of the LC-SS compared to the original LC can be further examined by verifying the forecasting power using out-of-sample comparison.

New alloys to conserve critical elements. [replacing chromium in steels

NASA Technical Reports Server (NTRS)

Stephens, J. R.

1978-01-01

Previous studies and surveys on availability of domestic reserves have shown that chromium is a most critical element within the U.S. metal industry. More precisely, the bulk of chromium is consumed in the production of stainless steels, specifically Type 304 stainless steel (304SS) which contains 18% Cr. The present paper deals with means of reducing chromium in commercial stainless steels by substituting more abundant or less expensive elements with the intent of maintaining the properties of 304SS. The discussion focuses on some of the oxidation and corrosion properties of new substitute stainless steels with only 12% Cr, which represents a potential saving of 33% of the chromium consumed in the production of 304SS. The alloying elements substituted for Cr in 304SS are selected according to their potential for protective oxide formation during high-temperature oxidation; these are Al, Si, Ti, Y, and misch metal which is 99.7% rare-earth metals containing 50 to 55% cerium. Other alloying elements to impart corrosion resistance are Mn, Mo, and V.

Discovery of fur seal feces-associated circular DNA virus in swine feces in Japan.

PubMed

Oba, Mami; Katayama, Yukie; Naoi, Yuki; Tsuchiaka, Shinobu; Omatsu, Tsutomu; Okumura, Atsushi; Nagai, Makoto; Mizutani, Tetsuya

2017-10-07

Fur seal feces-associated circular ssDNA virus (FSfaCV) was discovered in a pig for the first time in Japan using a next-generation sequencer with duplex-specific nuclease. Full genome of the virus showed approximately 92% similarity to FSfaCVs from New Zealand fur seals. Furthermore, we investigated the prevalence of the ssDNA virus in 85 piglets in Japan, and 65 piglets were positive (76%) for the virus.

Nasal potential difference outcomes support diagnostic decisions in cystic fibrosis.

PubMed

Tridello, Gloria; Menin, Laura; Pintani, Emily; Bergamini, Gabriella; Assael, Baroukh Maurice; Melotti, Paola

2016-09-01

When cystic fibrosis (CF) is suspected Nasal Potential Difference (NPD) measurements are proposed to support controversial diagnosis: we investigated appropriate outcomes at the CF Centre of Verona. NPD were measured in 196 subjects: 50 non-CF, 65 classical CF (the reference group) and 81 with uncertain CF (case group). Discriminating power was determined by comparison between several outcomes from the CF reference group versus non-CF: basal, amiloride, 0Cl, isoproterenol, ATP, Delta-amiloride, Delta-0Cl, Delta-isoproterenol, Delta-ATP, Delta-isoproterenol+Delta-0Cl, Wilschanski Index (WI) and Sermet score (SS). The most appropriate cut-off values for variables with the best discriminating power were then applied to the case group. Descriptive statistics, logistic regression models and ROC curve analysis were applied. WI and SS were the most powerful in discriminating CF from non-CF subjects. In the reference group sensitivity of the 0.82 WI cut-off was 98%, specificity 96%; both sensitivity and specificity of the -0.44 SS cut-off value were 100%. For the case group, WI and SS were, respectively, consistent with CF diagnosis in 94% and 92% of the cases. Formulae have the highest discriminating power and can support the diagnosis in uncertain cases; they should be utilized for standardized interpretation of NPD for diagnosis and possibly for clinical research. Copyright © 2016. Published by Elsevier B.V.

Accurate and rapid modeling of iron-bleomycin-induced DNA damage using tethered duplex oligonucleotides and electrospray ionization ion trap mass spectrometric analysis.

PubMed

Harsch, A; Marzilli, L A; Bunt, R C; Stubbe, J; Vouros, P

2000-05-01

Bleomycin B(2)(BLM) in the presence of iron [Fe(II)] and O(2)catalyzes single-stranded (ss) and double-stranded (ds) cleavage of DNA. Electrospray ionization ion trap mass spectrometry was used to monitor these cleavage processes. Two duplex oligonucleotides containing an ethylene oxide tether between both strands were used in this investigation, allowing facile monitoring of all ss and ds cleavage events. A sequence for site-specific binding and cleavage by Fe-BLM was incorporated into each analyte. One of these core sequences, GTAC, is a known hot-spot for ds cleavage, while the other sequence, GGCC, is a hot-spot for ss cleavage. Incubation of each oligo-nucleotide under anaerobic conditions with Fe(II)-BLM allowed detection of the non-covalent ternary Fe-BLM/oligonucleotide complex in the gas phase. Cleavage studies were then performed utilizing O(2)-activated Fe(II)-BLM. No work-up or separation steps were required and direct MS and MS/MS analyses of the crude reaction mixtures confirmed sequence-specific Fe-BLM-induced cleavage. Comparison of the cleavage patterns for both oligonucleotides revealed sequence-dependent preferences for ss and ds cleavages in accordance with previously established gel electrophoresis analysis of hairpin oligonucleotides. This novel methodology allowed direct, rapid and accurate determination of cleavage profiles of model duplex oligonucleotides after exposure to activated Fe-BLM.

Molecular Analysis of Colletotrichum Species in the Carposphere and Phyllosphere of Olive

PubMed Central

Mosca, Saveria; Li Destri Nicosia, Maria G.; Cacciola, Santa O.; Schena, Leonardo

2014-01-01

A metagenomic approach based on the use of genus specific primers was developed and utilized to characterize Colletotrichum species associated with the olive phyllosphere and carposphere. Selected markers enabled the specific amplification of almost the entire ITS1-5.8S-ITS2 region of the rDNA and its use as barcode gene. The analysis of different olive samples (green and senescent leaves, floral residues, symptomatic and asymptomatic fruits, and litter leaves and mummies) in three different phenological phases (June, October and December) enabled the detection of 12 genotypes associated with 4 phylotypes identified as C. godetiae, C. acutatum s.s., C. gloeosporioides s.s. and C. kahawae. Another three genotypes were not identified at the level of species but were associated with the species complexes of C. acutatum, C. gloeosporioides and C. boninense sensu lato. Colletotrichum godetiae and C. acutatum s.s. were by far the most abundant while C. gloeosporioides s.s. was detected in a limited number of samples whereas ther phylotypes were rarely found. The high incidence of C. acutatum s.s. represents a novelty for Italy and more generally for the Mediterranean basin since it had been previously reported only in Portugal. As regards to the phenological phase, Colletotrichum species were found in a few samples in June and were diffused on all assessed samples in December. According to data new infections on olive tissues mainly occur in the late fall. Furthermore, Colletotrichum species seem to have a saprophytic behavior on floral olive residues. The method developed in the present study proved to be valuable and its future application may contribute to the study of cycle and aetiology of diseases caused by Colletotrichum species in many different pathosystems. PMID:25501572

Evolutionarily Conserved nodE, nodO, T1SS, and Hydrogenase System in Rhizobia of Astragalus membranaceus and Caragana intermedia.

PubMed

Yan, Hui; Xie, Jian Bo; Ji, Zhao Jun; Yuan, Na; Tian, Chang Fu; Ji, Shou Kun; Wu, Zhong Yu; Zhong, Liang; Chen, Wen Xin; Du, Zheng Lin; Wang, En Tao; Chen, Wen Feng

2017-01-01

Mesorhizobium species are the main microsymbionts associated with the medicinal or sand-fixation plants Astragalus membranaceus and Caragana intermedia (AC) in temperate regions of China, while all the Mesorhizobium strains isolated from each of these plants could nodulate both of them. However, Rhizobium yanglingense strain CCBAU01603 could nodulate AC plants and it's a high efficiency symbiotic and competitive strain with Caragana . Therefore, the common features shared by these symbiotic rhizobia in genera of Mesorhizobium and Rhizobium still remained undiscovered. In order to study the genomic background influencing the host preference of these AC symbiotic strains, the whole genomes of two ( M. silamurunense CCBAU01550, M. silamurunense CCBAU45272) and five representative strains ( M. septentrionale CCBAU01583, M. amorphae CCBAU01570, M. caraganae CCBAU01502, M. temperatum CCBAU01399, and R. yanglingense CCBAU01603) originally isolated from AC plants were sequenced, respectively. As results, type III secretion systems (T3SS) of AC rhizobia evolved in an irregular pattern, while an evolutionarily specific region including nodE, nodO , T1SS, and a hydrogenase system was detected to be conserved in all these AC rhizobia. Moreover, nodO was verified to be prevalently distributed in other AC rhizobia and was presumed as a factor affecting the nodule formation process. In conclusion, this research interpreted the multifactorial features of the AC rhizobia that may be associated with their host specificity at cross-nodulation group, including nodE, nodZ , T1SS as the possible main determinants; and nodO , hydrogenase system, and T3SS as factors regulating the bacteroid formation or nitrogen fixation efficiency.

The effect of combined somatosensory stimulation and task-specific training on upper limb function in chronic stroke: a double-blind randomized controlled trial.

PubMed

Fleming, Melanie K; Sorinola, Isaac O; Roberts-Lewis, Sarah F; Wolfe, Charles D; Wellwood, Ian; Newham, Di J

2015-02-01

Somatosensory stimulation (SS) is a potential adjuvant to stroke rehabilitation, but the effect on function needs further investigation. To explore the effect of combining SS with task-specific training (TST) on upper limb function and arm use in chronic stroke survivors and determine underlying mechanisms. In this double-blinded randomized controlled trial (ISRCTN 05542931), 33 patients (mean 37.7 months poststroke) were block randomized to 2 groups: active or sham SS. They received 12 sessions of 2 hours of SS (active or sham) to all 3 upper limb nerves immediately before 30 minutes of TST. The primary outcome was the Action Research Arm Test (ARAT) score. Secondary outcomes were time to perform the ARAT, Fugl-Meyer Assessment score (FM), Motor Activity Log (MAL), and Goal Attainment Scale (GAS). Underlying mechanisms were explored using transcranial magnetic stimulation stimulus-response curves and intracortical inhibition. Outcomes were assessed at baseline, immediately following the intervention (mean 2 days), and 3 and 6 months (mean 96 and 190 days) after the intervention. The active group (n = 16) demonstrated greater improvement in ARAT score and time immediately postintervention (between-group difference; P < .05), but not at 3- or 6-month follow-ups (P > .2). Within-group improvements were seen for both groups for ARAT and GAS, but for the active group only for FM and MAL (P < .05). Corticospinal excitability did not change. Long-lasting improvements in upper limb function were observed following TST. Additional benefit of SS was seen immediately post treatment, but did not persist and the underlying mechanisms remain unclear. © The Author(s) 2014.

Evaluating preservation methods for identifying Anopheles gambiae s.s. and Anopheles arabiensis complex mosquitoes species using near infra-red spectroscopy.

PubMed

Mayagaya, Valeriana Simon; Ntamatungiro, Alex John; Moore, Sarah Jane; Wirtz, Robert Andrew; Dowell, Floyd Ercell; Maia, Marta Ferreira

2015-01-27

Near-infrared spectroscopy (NIRS) has been successfully used on fresh and RNAlater-preserved members of the Anopheles gambiae complex to identify sibling species and age. No preservation methods other than using RNAlater have been tested to preserve mosquitoes for species identification using NIRS. However, RNAlater is not the most practical preservative for field settings because it is expensive, requires basic laboratory conditions for storage and is not widely available in sub-Saharan Africa. The aim of this study was to test several cheaper and more field-friendly preservation methods for identifying sibling species of the An. gambiae complex using NIRS. In this study we describe the use of NIRS to identify sibling species of preserved An. gambiae s. s. and An. arabiensis. Mosquitoes of each species were placed in sample tubes and preserved using one of the following preservation methods: (i) refrigeration at 4°C, (ii) freezing at -20°C, (iii) drying over a silica-gel desiccant, (iv) submersion in RNAlater at room temperature, (v) submersion in RNAlater at 4°C, and (vi) submersion in RNAlater at -20°C. Mosquitoes were preserved for 1, 4, 10, 32 or 50 weeks before they were scanned. Storage at 4°C was the only preservation method that, up to 32 weeks, did not result in significantly lower predicted values than those obtained from fresh insects. After 50 weeks, however, refrigerated samples did not give meaningful results. When storing for 50 weeks, desiccating samples over silica gel was the best preservation method, with a partial least squares regression cross-validation of >80%. Predictive data values were analyzed using a generalized linear model. NIRS can be used to identify species of desiccated Anopheles gambiae s.s. and Anopheles arabiensis for up to 50 weeks of storage with more than 80% accuracy.

Three-dimensional imaging of aquifer and aquitard heterogeneity via transient hydraulic tomography at a highly heterogeneous field site

NASA Astrophysics Data System (ADS)

Zhao, Zhanfeng; Illman, Walter A.

2018-04-01

Previous studies have shown that geostatistics-based transient hydraulic tomography (THT) is robust for subsurface heterogeneity characterization through the joint inverse modeling of multiple pumping tests. However, the hydraulic conductivity (K) and specific storage (Ss) estimates can be smooth or even erroneous for areas where pumping/observation densities are low. This renders the imaging of interlayer and intralayer heterogeneity of highly contrasting materials including their unit boundaries difficult. In this study, we further test the performance of THT by utilizing existing and newly collected pumping test data of longer durations that showed drawdown responses in both aquifer and aquitard units at a field site underlain by a highly heterogeneous glaciofluvial deposit. The robust performance of the THT is highlighted through the comparison of different degrees of model parameterization including: (1) the effective parameter approach; (2) the geological zonation approach relying on borehole logs; and (3) the geostatistical inversion approach considering different prior information (with/without geological data). Results reveal that the simultaneous analysis of eight pumping tests with the geostatistical inverse model yields the best results in terms of model calibration and validation. We also find that the joint interpretation of long-term drawdown data from aquifer and aquitard units is necessary in mapping their full heterogeneous patterns including intralayer variabilities. Moreover, as geological data are included as prior information in the geostatistics-based THT analysis, the estimated K values increasingly reflect the vertical distribution patterns of permeameter-estimated K in both aquifer and aquitard units. Finally, the comparison of various THT approaches reveals that differences in the estimated K and Ss tomograms result in significantly different transient drawdown predictions at observation ports.

Detecting single-abasic residues within a DNA strand immobilized in a biological nanopore using an integrated CMOS sensor.

PubMed

Kim, Jungsuk; Maitra, Raj D; Pedrotti, Ken; Dunbar, William B

2013-02-01

In this paper, we demonstrate the application of a novel current-measuring sensor (CMS) customized for nanopore applications. The low-noise CMS is fabricated in a 0.35μm CMOS process and is implemented in experiments involving DNA captured in an α-hemolysin (α-HL) nanopore. Specifically, the CMS is used to build a current amplitude map as a function of varying positions of a single-abasic residue within a homopolymer cytosine single-stranded DNA (ssDNA) that is captured and held in the pore. Each ssDNA is immobilized using a biotin-streptavidin linkage. Five different DNA templates are measured and compared: one all-cytosine ssDNA, and four with a single-abasic residue substitution that resides in or near the ~1.5nm aperture of the α-HL channel when the strand is immobilized. The CMOS CMS is shown to resolves the ~5Å displacements of the abasic residue within the varying templates. The demonstration represents an advance in application-specific circuitry that is optimized for small-footprint nanopore applications, including genomic sequencing.

Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability

DOE PAGES

Tsutakawa, Susan E.; Thompson, Mark J.; Arvai, Andrew S.; ...

2017-06-27

DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5'-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 5'polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via phosphate steering', basic residues energetically steer an inverted ss 5'-flap through a gateway over FEN1's active site and shift dsDNA formore » catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA) n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 5'-flap specificity and catalysis, preventing genomic instability.« less

Sequence-specific activation of the DNA sensor cGAS by Y-form DNA structures as found in primary HIV-1 cDNA.

PubMed

Herzner, Anna-Maria; Hagmann, Cristina Amparo; Goldeck, Marion; Wolter, Steven; Kübler, Kirsten; Wittmann, Sabine; Gramberg, Thomas; Andreeva, Liudmila; Hopfner, Karl-Peter; Mertens, Christina; Zillinger, Thomas; Jin, Tengchuan; Xiao, Tsan Sam; Bartok, Eva; Coch, Christoph; Ackermann, Damian; Hornung, Veit; Ludwig, Janos; Barchet, Winfried; Hartmann, Gunther; Schlee, Martin

2015-10-01

Cytosolic DNA that emerges during infection with a retrovirus or DNA virus triggers antiviral type I interferon responses. So far, only double-stranded DNA (dsDNA) over 40 base pairs (bp) in length has been considered immunostimulatory. Here we found that unpaired DNA nucleotides flanking short base-paired DNA stretches, as in stem-loop structures of single-stranded DNA (ssDNA) derived from human immunodeficiency virus type 1 (HIV-1), activated the type I interferon-inducing DNA sensor cGAS in a sequence-dependent manner. DNA structures containing unpaired guanosines flanking short (12- to 20-bp) dsDNA (Y-form DNA) were highly stimulatory and specifically enhanced the enzymatic activity of cGAS. Furthermore, we found that primary HIV-1 reverse transcripts represented the predominant viral cytosolic DNA species during early infection of macrophages and that these ssDNAs were highly immunostimulatory. Collectively, our study identifies unpaired guanosines in Y-form DNA as a highly active, minimal cGAS recognition motif that enables detection of HIV-1 ssDNA.

Disruption of de Novo Adenosine Triphosphate (ATP) Biosynthesis Abolishes Virulence in Cryptococcus neoformans.

PubMed

Blundell, Ross D; Williams, Simon J; Arras, Samantha D M; Chitty, Jessica L; Blake, Kirsten L; Ericsson, Daniel J; Tibrewal, Nidhi; Rohr, Jurgen; Koh, Y Q Andre E; Kappler, Ulrike; Robertson, Avril A B; Butler, Mark S; Cooper, Matthew A; Kobe, Bostjan; Fraser, James A

2016-09-09

Opportunistic fungal pathogens such as Cryptococcus neoformans are a growing cause of morbidity and mortality among immunocompromised populations worldwide. To address the current paucity of antifungal therapeutic agents, further research into fungal-specific drug targets is required. Adenylosuccinate synthetase (AdSS) is a crucial enzyme in the adeosine triphosphate (ATP) biosynthetic pathway, catalyzing the formation of adenylosuccinate from inosine monophosphate and aspartate. We have investigated the potential of this enzyme as an antifungal drug target, finding that loss of function results in adenine auxotrophy in C. neoformans, as well as complete loss of virulence in a murine model. Cryptococcal AdSS was expressed and purified in Escherichia coli and the enzyme's crystal structure determined, the first example of a structure of this enzyme from fungi. Together with enzyme kinetic studies, this structural information enabled comparison of the fungal enzyme with the human orthologue and revealed species-specific differences potentially exploitable via rational drug design. These results validate AdSS as a promising antifungal drug target and lay a foundation for future in silico and in vitro screens for novel antifungal compounds.

Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsutakawa, Susan E.; Thompson, Mark J.; Arvai, Andrew S.

DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5'-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 5'polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via phosphate steering', basic residues energetically steer an inverted ss 5'-flap through a gateway over FEN1's active site and shift dsDNA formore » catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA) n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 5'-flap specificity and catalysis, preventing genomic instability.« less

Understanding transport pathways in a river system - Monitoring sediments contaminated by an incident

NASA Astrophysics Data System (ADS)

Dietrich, S.; Kleisinger, C.; Hillebrand, G.; Claus, E.; Schwartz, R.; Carls, I.; Winterscheid, A.; Schubert, B.

2016-12-01

Experiments to trace transport of sediments and suspended particulate matter on a river scale are an expensive and difficult venture, since it causes a lot of official requirements. In spring 2015, polychlorinated biphenyls (PCB) were released during restoration works at a bridge in the upper part of the Elbe River, near the Czech-German border. In this study, the particle-bound PCB-transport is applied as a tracer for monitoring transport pathways of suspended solids (SS) along a whole river stretch over 700 km length. The incident was monitored by concentration measurements of seven indicator PCB congeners along the inland part of the Elbe River as well as in the Elbe estuary. Data from 15 monitoring stations (settling tanks) as well as from two longitudinal campaigns (grab samples) along the river in July and August 2015 are considered. The total PCB load is calculated for all stations on the basis of monthly contaminant concentrations and daily suspended sediment concentrations. Monte-Carlo simulations assess the uncertainties of the calculated load. 1D water levels and GIS analysis were used to locate temporal storage areas for the SS. It is shown that the ratio of high versus low chlorinated PCB congeners is a suitable tracer to distinguish the PCB load of the incident from the long-term background signal. Furthermore, the reduction of total PCB load within the upper Elbe indicates that roughly 24% of the SS were transported with the water by wash load. Approximately 600 km downstream of the incident site, the PCB-marked wash load was first identified in July 2015. PCB load transported intermittently in suspension was detected roughly 400 km downstream of the incident site by August 2015. In the Elbe Estuary, PCB-marked SS were only found upstream of the steep slope of water depth (approx. 4 to 15 m) within Hamburg harbor that acts as a major sediment sink. Here, SS from the inland Elbe are mixed with lowly contaminated marine material, which may mask the effect of the PCB release.

Intracellular delivery and antitumor effects of a redox-responsive polymeric paclitaxel conjugate based on hyaluronic acid.

PubMed

Yin, Shaoping; Huai, Jue; Chen, Xi; Yang, Yong; Zhang, Xinxin; Gan, Yong; Wang, Guangji; Gu, Xiaochen; Li, Juan

2015-10-01

Polymer-drug conjugates have demonstrated application potentials in optimizing chemotherapeutics. In this study a new bioconjugate, HA-ss-PTX, was designed and synthesized with cooperative dual characteristics of active tumor targeting and selective intracellular drug release. Paclitaxel (PTX) was covalently attached to hyaluronic acid (HA) with various sizes (MW 9.5, 35, 770 kDa); a cross-linker containing disulfide bond was also used to shield drug leakage in blood circulation and to achieve rapid drug release in tumor cells in response to glutathione. Incorporation of HA to the conjugate enhanced the capabilities of drug loading, intracellular endocytosis and tumor targeting of micelles in comparison to mPEG. HA molecular weight showed significant effect on properties and antitumor efficacy of the synthesized conjugates. Intracellular uptake of HA-ss-PTX toward MCF-7 cells was mediated by CD44-caveolae-mediated endocytosis. Compared to Taxol and mPEG-ss-PTX, HA9.5-ss-PTX demonstrated improved tumor growth inhibition in vivo with a TIR of 83.27 ± 5.20%. It was concluded that HA9.5-ss-PTX achieved rapid intracellular release of PTX and enhanced its therapeutic efficacy, thus providing a platform for specific drug targeting and controlled intracellular release in chemotherapeutics. Polymer-drug conjugates, promising nanomedicines, still face some technical challenges including a lack of specific targeting and rapid intracellular drug release at the target site. In this manuscript we designed and constructed a novel bioconjugate HA-ss-PTX, which possessed coordinated dual characteristics of active tumor targeting and selective intracellular drug release. Redox-responsive disulfide bond was introduced to the conjugate to shield drug leakage in blood circulation and to achieve rapid drug release at tumor site in response to reductant like glutathione. Paclitaxel was selected as a model drug to be covalently attached to hyaluronic acid (HA) with various sizes to elucidate the structure-activity relationship and to address whether HA could substitute PEG as a carrier for polymeric conjugates. Based on a series of in vitro and in vivo experiments, HA-ss-PTX performed well in drug loading, cellular internalization, tumor targeting by entering tumor cells via CD44-caveolae-mediated endocytosis and rapidly release drug at target in the presence of GSH. One of the key issues in clinical oncology is to enhance drug delivery efficacy while minimizing side effects. The study indicated that this new polymeric conjugate system would be useful in delivering anticancer agents to improve therapeutic efficacy and to minimize adverse effects, thus providing a platform for specific drug targeting and controlled intracellular release in chemotherapeutics. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Construct validity of the items on the Stroke Specific Quality of Life (SS-QOL) questionnaire that evaluate the participation component of the International Classification of Functioning, Disability and Health.

PubMed

Silva, Soraia Micaela; Corrêa, Fernanda Ishida; Pereira, Gabriela Santos; Faria, Christina Danielli Coelho de Morais; Corrêa, João Carlos Ferrari

2018-01-01

Analyze the construct validity and internal consistency of the Stroke Specific Quality of Life (SS-QOL) items that address the participation component of the ICF as well as analyze the ceiling and floor effects. One hundred subjects were analyzed: 85 community-dwelling and 15 institutionalized individuals. The analysis of construct validity was performed using classic psychometrics: (1) the comparison of known groups (individuals without restriction to participation vs. those with restriction to participation) using the Mann-Whitney test and (2) convergent validity - correlation between the scores on the SS-QOL items that address participation and the subscale scores of measures used to evaluate the similar constructs and concepts [the Short-Form Health Survey (SF-36), Functional Independence Measure (FIM) and grip strength test]. Spearman's correlation coefficients were calculated for this analysis. Cronbach's α was used for the analysis of internal consistency and both the ceiling and floor effects were analyzed. The level of significance for all analyses was α = 0.05. The a priori hypotheses regarding construct validity were partially demonstrated, as only five of the eight domains exhibited positive moderate to strong correlations (r > 0.40) with measures that address constructs similar to those addressed on the SS-QOL questionnaire. The items demonstrated adequate internal consistency and are capable of differentiating individuals with and without restriction to participation. The ceiling and floor effects were considered adequate for the total SS-QOL score, but beyond acceptable standards for some domains. The 26 items of the SS-QOL questionnaire measure a multidimensional construct and therefore do not only address participation. However, the items demonstrated adequate internal consistency and are capable of differentiating individuals with and without restriction to participation. Implications for rehabilitation The 26 items of the SS-QOL questionnaire demonstrated adequate internal consistency and are capable of differentiating individuals with and without restriction to participation. The present findings can guide healthcare professionals regarding the selection of an assessment tool for the evaluation of post-stroke participation. The findings can lead to consistent and standardization evaluations, which facilitates comparisons and discussion on functional health and social participation after stroke.

Identification of ssDNA aptamers specific to clinical isolates of Streptococcus mutans strains with different cariogenicity.

PubMed

Cui, Wei; Liu, Jiaojiao; Su, Donghua; Hu, Danyang; Hou, Shuai; Hu, Tongnan; Yang, Jiyong; Luo, Yanping; Xi, Qing; Chu, Bingfeng; Wang, Chenglong

2016-06-01

Streptococcus mutans, a Gram-positive facultative anaerobic bacterium, is considered to be a major etiological factor for dental caries. In this study, plaques from dental enamel surfaces of caries-active and caries-free individuals were obtained and cultivated for S. mutans isolation. Morphology examination, biochemical characterization, and polymerase chain reaction were performed to identify S. mutans The cariogenicity of S. mutans strains isolated from clinical specimens was evaluated by testing the acidogenicity, aciduricity, extracellular polysaccharide production, and adhesion ability of the bacteria. Finally, subtractive SELEX (systematic evolution of ligands by exponential enrichment) technology targeting whole intact cells was used to screen for ssDNA aptamers specific to the strains with high cariogenicity. After nine rounds of subtractive SELEX, sufficient pool enrichment was achieved as shown by radioactive isotope analysis. The enriched pool was cloned and sequenced randomly, followed by MEME online and RNA structure software analysis of the sequences. Results from the flow cytometry indicated that aptamers H1, H16, H4, L1, L10, and H19 could discriminate highly cariogenic S. mutans strains from poorly cariogenic strains. Among these, Aptamer H19 had the strongest binding capacity with cariogenic S. mutans strains with a dissociation constant of 69.45 ± 38.53 nM. In conclusion, ssDNA aptamers specific to highly cariogenic clinical S. mutans strains were successfully obtained. These ssDNA aptamers might be used for the early diagnosis and treatment of dental caries. © The Author 2016. Published by Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

RE-PERG, a new procedure for electrophysiologic diagnosis of glaucoma that may improve PERG specificity.

PubMed

Mavilio, Alberto; Sisto, Dario; Ferreri, Paolo; Cardascia, Nicola; Alessio, Giovanni

2017-01-01

A significant variability of the second harmonic (2ndH) phase of steady-state pattern electroretinogram (SS-PERG) in intrasession retest has been recently described in glaucoma patients (GP), which has not been found in healthy subjects. To evaluate the reliability of phase variability in retest (a procedure called RE-PERG or REPERG) in the presence of cataract, which is known to affect standard PERG, we tested this procedure in GP, normal controls (NC), and cataract patients (CP). The procedure was performed on 50 GP, 35 NC, and 27 CP. All subjects were examined with RE-PERG and SS-PERG and also with spectral domain optical coherence tomography and standard automated perimetry. Standard deviation of phase and amplitude value of 2ndH were correlated by means of one-way analysis of variance and Pearson correlation, with the mean deviation and pattern standard deviation assessed by standard automated perimetry and retinal nerve fiber layer and the ganglion cell complex thickness assessed by spectral domain optical coherence tomography. Receiver operating characteristics were calculated in cohort populations with and without cataract. Standard deviation of phase of 2ndH was significantly higher in GP with respect to NC ( P <0.001) and CP ( P <0.001), and it correlated with retinal nerve fiber layer ( r =-0.5, P <0.001) and ganglion cell complex ( r =-0.6, P <0.001) defects in GP. Receiver operating characteristic evaluation showed higher specificity of RE-PERG (86.4%; area under the curve 0.93) with respect to SS-PERG (54.5%; area under the curve 0.68) in CP. RE-PERG may improve the specificity of SS-PERG in clinical practice in the discrimination of GP.

Discovering weighted patterns in intron sequences using self-adaptive harmony search and back-propagation algorithms.

PubMed

Huang, Yin-Fu; Wang, Chia-Ming; Liou, Sing-Wu

2013-01-01

A hybrid self-adaptive harmony search and back-propagation mining system was proposed to discover weighted patterns in human intron sequences. By testing the weights under a lazy nearest neighbor classifier, the numerical results revealed the significance of these weighted patterns. Comparing these weighted patterns with the popular intron consensus model, it is clear that the discovered weighted patterns make originally the ambiguous 5SS and 3SS header patterns more specific and concrete.

Discovering Weighted Patterns in Intron Sequences Using Self-Adaptive Harmony Search and Back-Propagation Algorithms

PubMed Central

Wang, Chia-Ming; Liou, Sing-Wu

2013-01-01

A hybrid self-adaptive harmony search and back-propagation mining system was proposed to discover weighted patterns in human intron sequences. By testing the weights under a lazy nearest neighbor classifier, the numerical results revealed the significance of these weighted patterns. Comparing these weighted patterns with the popular intron consensus model, it is clear that the discovered weighted patterns make originally the ambiguous 5SS and 3SS header patterns more specific and concrete. PMID:23737711

Do pre-existing diabetes social support or depressive symptoms influence the effectiveness of a diabetes management intervention?

PubMed

Rosland, Ann-Marie; Kieffer, Edith; Spencer, Michael; Sinco, Brandy; Palmisano, Gloria; Valerio, Melissa; Nicklett, Emily; Heisler, Michele

2015-11-01

Examine influences of diabetes-specific social support (D-SS) and depressive symptoms on glycemic control over time, among adults randomized to a diabetes self-management education and support (DSME/S) intervention or usual care. Data were from 108 African-American and Latino participants in a 6-month intervention trial. Multivariable linear regression models assessed associations between baseline D-SS from family and friends and depressive symptoms with changes in HbA1c. We then examined whether baseline D-SS or depression moderated intervention-associated effects on HbA1c. Higher baseline D-SS was associated with larger improvements in HbA1c (adjusted ΔHbA1c -0.39% for each +1-point D-SS, p=0.02), independent of intervention-associated HbA1c decreases. Baseline depressive symptoms had no significant association with subsequent HbA1c change. Neither D-SS nor depression moderated intervention-associated effects on HbA1c. Diabetes self-management education and support programs have potential to improve glycemic control for participants starting with varying levels of social support and depressive symptoms. Participants starting with more support for diabetes management from family and friends improved HbA1c significantly more over 6 months than those with less support, independent of additional significant DSME/S intervention-associated HbA1c improvements. Social support from family and friends may improve glycemic control in ways additive to DSME/S. Published by Elsevier Ireland Ltd.

Quantification of Functionalised Gold Nanoparticle-Targeted Knockdown of Gene Expression in HeLa Cells

PubMed Central

Jiwaji, Meesbah; Sandison, Mairi E.; Reboud, Julien; Stevenson, Ross; Daly, Rónán; Barkess, Gráinne; Faulds, Karen; Kolch, Walter; Graham, Duncan; Girolami, Mark A.; Cooper, Jonathan M.; Pitt, Andrew R.

2014-01-01

Introduction Gene therapy continues to grow as an important area of research, primarily because of its potential in the treatment of disease. One significant area where there is a need for better understanding is in improving the efficiency of oligonucleotide delivery to the cell and indeed, following delivery, the characterization of the effects on the cell. Methods In this report, we compare different transfection reagents as delivery vehicles for gold nanoparticles functionalized with DNA oligonucleotides, and quantify their relative transfection efficiencies. The inhibitory properties of small interfering RNA (siRNA), single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) sequences targeted to human metallothionein hMT-IIa are also quantified in HeLa cells. Techniques used in this study include fluorescence and confocal microscopy, qPCR and Western analysis. Findings We show that the use of transfection reagents does significantly increase nanoparticle transfection efficiencies. Furthermore, siRNA, ssRNA and ssDNA sequences all have comparable inhibitory properties to ssDNA sequences immobilized onto gold nanoparticles. We also show that functionalized gold nanoparticles can co-localize with autophagosomes and illustrate other factors that can affect data collection and interpretation when performing studies with functionalized nanoparticles. Conclusions The desired outcome for biological knockdown studies is the efficient reduction of a specific target; which we demonstrate by using ssDNA inhibitory sequences targeted to human metallothionein IIa gene transcripts that result in the knockdown of both the mRNA transcript and the target protein. PMID:24926959

Cystic Lung Disease Among Patients With Sjögren Syndrome: Frequency, Natural History, and Associated Risk Factors.

PubMed

Martínez-Balzano, Carlos D; Touray, Sunkaru; Kopec, Scott

2016-09-01

Cystic lung disease (CLD) in Sjögren syndrome (SS) is a condition with unclear prognostic implications. Our objectives in this study are to determine its frequency, progression over time, and associated risk factors and complications. Eighty-four patients with primary or secondary SS and chest imaging, chest radiograph, or CT scan were retrospectively evaluated for CLD. Thirteen patients with cysts were found. Baseline characteristics of all patients were collected. A multivariate logistic regression model was used to look for predictors of CLD in patients with CT scan. Additional imaging, SS activity, and complications from CLD and SS were collected for the patients with cysts. CLD had a frequency of 15.4% for all patients with chest imaging. Not all cysts were evident on radiography, and CLD frequency was 30.9% for the patients with chest CT scan. Six patients had cysts without other radiographic findings. CLD was associated with older age (OR, 1.1; 95% CI, 1.0-1.16), a diagnosis of secondary SS (OR, 12.1; 95% CI, 1.12-130.4), and seropositivity for anti-SS-related antigen A/Ro autoantibodies (OR, 26.9; 95% CI, 1.44-93.61). There was no radiologic progression of CLD for 12 patients after a 4-year median follow-up. Lung function did not exhibit temporal worsening. CLD did not correlate with a specific pattern in pulmonary function testing. Two patients had secondary infectious complications of the cysts. CLD is a relatively common condition in SS that does not progress on serial radiologic and lung function follow-up. CLD, without other radiographic findings, may represent a direct manifestation of SS. Copyright © 2016 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

Motion artifacts in kidney stone imaging using single-source and dual-source dual-energy CT scanners: a phantom study.

PubMed

Ibrahim, El-Sayed H; Cernigliaro, Joseph G; Pooley, Robert A; Williams, James C; Haley, William E

2015-10-01

Dual-energy computed tomography (DECT) has shown the capability of differentiating uric acid (UA) from non-UA stones with 90-100% accuracy. With the invention of dual-source (DS) scanners, both low- and high-energy images are acquired simultaneously. However, DECT can also be performed by sequential acquisition of both images on single-source (SS) scanners. The objective of this study is to investigate the effects of motion artifacts on stone classification using both SS-DECT and DS-DECT. 114 kidney stones of different types and sizes were imaged on both DS-DECT and SS-DECT scanners with tube voltages of 80 and 140 kVp with and without induced motion. Postprocessing was conducted to create material-specific images from corresponding low- and high-energy images. The dual-energy ratio (DER) and stone material were determined and compared among different scans. For the motionless scans, all stones were correctly classified with SS-DECT, while two cystine stones were misclassified with DS-DECT. When motion was induced, 94% of the stones were misclassified with SS-DECT versus 11% with DS-DECT (P < 0.0001). Stone size was not a factor in stone misclassification under motion. Stone type was not a factor in stone misclassification under motion with SS-DECT, although with DS-DECT, cystine showed higher number of stone misclassification. Motion artifacts could result in stone misclassification in DECT. This effect is more pronounced in SS-DECT versus DS-DECT, especially if stones of different types lie in close proximity to each other. Further, possible misinterpretation of the number of stones (i.e., missing one, or thinking that there are two) in DS-DECT could be a potentially significant problem.

The non-conserved region of MRP is involved in the virulence of Streptococcus suis serotype 2

PubMed Central

Li, Quan; Fu, Yang; Ma, Caifeng; He, Yanan; Yu, Yanfei; Du, Dechao; Yao, Huochun; Lu, Chengping; Zhang, Wei

2017-01-01

ABSTRACT Muramidase-released protein (MRP) of Streptococcus suis serotype 2 (SS2) is an important epidemic virulence marker with an unclear role in bacterial infection. To investigate the biologic functions of MRP, 3 mutants named Δmrp, Δmrp domain 1 (Δmrp-d1), and Δmrp domain 2 (Δmrp-d2) were constructed to assess the phenotypic changes between the parental strain and the mutant strains. The results indicated that MRP domain 1 (MRP-D1, the non-conserved region of MRP from a virulent strain, a.a. 242–596) played a critical role in adherence of SS2 to host cells, compared with MRP domain 1* (MRP-D1*, the non-conserved region of MRP from a low virulent strain, a.a. 239–598) or MRP domain 2 (MRP-D2, the conserved region of MRP, a.a. 848–1222). We found that MRP-D1 but not MRP-D2, could bind specifically to fibronectin (FN), factor H (FH), fibrinogen (FG), and immunoglobulin G (IgG). Additionally, we confirmed that mrp-d1 mutation significantly inhibited bacteremia and brain invasion in a mouse infection model. The mrp-d1 mutation also attenuated the intracellular survival of SS2 in RAW246.7 macrophages, shortened the growth ability in pig blood and decreased the virulence of SS2 in BALB/c mice. Furthermore, antiserum against MRP-D1 was found to dramatically impede SS2 survival in pig blood. Finally, immunization with recombinant MRP-D1 efficiently enhanced murine viability after SS2 challenge, indicating its potential use in vaccination strategies. Collectively, these results indicated that MRP-D1 is involved in SS2 virulence and eloquently demonstrate the function of MRP in pathogenesis of infection. PMID:28362221

The non-conserved region of MRP is involved in the virulence of Streptococcus suis serotype 2.

PubMed

Li, Quan; Fu, Yang; Ma, Caifeng; He, Yanan; Yu, Yanfei; Du, Dechao; Yao, Huochun; Lu, Chengping; Zhang, Wei

2017-10-03

Muramidase-released protein (MRP) of Streptococcus suis serotype 2 (SS2) is an important epidemic virulence marker with an unclear role in bacterial infection. To investigate the biologic functions of MRP, 3 mutants named Δmrp, Δmrp domain 1 (Δmrp-d1), and Δmrp domain 2 (Δmrp-d2) were constructed to assess the phenotypic changes between the parental strain and the mutant strains. The results indicated that MRP domain 1 (MRP-D1, the non-conserved region of MRP from a virulent strain, a.a. 242-596) played a critical role in adherence of SS2 to host cells, compared with MRP domain 1* (MRP-D1*, the non-conserved region of MRP from a low virulent strain, a.a. 239-598) or MRP domain 2 (MRP-D2, the conserved region of MRP, a.a. 848-1222). We found that MRP-D1 but not MRP-D2, could bind specifically to fibronectin (FN), factor H (FH), fibrinogen (FG), and immunoglobulin G (IgG). Additionally, we confirmed that mrp-d1 mutation significantly inhibited bacteremia and brain invasion in a mouse infection model. The mrp-d1 mutation also attenuated the intracellular survival of SS2 in RAW246.7 macrophages, shortened the growth ability in pig blood and decreased the virulence of SS2 in BALB/c mice. Furthermore, antiserum against MRP-D1 was found to dramatically impede SS2 survival in pig blood. Finally, immunization with recombinant MRP-D1 efficiently enhanced murine viability after SS2 challenge, indicating its potential use in vaccination strategies. Collectively, these results indicated that MRP-D1 is involved in SS2 virulence and eloquently demonstrate the function of MRP in pathogenesis of infection.

Is salivary gland ultrasonography a useful tool in Sjögren's syndrome? A systematic review.

PubMed

Jousse-Joulin, Sandrine; Milic, Vera; Jonsson, Malin V; Plagou, Athena; Theander, Elke; Luciano, Nicoletta; Rachele, Pascale; Baldini, Chiara; Bootsma, Hendrika; Vissink, Arjan; Hocevar, Alojzija; De Vita, Salvatore; Tzioufas, Athanasios G; Alavi, Zarin; Bowman, Simon J; Devauchelle-Pensec, Valerie

2016-05-01

Ultrasonography (US) is a sensitive tool in the diagnosis of major salivary gland abnormalities in primary Sjögren's syndrome (pSS). The aim of this systematic review was to assess the metric properties of this technique. PUBMED and EMBASE databases were searched. All publications between January 1988 and January 2013 were considered. Data were extracted from the articles meeting the inclusion criteria according to US definition of salivary gland scoring system and metric properties studied. The type and number of glands tested, study design and metric properties according to OMERACT filter (truth, discrimination, feasibility) were assessed. Of 167 publications identified initially with PUBMED and EMBASE, 31 met the inclusion criteria. The number of pSS patients varied among the studies from 16 to 140. The diagnosis of pSS was in line in most of the cases with the American-European Consensus Group (AECG) classification criteria for Sjögren's syndrome. The US examination was performed in suspected pSS only in studies in which the sensitivity ranged from 45.8 to 91.6% and specificity from 73 to 98.1%. There was heterogeneity in regard to the definition of US in B-mode and few studies used US in colour Doppler. Few studies reported reliability of US and sensitivity to change in pSS. US is a valuable tool for detecting salivary gland abnormalities in pSS. Its reliability has been poorly investigated and there is considerable variation in the definition of US abnormalities. Further studies are required to validate and standardize the US definition of salivary gland in pSS. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Comparison of gel properties and biochemical characteristics of myofibrillar protein from bighead carp (Aristichthys nobilis) affected by frozen storage and a hydroxyl radical-generation oxidizing system.

PubMed

Lu, Han; Zhang, Longteng; Li, Qingzheng; Luo, Yongkang

2017-05-15

We wanted to clarify whether gel properties can be affected by in vivo or in vitro myofibrillar protein oxidation and, thus, to provide relevant information and a scientific foundation for the processing of gel products. To accomplish this, we measured the changes in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), total disulfide (SS) content, surface hydrophobicity (So-ANS), carbonyl content, and gel texture and water-holding capacity (WHC) of isolated myofibrillar protein from bighead carp fillets during frozen storage and under different H 2 O 2 concentrations, which were used to represent in vivo and in vitro conditions, respectively. The results indicated that a certain range in content of disulfide crosslinks (0.91mol/10 5 g protein) would promote gel hardness. Mild protein oxidation caused by a certain degree of frozen storage and hydroxyl radicals can promote gel texture and WHC. Based on those results, freezing bighead carp for a certain period can be used to produce gel products. Copyright © 2016 Elsevier Ltd. All rights reserved.

Sediment source detection by stable isotope analysis, carbon and nitrogen content and CSSI in a small river of the Swiss Plateau

NASA Astrophysics Data System (ADS)

SchindlerWildhaber, Yael; Alewell, Christine; Birkholz, Axel

2014-05-01

Suspended sediment (SS) and organic matter in rivers can harm the fauna by affecting health and fitness of free swimming fish and by causing siltation of the riverbed. The temporal and spatial dynamics of sediment, carbon (C) and nitrogen (N) during the brown trout spawning season in a small river of the Swiss Plateau were assessed and C isotopes as well as the C/N atomic ratio were used to distinguish autochthonous and allochthonous sources of organic matter in SS loads. The visual basic program IsoSource with 13Ctot and 15N as input isotopes was used to quantify the temporal and spatial sources of SS. We determined compound specific stable carbon isotopes (CSSI) in fatty acids of possible sediment source areas to the stream in addition and compared them to SS from selected high flow and low flow events. Organic matter concentrations in the infiltrated and suspended sediment were highest during low flow periods with small sediment loads and lowest during high flow periods with high sediment loads. Peak values in nitrate and dissolved organic C were measured during high flow and high rainfall, probably due to leaching from pasture and arable land. The organic matter was of allochthonous sources as indicated by the C/N atomic ratio and δ13Corg. Organic matter in SS increased from up- to downstream due to an increase in sediment delivery from pasture and arable land downstream of the river. While the major sources of SS are pasture and arable land during base flow conditions, SS from forest soils increased during heavy rain events and warmer winter periods most likely due to snow melt which triggered erosion. Preliminary results of CSSI analysis of sediment source areas and comparison to SS of selected events indicate that differences in d13C values of individual fatty acids are too small to differentiate unambiguously between sediment sources.

Magnetic porous carbon nanocomposites derived from metal-organic frameworks as a sensing platform for DNA fluorescent detection.

PubMed

Tan, Hongliang; Tang, Gonge; Wang, Zhixiong; Li, Qian; Gao, Jie; Wu, Shimeng

2016-10-12

Metal-organic frameworks (MOFs) have emerged as very fascinating functional materials due to their tunable nature and diverse applications. In this work, we prepared a magnetic porous carbon (MPC) nanocomposite by employing iron-containing MOFs (MIL-88A) as precursors through a one-pot thermolysis method. It was found that the MPC can absorb selectively single-stranded DNA (ssDNA) probe to form MPC/ssDNA complex and subsequently quench the labelled fluorescent dye of the ssDNA probe, which is resulted from the synergetic effect of magnetic nanoparticles and carbon matrix. Upon the addition of complementary target DNA, however, the absorbed ssDNA probe could be released from MPC surface by forming double-stranded DNA with target DNA, and accompanied by the recovery of the fluorescence of ssDNA probe. Based on these findings, a sensing platform with low background signal for DNA fluorescent detection was developed. The proposed sensing platform exhibits high sensitivity with detection limit of 1 nM and excellent selectivity to specific target DNA, even single-base mismatched nucleotide can be distinguished. We envision that the presented study would provide a new perspective on the potential applications of MOF-derived nanocomposites in biomedical fields. Copyright © 2016 Elsevier B.V. All rights reserved.

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

PubMed Central

Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin

2014-01-01

Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80% and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test data set of 198 proteins, achieving a Q3 accuracy of 80.7% and a Sov accuracy of 74.2%. PMID:25750595

Earthquake and tsunami forecasts: Relation of slow slip events to subsequent earthquake rupture

PubMed Central

Dixon, Timothy H.; Jiang, Yan; Malservisi, Rocco; McCaffrey, Robert; Voss, Nicholas; Protti, Marino; Gonzalez, Victor

2014-01-01

The 5 September 2012 Mw 7.6 earthquake on the Costa Rica subduction plate boundary followed a 62-y interseismic period. High-precision GPS recorded numerous slow slip events (SSEs) in the decade leading up to the earthquake, both up-dip and down-dip of seismic rupture. Deeper SSEs were larger than shallower ones and, if characteristic of the interseismic period, release most locking down-dip of the earthquake, limiting down-dip rupture and earthquake magnitude. Shallower SSEs were smaller, accounting for some but not all interseismic locking. One SSE occurred several months before the earthquake, but changes in Mohr–Coulomb failure stress were probably too small to trigger the earthquake. Because many SSEs have occurred without subsequent rupture, their individual predictive value is limited, but taken together they released a significant amount of accumulated interseismic strain before the earthquake, effectively defining the area of subsequent seismic rupture (rupture did not occur where slow slip was common). Because earthquake magnitude depends on rupture area, this has important implications for earthquake hazard assessment. Specifically, if this behavior is representative of future earthquake cycles and other subduction zones, it implies that monitoring SSEs, including shallow up-dip events that lie offshore, could lead to accurate forecasts of earthquake magnitude and tsunami potential. PMID:25404327

Earthquake and tsunami forecasts: relation of slow slip events to subsequent earthquake rupture.

PubMed

Dixon, Timothy H; Jiang, Yan; Malservisi, Rocco; McCaffrey, Robert; Voss, Nicholas; Protti, Marino; Gonzalez, Victor

2014-12-02

The 5 September 2012 M(w) 7.6 earthquake on the Costa Rica subduction plate boundary followed a 62-y interseismic period. High-precision GPS recorded numerous slow slip events (SSEs) in the decade leading up to the earthquake, both up-dip and down-dip of seismic rupture. Deeper SSEs were larger than shallower ones and, if characteristic of the interseismic period, release most locking down-dip of the earthquake, limiting down-dip rupture and earthquake magnitude. Shallower SSEs were smaller, accounting for some but not all interseismic locking. One SSE occurred several months before the earthquake, but changes in Mohr-Coulomb failure stress were probably too small to trigger the earthquake. Because many SSEs have occurred without subsequent rupture, their individual predictive value is limited, but taken together they released a significant amount of accumulated interseismic strain before the earthquake, effectively defining the area of subsequent seismic rupture (rupture did not occur where slow slip was common). Because earthquake magnitude depends on rupture area, this has important implications for earthquake hazard assessment. Specifically, if this behavior is representative of future earthquake cycles and other subduction zones, it implies that monitoring SSEs, including shallow up-dip events that lie offshore, could lead to accurate forecasts of earthquake magnitude and tsunami potential.

Respiration and enzymatic activities as indicators of stabilization of sewage sludge composting.

PubMed

Nikaeen, Mahnaz; Nafez, Amir Hossein; Bina, Bijan; Nabavi, BiBi Fatemeh; Hassanzadeh, Akbar

2015-05-01

The objective of this work was to study the evolution of physico-chemical and microbial parameters in the composting process of sewage sludge (SS) with pruning wastes (PW) in order to compare these parameters with respect to their applicability in the evaluation of organic matter (OM) stabilization. To evaluate the composting process and organic matter stability, different microbial activities were compared during composting of anaerobically digested SS with two volumetric ratios, 1:1 and 3:1 of PW:SS and two aeration techniques including aerated static piles (ASP) and turned windrows (TW). Dehydrogenase activity, fluorescein diacetate hydrolysis, and specific oxygen uptake rate (SOUR) were used as microbial activity indices. These indices were compared with traditional parameters, including temperature, pH, moisture content, organic matter, and C/N ratio. The results showed that the TW method and 3:1 (PW:SS) proportion was superior to the ASP method and 1:1 proportion, since the former accelerate the composting process by catalyzing the OM stabilization. Enzymatic activities and SOUR, which reflect microbial activity, correlated well with temperature fluctuations. Based on these results it appears that SOUR and the enzymatic activities are useful parameters to monitor the stabilization of SS compost. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.

PubMed

Spencer, Matt; Eickholt, Jesse; Jianlin Cheng

2015-01-01

Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent.

Role of beta 1-4 linked polymers in the biofilm structure of marine Pseudomonas sp. CE-2 on 304 stainless steel coupons.

PubMed

Jain, Anand; Bhosle, Narayan B

2008-01-01

Pseudomonas sp CE-2 cells attach and form biofilms on 304-stainless steel (SS) coupons. A series of experiments were carried out in order to understand the role of exopolysaccharides (EPS) in the formation and maintenance of CE-2 biofilms on SS coupons. The biofilm density and EPS concentration increased over the period of incubation and the highest values for both were recorded after 72 h. Calcofluor and the lectin concanavalin A (Con A) showed a positive interaction with 72-h old biofilms, indicating the presence of beta 1-4 linked polymers, and alpha-d-glucose and alpha-d-mannose in the biofilm matrix of CE-2. When the CE-2 cells were grown in the presence of calcofluor (200 microg ml(-1)), biofilm formation was significantly reduced (approximately 85%). Conversely, the lectins Con A or WGA did not influence the CE-2 biofilms on the SS coupons. Furthermore, treatment with cellulase, an enzyme specific for the degradation of beta 1-4 linked polymers, removed substantial amounts of CE-2 biofilm from SS coupons. These results strongly suggest the involvement of beta 1-4 linked polymers in the formation and maintenance of Pseudomonas sp. CE-2 biofilms on SS coupons.

The Drosophila telomere-capping protein Verrocchio binds single-stranded DNA and protects telomeres from DNA damage response

PubMed Central

Cicconi, Alessandro; Micheli, Emanuela; Vernì, Fiammetta; Jackson, Alison; Gradilla, Ana Citlali; Cipressa, Francesca; Raimondo, Domenico; Bosso, Giuseppe; Wakefield, James G.; Ciapponi, Laura; Cenci, Giovanni; Gatti, Maurizio

2017-01-01

Abstract Drosophila telomeres are sequence-independent structures maintained by transposition to chromosome ends of three specialized retroelements rather than by telomerase activity. Fly telomeres are protected by the terminin complex that includes the HOAP, HipHop, Moi and Ver proteins. These are fast evolving, non-conserved proteins that localize and function exclusively at telomeres, protecting them from fusion events. We have previously suggested that terminin is the functional analogue of shelterin, the multi-protein complex that protects human telomeres. Here, we use electrophoretic mobility shift assay (EMSA) and atomic force microscopy (AFM) to show that Ver preferentially binds single-stranded DNA (ssDNA) with no sequence specificity. We also show that Moi and Ver form a complex in vivo. Although these two proteins are mutually dependent for their localization at telomeres, Moi neither binds ssDNA nor facilitates Ver binding to ssDNA. Consistent with these results, we found that Ver-depleted telomeres form RPA and γH2AX foci, like the human telomeres lacking the ssDNA-binding POT1 protein. Collectively, our findings suggest that Drosophila telomeres possess a ssDNA overhang like the other eukaryotes, and that the terminin complex is architecturally and functionally similar to shelterin. PMID:27940556

Chinese isms dimensions in mainland China and Taiwan: Convergence and extension of American isms dimensions.

PubMed

Chen, Zhuo Job; Hsu, Kung-Yu; Zhou, Xinyue; Saucier, Gerard

2017-07-21

Previous studies of American English isms terms have uncovered as many as five broad factors: tradition-oriented religiousness (TR), subjective spirituality (SS), communal rationalism (CR), unmitigated self-interest (USI), and inequality aversion (IA). The present studies took a similar lexical approach to investigate the Chinese-language isms structures in both mainland China and Taiwan. In Study 1, exploratory factor analyses with 915 mainland Chinese subjects uncovered four interpretable factors dimensionalizing 165 mainland Chinese dictionary isms terms. These factors represented contents of a combination of TR and SS, USI, CR, and a culturally unique Communist Party of China (CPC) ideology factor. In Study 2, exploratory factor analyses with 467 Taiwan Chinese subjects revealed four interpretable factors categorizing 291 Taiwan Chinese dictionary isms terms. These factors represented contents of a combination of TR and SS, USI, CR, and a culturally unique dimension expressing aspirations for happiness. The results gave evidence for the existence of the isms factors TR and SS, USI, and CR in Chinese culture. Cultural uniqueness was reflected in the merging of TR and SS into the factor Syncretic Religiousness and the culture-specific factors of CPC ideology in China and Happiness/Peace Promotion in Taiwan. © 2017 Wiley Periodicals, Inc.

The unique response of renin and aldosterone to dietary sodium intervention in sodium sensitivity.

PubMed

Shin, Sung Joon; Lim, ChiYeon; Oh, Sang Woo; Rhee, Moo-Yong

2014-06-01

Sodium sensitivity (SS) is a phenomenon in which significant changes in blood pressure (BP) are observed based on sodium intake. The renin-angiotensin-aldosterone system plays a critical role in sodium handling and hypertension. We identified the specific responses of renin and aldosterone based on dietary sodium intake and revealed the relationship between these hormonal changes and dietary sodium intake in patients with SS. In total, 61 subjects were available to analyze full data including plasma renin activity (PRA) and aldosterone. Participants were given a low-sodium DASH diet (LSD) for 7 days and a high-sodium DASH diet (HSD) for the following 7 days. SS was found in five (14.71%) in normotensives, and 14 (51.85%) in hypertensives. In sodium-resistant (SR) subjects, both PRA and aldosterone decreased significantly after consuming HSD. Moreover, a significant correlation was observed between PRA and aldosterone in SR subjects. In contrast, only hypertensive subjects showed a marked fall in PRA after consuming HSD (1.299 ± 0.904 vs. 0.593 ± 0.479) among SS subjects. This study demonstrated the different responses of renin and aldosterone in SS and SR subjects based on dietary sodium intake whether or not they had hypertension. © The Author(s) 2014.

Evaluation of Autoantibodies in Patients with Primary and Secondary Sjogren's Syndrome.

PubMed

De Langhe, Ellen; Bossuyt, Xavier; Shen, Long; Malyavantham, Kishore; Ambrus, Julian L; Suresh, Lakshmanan

2017-01-01

Antibodies to salivary gland protein 1 (SP1), carbonic anhydrase 6 (CA6) and parotid secretory protein (PSP) were discovered in an animal model of Sjogren's syndrome (SS). Their expression was noted in patients with SS, especially those with lower focus scores on lip biopsies and those with early disease lacking antibodies to Ro and La. The current studies evaluated these autoantibodies in patients with long-standing SS expressing high levels of anti-Ro antibodies and in patients with Sjogren's syndrome secondary to systemic lupus erythematosus (SLE), systemic sclerosis (SSc) and mixed connective tissue disease (MCTD). Sera were obtained from patients and evaluated by ELISA for IgG, IgA and IgM antibodies to SP1, CA6 and PSP. IgA anti-CA6 antibodies were noted in 38% of these patients, but anti-SP1, CA6 and PSP IgM or IgG antibodies were identified only in a minority of patients. In patients with secondary SS, antibodies to SP1/CA6/PSP were more sensitive and specific than anti-Ro . While more studies are needed, antibodies to SP1, CA6 and PSP provide valuable markers for the diagnosis of primary and secondary SS, especially early in the course of the disease.

Development and evaluation of an in-house single step loop-mediated isothermal amplification (SS-LAMP) assay for the detection of Mycobacterium tuberculosis complex in sputum samples from Moroccan patients.

PubMed

Bentaleb, El Mehdi; Abid, Mohammed; El Messaoudi, My Driss; Lakssir, Brahim; Ressami, El Mostafa; Amzazi, Saaïd; Sefrioui, Hassan; Ait Benhassou, Hassan

2016-09-27

Tuberculosis (TB) is a major global health problem and remains the leading cause of morbidity and mortality in developing countries. Routinely used TB diagnostic methods, in most endemic areas, are time-consuming, often less-sensitive, expensive and inaccessible to most patients. Therefore, there is an urgent need for the development of early, easy to use and effective diagnosis tools of TB, which can be effectively integrated into resource limited settings, to anticipate the early treatment and limit further spread of the disease. Over the last decade, Loop-mediated isothermal amplification (LAMP) assays have become a powerful tool for rapid diagnosis of infectious diseases because of the simplicity of device requirements. Indeed, LAMP is a simple, quick and cost effective Isothermal Nucleic Acid Amplification diagnostic test (INAAT) that has the potential to be used in TB endemic settings of resource-poor countries. In the present study, we have developed a simple and rapid TB molecular diagnostic test using a Single-Step Loop-mediated isothermal DNA amplification (SS-LAMP) method for the detection of Mycobacterium tuberculosis complex (MTBC) strains, with a simplified sample preparation procedure, eliminating DNA extraction prior to LAMP amplification, DNA initial denaturation and enzymatic inactivation steps during the amplification process. To perform our in-house SS-LAMP assay, a set of six specific primers was specifically designed to recognize eight distinct regions on the MTBC species-specific repetitive insertion sequence 6110 (IS6110). The amplification of the targeted DNA was carried out under isothermal conditions at 65 °C within 1 h. Our protocol was firstly optimized using 60 of confirmed MTBC isolates and a recombinant pGEMeasy-IS6110 vector for sensitivity testing. Thereafter, the assay was evaluated on liquefied sputum specimens collected from 157 Moroccan patients suspected of having TB. Our SS-LAMP developed assay was able to detect MTBC DNA directly from liquefied sputum samples without any prior DNA extraction, denaturation nor the final enzymatic inactivation step. When compared to routinely used Löwenstein Jensen (LJ) Culture method, our SS-LAMP assay is rapid and showed specificity and sensitivity of 99.14 % and 82.93 % respectively which are within the international standards. In addition, the limit of detection of our assay was found to be as little as 10 copies of bacterial DNA. To our knowledge, this is the first study using a single step LAMP (SS-LAMP) procedure as a rapid, easy to perform and cost effective testing for TB early detection. This innovative assay could be suitable for low-income countries with restricted health equipment facilities.

Cloning, characterisation and comparative analysis of a starch synthase IV gene in wheat: functional and evolutionary implications

PubMed Central

Leterrier, Marina; Holappa, Lynn D; Broglie, Karen E; Beckles, Diane M

2008-01-01

Background Starch is of great importance to humans as a food and biomaterial, and the amount and structure of starch made in plants is determined in part by starch synthase (SS) activity. Five SS isoforms, SSI, II, III, IV and Granule Bound SSI, have been identified, each with a unique catalytic role in starch synthesis. The basic mode of action of SSs is known; however our knowledge of several aspects of SS enzymology at the structural and mechanistic level is incomplete. To gain a better understanding of the differences in SS sequences that underscore their specificity, the previously uncharacterised SSIVb from wheat was cloned and extensive bioinformatics analyses of this and other SSs sequences were done. Results The wheat SSIV cDNA is most similar to rice SSIVb with which it shows synteny and shares a similar exon-intron arrangement. The wheat SSIVb gene was preferentially expressed in leaf and was not regulated by a circadian clock. Phylogenetic analysis showed that in plants, SSIV is closely related to SSIII, while SSI, SSII and Granule Bound SSI clustered together and distinctions between the two groups can be made at the genetic level and included chromosomal location and intron conservation. Further, identified differences at the amino acid level in their glycosyltransferase domains, predicted secondary structures, global conformations and conserved residues might be indicative of intragroup functional associations. Conclusion Based on bioinformatics analysis of the catalytic region of 36 SSs and 3 glycogen synthases (GSs), it is suggested that the valine residue in the highly conserved K-X-G-G-L motif in SSIII and SSIV may be a determining feature of primer specificity of these SSs as compared to GBSSI, SSI and SSII. In GBSSI, the Ile485 residue may partially explain that enzyme's unique catalytic features. The flexible 380s Loop in the starch catalytic domain may be important in defining the specificity of action for each different SS and the G-X-G in motif VI could define SSIV and SSIII action particularly. PMID:18826586

Corrosion resistance of MCrAlX coatings in a molten chloride for thermal storage in concentrating solar power applications

DOE PAGES

Gomez-Vidal, Judith C.

2017-09-18

Corrosion evaluations of Incoloy 800 H (In800H) and stainless steel AISI 310 (310SS), in bare and coated conditions, were performed in 34.42 wt% NaCl – 55.47 wt% KCl at 700 °C in a nitrogen atmosphere. This NaCl–KCl composition has a melting point of 657 °C, which makes it suitable for latent-heat thermal energy storage in concentrating solar power applications. Several nickel-based MCrAlX coatings were tested, where M = Ni and/or Co and X = Y, Ta, Hf, and/or Si. Electrochemical testing was carried out to determine corrosion rates. The bare In800H and 310SS alloys corroded rapidly (~2500 and 4500 µm/yr,more » respectively, assuming uniform corrosion). Concentrating solar power plants need containment materials with a lifetime of at least 30 years; thus, these corrosion rates are excessive. Corrosion mitigation approaches are being investigated to obtain degradation on the order of 20 µm/yr or lower. The lowest corrosion rate of 190 µm/yr was obtained for atmospheric plasma spray NiCoCrAlY coatings pre-oxidized in air at 900 °C for 24 h with a heating/cooling rate of 0.5 °C/min. Metallographic characterization of the corroded surfaces showed that the formation of a uniform thin alumina scale before exposure to the molten chloride system considerably reduced the corrosion of the alloy. However, the rates of corrosion determined herein are considerable, highlighting the relevance of testing materials durability in solar power applications.« less

Corrosion resistance of MCrAlX coatings in a molten chloride for thermal storage in concentrating solar power applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gomez-Vidal, Judith C.

Corrosion evaluations of Incoloy 800 H (In800H) and stainless steel AISI 310 (310SS), in bare and coated conditions, were performed in 34.42 wt% NaCl – 55.47 wt% KCl at 700 °C in a nitrogen atmosphere. This NaCl–KCl composition has a melting point of 657 °C, which makes it suitable for latent-heat thermal energy storage in concentrating solar power applications. Several nickel-based MCrAlX coatings were tested, where M = Ni and/or Co and X = Y, Ta, Hf, and/or Si. Electrochemical testing was carried out to determine corrosion rates. The bare In800H and 310SS alloys corroded rapidly (~2500 and 4500 µm/yr,more » respectively, assuming uniform corrosion). Concentrating solar power plants need containment materials with a lifetime of at least 30 years; thus, these corrosion rates are excessive. Corrosion mitigation approaches are being investigated to obtain degradation on the order of 20 µm/yr or lower. The lowest corrosion rate of 190 µm/yr was obtained for atmospheric plasma spray NiCoCrAlY coatings pre-oxidized in air at 900 °C for 24 h with a heating/cooling rate of 0.5 °C/min. Metallographic characterization of the corroded surfaces showed that the formation of a uniform thin alumina scale before exposure to the molten chloride system considerably reduced the corrosion of the alloy. However, the rates of corrosion determined herein are considerable, highlighting the relevance of testing materials durability in solar power applications.« less

Effects of instrumentation time on microleakage of resin-modified glass ionomer cements.

PubMed

Yap, Adrian U J; Yeo, Egwin J C; Yap, W Y; Ong, Debbie S B; Tan, Jane W S

2003-01-01

This study investigated the effect of instrumentation time on the microleakage of resin-modified glass ionomer cements (RMGICs). Class V cavities were prepared on buccal and lingual/ palatal surfaces of 64 freshly extracted non-carious premolars. The cavities on each tooth were restored with Fuji II LC (FT [GC]) and Photac-Fil Quick (PF [3M-ESPE]). The restored teeth were randomly divided into two groups of 32 teeth. Finishing/polishing was done immediately after light-polymerization in one group and was delayed for one week in the other group. The following finishing/polishing systems were evaluated: (a) Robot Carbides (RC); (b) SuperSnap (SS); (c) OneGloss (OG) and (d) CompoSite Polishers (CS). The sample size for each instrumentation time, material and finishing/polishing system combination was 8. Storage medium for both immediate and delayed instrumentation groups was distilled water at 37 degrees C during the hiatus period. The teeth were subsequently subjected to dye penetration testing (0.5% basic fushcin), sectioned and scored. Data were analyzed using Kruskal-Wallis and Mann-Whitney U tests at significance level 0.05. For PF, significant difference in enamel leakage was observed between immediate and delayed instrumentation with SS and CS. Significant differences in dentin leakage were also observed between the two instrumentation times for SS. For FT, significant differences in leakage between instrumentation times were observed only in dentin and with RC. Where significant differences in dye penetration scores existed, delayed finishing/polishing resulted in less microleakage.

Mechanical Strength of the Side-to-Side Versus Pulvertaft Weave Tendon Repair

PubMed Central

Brown, Stephen H. M.; Hentzen, Eric R.; Kwan, Alan; Ward, Samuel R.; Fridén, Jan; Lieber, Richard L.

2010-01-01

Purpose The side-to-side (SS) tendon suture technique was designed to function as a repair that permits immediate post-operative activation and mobilization of a transferred muscle. This study was designed to test the strength and stiffness of the SS technique against a variation of the Pulvertaft (PT) repair technique. Methods Flexor digitorum superficialis (FDS) and flexor digitorum profundus (FDP) tendons were harvested from four fresh cadavers and used as a model system. Seven SS and six PT repairs were performed using the FDS as the donor and the FDP as the recipient tendon. For SS repairs, the FDS was woven through one incision in the FDP, and was joined with four cross-stitch running sutures down both sides, and one double-loop suture at each tendon free end; for PT repairs, FDS was woven through three incisions in FDP, joined with a double-loop suture at both ends of the overlap, and four evenly spaced mattress sutures between the ends. Tendon repairs were placed in a tensile testing machine, pre-conditioned and tested to failure. Results There were no statistically significant differences in cross-sectional area (p=0.99) or initial length (p=0.93) between SS and PT repairs. Therefore, all comparisons between methods were made using measures of loads and deformations, rather than stresses and strains.. All failures occurred in the repair region, rather than at the clamps. However, failure mechanisms were different between the two techniques—PT repairs failed by the suture knots either slipping or pulling through the tendon material, followed by the FDS tendon pulling through the FDP tendon; SS repairs failed by shearing of fibers within the FDS. Load at first failure (p < 0.01), ultimate load (p < 0.001), and repair stiffness (p < 0.05) were all significantly different between SS and PT techniques; in all cases the mean value for SS was higher than for PT. Discussion The SS repair, using a cross-stitch suture technique, was significantly stronger and stiffer compared to the PT repair using a mattress suture technique. This suggests that using SS repairs could enable patients to load the repair soon after surgery. Ultimately, this should reduce the risk of developing adhesions and result in improved functional outcome and fewer complications in the acute post-operative period. Future work will address the specific mechanisms (for example, suture-throw technique, tendon-weave technique) that underlie the improved strength and stiffness of the SS repair. PMID:20223604

Competitive regulation of alternative splicing and alternative polyadenylation by hnRNP H and CstF64 determines acetylcholinesterase isoforms

PubMed Central

Nazim, Mohammad; Masuda, Akio; Rahman, Mohammad Alinoor; Nasrin, Farhana; Takeda, Jun-ichi; Ohe, Kenji; Ohkawara, Bisei; Ito, Mikako

2017-01-01

Abstract Acetylcholinesterase (AChE), encoded by the ACHE gene, hydrolyzes the neurotransmitter acetylcholine to terminate synaptic transmission. Alternative splicing close to the 3΄ end generates three distinct isoforms of AChET, AChEH and AChER. We found that hnRNP H binds to two specific G-runs in exon 5a of human ACHE and activates the distal alternative 3΄ splice site (ss) between exons 5a and 5b to generate AChET. Specific effect of hnRNP H was corroborated by siRNA-mediated knockdown and artificial tethering of hnRNP H. Furthermore, hnRNP H competes for binding of CstF64 to the overlapping binding sites in exon 5a, and suppresses the selection of a cryptic polyadenylation site (PAS), which additionally ensures transcription of the distal 3΄ ss required for the generation of AChET. Expression levels of hnRNP H were positively correlated with the proportions of the AChET isoform in three different cell lines. HnRNP H thus critically generates AChET by enhancing the distal 3΄ ss and by suppressing the cryptic PAS. Global analysis of CLIP-seq and RNA-seq also revealed that hnRNP H competitively regulates alternative 3΄ ss and alternative PAS in other genes. We propose that hnRNP H is an essential factor that competitively regulates alternative splicing and alternative polyadenylation. PMID:28180311

Competitive regulation of alternative splicing and alternative polyadenylation by hnRNP H and CstF64 determines acetylcholinesterase isoforms.

PubMed

Nazim, Mohammad; Masuda, Akio; Rahman, Mohammad Alinoor; Nasrin, Farhana; Takeda, Jun-Ichi; Ohe, Kenji; Ohkawara, Bisei; Ito, Mikako; Ohno, Kinji

2017-02-17

Acetylcholinesterase (AChE), encoded by the ACHE gene, hydrolyzes the neurotransmitter acetylcholine to terminate synaptic transmission. Alternative splicing close to the 3΄ end generates three distinct isoforms of AChET, AChEH and AChER. We found that hnRNP H binds to two specific G-runs in exon 5a of human ACHE and activates the distal alternative 3΄ splice site (ss) between exons 5a and 5b to generate AChET. Specific effect of hnRNP H was corroborated by siRNA-mediated knockdown and artificial tethering of hnRNP H. Furthermore, hnRNP H competes for binding of CstF64 to the overlapping binding sites in exon 5a, and suppresses the selection of a cryptic polyadenylation site (PAS), which additionally ensures transcription of the distal 3΄ ss required for the generation of AChET. Expression levels of hnRNP H were positively correlated with the proportions of the AChET isoform in three different cell lines. HnRNP H thus critically generates AChET by enhancing the distal 3΄ ss and by suppressing the cryptic PAS. Global analysis of CLIP-seq and RNA-seq also revealed that hnRNP H competitively regulates alternative 3΄ ss and alternative PAS in other genes. We propose that hnRNP H is an essential factor that competitively regulates alternative splicing and alternative polyadenylation.

The nature of the force-induced conformation transition of dsDNA studied by using single molecule force spectroscopy.

PubMed

Liu, Ningning; Bu, Tianjia; Song, Yu; Zhang, Wei; Li, Jinjing; Zhang, Wenke; Shen, Jiacong; Li, Hongbin

2010-06-15

Single-stranded DNA binding proteins (SSB) interact with single-stranded DNA (ssDNA) specifically. Taking advantage of this character, we have employed Bacillus subtilis SSB protein to investigate the nature of force-induced conformation transition of double-stranded DNA (dsDNA) by using AFM-based single molecule force spectroscopy (SMFS) technique. Our results show that, when a dsDNA is stretched beyond its contour length, the dsDNA is partially melted, producing some ssDNA segments which can be captured by SSB proteins. We have also systematically investigated the effects of stretching length, waiting time, and salt concentration on the conformation transition of dsDNA and SSB-ssDNA interactions, respectively. Furthermore, the effect of proflavine, a DNA intercalator, on the SSB-DNA interactions has been investigated, and the results indicate that the proflavine-saturated dsDNA can be stabilized to the extent that the dsDNA will no longer melt into ssDNA under the mechanical force even up to 150 pN, and no SSB-DNA interactions are detectable.

Efficient performance and the microbial community changes of submerged anaerobic membrane bioreactor in treatment of sewage containing cellulose suspended solid at 25°C.

PubMed

Watanabe, Ryoya; Nie, Yulun; Takahashi, Shintaro; Wakahara, Shinichiro; Li, Yu-You

2016-09-01

Influence of cellulose as suspended solid (SS) on the performance of submerged anaerobic membrane bioreactor (SAnMBR) was evaluated at 25°C using two types of synthetic sewage (SS contained or not). During the 110days operation, COD and BOD removal, CH4 gas recovery and cellulose accumulation were investigated in detail. The influence of cellulose as SS in sewage on the SAnMBR performance was not significant at HRT longer than12h and 65-72% of the influent COD was recovered as methane gas at HRT of 12h. At HRT of 6h, the quality of effluent got worse and the accumulation of cellulose was found in reactor. 16S rRNA analysis revealed that the microbial diversity distribution including Archaea and Bacteria changed due to the addition of SS in sewage and specific microbe for cellulose degradation such as Proteobacteria was detected. Sludge in SAnMBR could acclimate to characteristics of sewage by self-adaptation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Composition of the Active Fleet, U.S. Navy, 1961-1985.

DTIC Science & Technology

1980-12-01

Amberjack SS 324 Blenny SS 523 Grampus SS 331 Bugara SS 524 Pickerel SS 337 Carbonero SS 525 Grenadier SS 338 Carp SS 550 Barracuda SS 339 Catfish SS...LKA 57 Bordelon DD 881 Carbonero SS 337 Borie DD 704 Carl Vinson CVN 70 Boston CA 69 Caroline County LST 525 Boston SSN 703 Caron DD 970 Botetourt LPA

Identification of cytotoxic agents disrupting synovial sarcoma oncoprotein interactions by proximity ligation assay.

PubMed

Laporte, Aimée N; Ji, Jennifer X; Ma, Limin; Nielsen, Torsten O; Brodin, Bertha A

2016-06-07

Conventional cytotoxic therapies for synovial sarcoma provide limited benefit. Drugs specifically targeting the product of its driver translocation are currently unavailable, in part because the SS18-SSX oncoprotein functions via aberrant interactions within multiprotein complexes. Proximity ligation assay is a recently-developed method that assesses protein-protein interactions in situ. Here we report use of the proximity ligation assay to confirm the oncogenic association of SS18-SSX with its co-factor TLE1 in multiple human synovial sarcoma cell lines and in surgically-excised human tumor tissue. SS18-SSX/TLE1 interactions are disrupted by class I HDAC inhibitors and novel small molecule inhibitors. This assay can be applied in a high-throughput format for drug discovery in fusion-oncoprotein associated cancers where key effector partners are known.

Analysis of activation and shutdown contact dose rate for EAST neutral beam port

NASA Astrophysics Data System (ADS)

Chen, Yuqing; Wang, Ji; Zhong, Guoqiang; Li, Jun; Wang, Jinfang; Xie, Yahong; Wu, Bin; Hu, Chundong

2017-12-01

For the safe operation and maintenance of neutral beam injector (NBI), specific activity and shutdown contact dose rate of the sample material SS316 are estimated around the experimental advanced superconducting tokamak (EAST) neutral beam port. Firstly, the neutron emission intensity is calculated by TRANSP code while the neutral beam is co-injected to EAST. Secondly, the neutron activation and shutdown contact dose rates for the neutral beam sample materials SS316 are derived by the Monte Carlo code MCNP and the inventory code FISPACT-2007. The simulations indicate that the primary radioactive nuclides of SS316 are 58Co and 54Mn. The peak contact dose rate is 8.52 × 10-6 Sv/h after EAST shutdown one second. That is under the International Thermonuclear Experimental Reactor (ITER) design values 1 × 10-5 Sv/h.

Linguistic nonimmediacy and self-presentation.

PubMed

Conville, R L

1975-07-01

It has been previously shown that Ss accurately infer communicators' levels of negative effect on the basis of communicators' levels of linguistic nonimmediacy (the degree of verbal indirectness with which a communicator refers to himself or to that about which he communicates). It was hypothesized that Ss would also rely on communicators' levels of linguistic nonimmediacy for impression formation, specifically that Ss would perceive communicators using lower levels of linguistic nonimmediacy as more authoritative and as having a more positive character than communicators using higher levels of linguistic nonimmediacy. The hypothesis was partially confirmed in a study of 12 college students who rated samples of student speeches by means of McCroskey's impression formation instrument for public speakers. The results were discussed in terms of the role of language in self-presentation and the role of interpretative procedures in social interaction.

Knowledge Insufficient: The Management of Haemoglobin SC Disease

PubMed Central

Pecker, Lydia H.; Schaefer, Beverly A.; Luchtman-Jones, Lori

2016-01-01

Although haemoglobin SC (HbSC) accounts for 30% of sickle cell disease (SCD) in the United States and United Kingdom, evidence-based guidelines for genotype specific management are lacking. The unique pathology of HbSC disease is complex, characterized by erythrocyte dehydration, intracellular sickling and increased blood viscosity. The evaluation and treatment of patients with HbSC is largely inferred from studies of SCD consisting mostly of haemoglobin SS (HbSS) patients. These studies are underpowered to allow definitive conclusions about HbSC. We review the pathophysiology of HbSC disease, including known and potential differences between HbSS and HbSC, and highlight knowledge gaps in HbSC disease management. Clinical and translational research is needed to develop targeted treatments and to validate management recommendations for efficacy, safety and impact on quality of life for people with HbSC. PMID:27982424

The design and networking of dynamic satellite constellations for global mobile communication systems

NASA Technical Reports Server (NTRS)

Cullen, Cionaith J.; Benedicto, Xavier; Tafazolli, Rahim; Evans, Barry

1993-01-01

Various design factors for mobile satellite systems, whose aim is to provide worldwide voice and data communications to users with hand-held terminals, are examined. Two network segments are identified - the ground segment (GS) and the space segment (SS) - and are seen to be highly dependent on each other. The overall architecture must therefore be adapted to both of these segments, rather than each being optimized according to its own criteria. Terrestrial networks are grouped and called the terrestrial segment (TS). In the SS, of fundamental importance is the constellation altitude. The effect of the altitude on decisions such as constellation design choice and on network aspects like call handover statistics are fundamental. Orbit resonance is introduced and referred to throughout. It is specifically examined for its useful properties relating to GS/SS connectivities.

Noninvasive characterisation of foot reflexology areas by swept source-optical coherence tomography in patients with low back pain.

PubMed

Dalal, Krishna; Elanchezhiyan, D; Das, Raunak; Dalal, Devjyoti; Pandey, Ravindra Mohan; Chatterjee, Subhamoy; Upadhyay, Ashish Datt; Maran, V Bharathi; Chatterjee, Jyotirmoy

2013-01-01

Objective. When exploring the scientific basis of reflexology techniques, elucidation of the surface and subsurface features of reflexology areas (RAs) is crucial. In this study, the subcutaneous features of RAs related to the lumbar vertebrae were evaluated by swept source-optical coherence tomography (SS-OCT) in subjects with and without low back pain (LBP). Methods. Volunteers without LBP (n = 6 (male : female = 1 : 1)) and subjects with LBP (n = 15 (male : female = 2 : 3)) were clinically examined in terms of skin colour (visual perception), localised tenderness (visual analogue scale) and structural as well as optical attributes as per SS-OCT. From each subject, 6 optical tomograms were recorded from equidistant transverse planes along the longitudinal axis of the RAs, and from each tomogram, 25 different spatial locations were considered for recording SS-OCT image attributes. The images were analysed with respect to the optical intensity distributions and thicknesses of different skin layers by using AxioVision Rel. 4.8.2 software. The SS-OCT images could be categorised into 4 pathological grades (i.e., 0, 1, 2, and 3) according to distinctness in the visible skin layers. Results. Three specific grades for abnormalities in SS-OCT images were identified considering gradual loss of distinctness and increase in luminosity of skin layers. Almost 90.05% subjects were of mixed type having predominance in certain grades. Conclusion. The skin SS-OCT system demonstrated a definite association of the surface features of healthy/unhealthy RAs with cutaneous features and the clinical status of the lumbar vertebrae.

Noninvasive Characterisation of Foot Reflexology Areas by Swept Source-Optical Coherence Tomography in Patients with Low Back Pain

PubMed Central

Dalal, Krishna; Elanchezhiyan, D.; Das, Raunak; Dalal, Devjyoti; Pandey, Ravindra Mohan; Chatterjee, Subhamoy; Upadhyay, Ashish Datt; Maran, V. Bharathi; Chatterjee, Jyotirmoy

2013-01-01

Objective. When exploring the scientific basis of reflexology techniques, elucidation of the surface and subsurface features of reflexology areas (RAs) is crucial. In this study, the subcutaneous features of RAs related to the lumbar vertebrae were evaluated by swept source-optical coherence tomography (SS-OCT) in subjects with and without low back pain (LBP). Methods. Volunteers without LBP (n = 6 (male : female = 1 : 1)) and subjects with LBP (n = 15 (male : female = 2 : 3)) were clinically examined in terms of skin colour (visual perception), localised tenderness (visual analogue scale) and structural as well as optical attributes as per SS-OCT. From each subject, 6 optical tomograms were recorded from equidistant transverse planes along the longitudinal axis of the RAs, and from each tomogram, 25 different spatial locations were considered for recording SS-OCT image attributes. The images were analysed with respect to the optical intensity distributions and thicknesses of different skin layers by using AxioVision Rel. 4.8.2 software. The SS-OCT images could be categorised into 4 pathological grades (i.e., 0, 1, 2, and 3) according to distinctness in the visible skin layers. Results. Three specific grades for abnormalities in SS-OCT images were identified considering gradual loss of distinctness and increase in luminosity of skin layers. Almost 90.05% subjects were of mixed type having predominance in certain grades. Conclusion. The skin SS-OCT system demonstrated a definite association of the surface features of healthy/unhealthy RAs with cutaneous features and the clinical status of the lumbar vertebrae. PMID:23662156

Do Pre-Existing Diabetes Social Support or Depressive Symptoms Influence the Effectiveness of a Diabetes Management Intervention?

PubMed Central

Rosland, Ann-Marie; Kieffer, Edith; Spencer, Michael; Sinco, Brandy; Palmisano, Gloria; Valerio, Melissa; Nicklett, Emily; Heisler, Michele

2015-01-01

Objective Examine influences of diabetes-specific social support (D-SS) and depressive symptoms on glycemic control over time, among adults randomized to a diabetes self-management education and support (DSME/S) intervention or usual care. Methods Data were from 108 African-American and Latino participants in a six-month intervention trial. Multivariable linear regression models assessed associations between baseline D-SS from family and friends and depressive symptoms with changes in HbA1c. We then examined whether baseline D-SS or depression moderated intervention-associated effects on HbA1c. Results Higher baseline D-SS was associated with larger improvements in HbA1c (adjusted ΔHbA1c -0.39% for each +1-point D-SS, p=0.02), independent of intervention-associated HbA1c decreases. Baseline depressive symptoms had no significant association with subsequent HbA1c change. Neither D-SS nor depression moderated intervention-associated effects on HbA1c. Conclusions and Practice Implications Diabetes self-management education and support programs have potential to improve glycemic control for participants starting with varying levels of social support and depressive symptoms. Participants starting with more support for diabetes management from family and friends improved HbA1c significantly more over six months than those with less support, independent of additional significant DSME/S intervention-associated HbA1c improvements. Social support from family and friends may improve glycemic control in ways additive to DSME/S. PMID:26234800

Metabolic half-life of somatostatin and peptidase activities are altered in Alzheimer's disease.

PubMed

Weber, S J; Louis, R B; Trombley, L; Bissette, G; Davies, P; Davis, T P

1992-01-01

Several reports have described decreased immunoreactive somatostatin levels in specific regions of post-mortem brain tissue from patients diagnosed with senile dementia of the Alzheimer type (SDAT). In an attempt to determine if the metabolism of somatostatin is also altered as a result of SDAT, we examined the regional metabolic half-life of somatostatin-28 (SS-28) and somatostatin-14 (SS-14). The activity of the following peptidases was also determined: neutral endopeptidase E.C. 3.4.24.11; metalloendopeptidase E.C. 3.4.24.15; carboxypeptidase E (E.C. 3.4.17.10); and trypsin-like serine protease. The metabolic half-life of SS-28 was significantly reduced in post-mortem Brodmann Area 22 of SDAT tissue. This decrease in SS-28 metabolic half-life was correlated with a significant increase in trypsin-like serine protease activity in the same SDAT brain region. The formation rate of SS-14 from SS-28 incubated with Brodmann Area 22 homogenates was also increased in SDAT tissues as compared to controls. A regional variation in neutral endopeptidase E.C. 3.4.24.11 was also noted in both controls and SDAT samples. Although postmortem intervals of samples varied significantly, no effect was seen on any biochemical parameter measured. Results from this study provide evidence that a correlation can be made between changes in metabolic half-life somatostatin and alterations in neuropeptidase activities due to SDAT. As these data show alterations in both proteolytic metabolism and peptidase activities, many other biologically active peptide substrates could also be affected in SDAT.

Navigational Style Influences Eye Movement Pattern during Exploration and Learning of an Environmental Map

PubMed Central

Piccardi, Laura; De Luca, Maria; Nori, Raffaella; Palermo, Liana; Iachini, Fabiana; Guariglia, Cecilia

2016-01-01

During navigation people may adopt three different spatial styles (i.e., Landmark, Route, and Survey). Landmark style (LS) people are able to recall familiar landmarks but cannot combine them with directional information; Route style (RS) people connect landmarks to each other using egocentric information about direction; Survey style (SS) people use a map-like representation of the environment. SS individuals generally navigate better than LS and RS people. Fifty-one college students (20 LS; 17 RS, and 14 SS) took part in the experiment. The spatial cognitive style (SCS) was assessed by means of the SCS test; participants then had to learn a schematic map of a city, and after 5 min had to recall the path depicted on it. During the learning and delayed recall phases, eye-movements were recorded. Our intent was to investigate whether there is a peculiar way to explore an environmental map related to the individual’s spatial style. Results support the presence of differences in the strategy used by the three spatial styles for learning the path and its delayed recall. Specifically, LS individuals produced a greater number of fixations of short duration, while the opposite eye movement pattern characterized SS individuals. Moreover, SS individuals showed a more spread and comprehensive explorative pattern of the map, while LS individuals focused their exploration on the path and related targets. RS individuals showed a pattern of exploration at a level of proficiency between LS and SS individuals. We discuss the clinical and anatomical implications of our data. PMID:27445735

The therapy of Sjogren's syndrome: a review.

PubMed

Coaccioli, S; Giuliani, M; Puxeddu, A

2007-01-01

The Sjogren's syndrome (SS) is an chronic inflammatory autoimmune disease of the exocrine glands as well as of internal apparatus. The therapy of exocrinopathy is represented by parasympathomimetic drugs such as pilocarpine and cevimeline. The therapy of systemic manifestations, actually is represented by the inhibitors of TNF alfa, as well as leflunomide, methotrexate and cyclosporine-A, but the results are quite insufficient and disappointed. In order to the involvement of B-cell function in the pathogenesis of SS, one of the most important option in the future should be specific inhibitors of that cells.

[Willingness to implement mental health measures among small-scale enterprise employers in Ohta ward, Tokyo, Japan].

PubMed

Ikeda, Tomoko; Nakata, Akinori; Kobori, Shun-ichi; Hojo, Minoru; Sugishita, Chieko

2002-09-01

Due to the increase in mental health problems among Japanese workers in recent years, effective approaches to address these problems are of growing concern. Although such an effort is now under way in largescale enterprises (LSEs), small-scale enterprises (SSEs) are lagging behind LSEs for a number of reasons. In the present study, to know the reason, the presidents of 263 SSEs (fewer than 50 employees) in the Ohta ward of Tokyo were surveyed with a self-administered questionnaire from October 1999 to March 2000 (response rate, 51.0%). The main business types were manufacturing (71.2%), transportation & storage (6.1%), and construction (5.3%). The results revealed that employers attribute the mental health problems of employees to "Job content/Aptitude for job (78.6%)", "Communication among employees (71.0%)", "Physical problems/Illness (50.4%)", "Family problems (33.6%)". These results are very similar to those obtained in the same enterprises employees survey in 1996, suggesting that employers perceive the factors responsible for employees' mental health problems with substantial accuracy. Sixty-nine point five percent of the employers answered that they need mental health measures for employees. And 62.7% of employers agreed to take mental health measures in their enterprises. Taken together, it is considered that employers are willing to improve their employees' mental health problems. Nevertheless, 95% of employers are doing nothing to improve the situation. The major reasons cited were 1) Cannot obtain a consultant or counselor (44.8%), 2) Lack of time (43.1%), 3) Manpower shortage (41.4%), 4) Difficulty in ensuring employees' privacy (36.2%), and 5) Lack of financial resources (30.2%). The results of the present study suggest that perception of the mental health problems among employers and employees of SSEs in the Ohta area were close to each other. Effective strategies are needed to improve mental health problems in SSEs.

About the structural role of disulfide bridges in serum albumins: evidence from protein simulated unfolding.

PubMed

Paris, Guillaume; Kraszewski, Sebastian; Ramseyer, Christophe; Enescu, Mironel

2012-11-01

The role of the 17 disulfide (S-S) bridges in preserving the native conformation of human serum albumin (HSA) is investigated by performing classical molecular dynamics (MD) simulations on protein structures with intact and, respectively, reduced S-S bridges. The thermal unfolding simulations predict a clear destabilization of the protein secondary structure upon reduction of the S-S bridges as well as a significant distortion of the tertiary structure that is revealed by the changes in the protein native contacts fraction. The effect of the S-S bridges reduction on the protein compactness was tested by calculating Gibbs free energy profiles with respect to the protein gyration radius. The theoretical results obtained using the OPLS-AA and the AMBER ff03 force fields are in agreement with the available experimental data. Beyond the validation of the simulation method, the results here reported provide new insights into the mechanism of the protein reductive/oxidative unfolding/folding processes. It is predicted that in the native conformation of the protein, the thiol (-SH) groups belonging to the same reduced S-S bridge are located in potential wells that maintain them in contact. The -SH pairs can be dispatched by specific conformational transitions of the peptide chain located in the neighborhood of the cysteine residues. Copyright © 2012 Wiley Periodicals, Inc.

Salivary dysfunction associated with systemic diseases: systematic review and clinical management recommendations.

PubMed

von Bültzingslöwen, Inger; Sollecito, Thomas P; Fox, Philip C; Daniels, Troy; Jonsson, Roland; Lockhart, Peter B; Wray, David; Brennan, Michael T; Carrozzo, Marco; Gandera, Beatrice; Fujibayashi, Takashi; Navazesh, Mahvash; Rhodus, Nelson L; Schiødt, Morten

2007-03-01

The objective of this study was to identify systemic diseases associated with hyposalivation and xerostomia and develop evidence-based management recommendations for hyposalivation/xerostomia. Literature searches covered the English language medical literature from 1966 to 2005. An evidence-based review process was applied to management studies published from 2002 to 2005. Several systemic diseases were identified. From studies published 2002 to 2005, 15 were identified as high-quality studies and were used to support management recommendations: pilocarpine and cevimeline are recommended for treating hyposalivation and xerostomia in primary and secondary Sjögren's syndrome (SS). IFN-alpha lozenges may enhance saliva flow in primary SS patients. Anti-TNF-alpha agents, such as infliximab or etanercept, are not recommended to treat hyposalivation in SS. Dehydroepiandrosterone is not recommended to relieve hyposalivation or xerostomia in primary SS. There was not enough evidence to support any recommendations for the use of local stimulants, lubricants, and protectants for hyposalivation/xerostomia. However, professional judgment and patient preferences may support the use of a specific product for an individual patient. These evidence-based management recommendations should guide the clinician's management decisions for patients with salivary dysfunction related to systemic disease. Future treatment strategies may include new formulations of existing drugs, e.g., local application of pilocarpine. Recent discoveries on gene expression and a better understanding of the etiopathogenesis of SS may open new treatment options in the future.

Zinc-finger Nuclease-induced Gene Repair With Oligodeoxynucleotides: Wanted and Unwanted Target Locus Modifications

PubMed Central

Radecke, Sarah; Radecke, Frank; Cathomen, Toni; Schwarz, Klaus

2010-01-01

Correcting a mutated gene directly at its endogenous locus represents an alternative to gene therapy protocols based on viral vectors with their risk of insertional mutagenesis. When solely a single-stranded oligodeoxynucleotide (ssODN) is used as a repair matrix, the efficiency of the targeted gene correction is low. However, as shown with the homing endonuclease I-SceI, ssODN-mediated gene correction can be enhanced by concomitantly inducing a DNA double-strand break (DSB) close to the mutation. Because I-SceI is hardly adjustable to cut at any desired position in the human genome, here, customizable zinc-finger nucleases (ZFNs) were used to stimulate ssODN-mediated repair of a mutated single-copy reporter locus stably integrated into human embryonic kidney-293 cells. The ZFNs induced faithful gene repair at a frequency of 0.16%. Six times more often, ZFN-induced DSBs were found to be modified by unfaithful addition of ssODN between the termini and about 60 times more often by nonhomologous end joining-related deletions and insertions. Additionally, ZFN off-target activity based on binding mismatch sites at the locus of interest was detected in in vitro cleavage assays and also in chromosomal DNA isolated from treated cells. Therefore, the specificity of ZFN-induced ssODN-mediated gene repair needs to be improved, especially regarding clinical applications. PMID:20068556

Characterization of the Interaction between the Salmonella Type III Secretion System Tip Protein SipD and the Needle Protein PrgI by Paramagnetic Relaxation Enhancement*

PubMed Central

Rathinavelan, Thenmalarchelvi; Tang, Chun; De Guzman, Roberto N.

2011-01-01

Many Gram-negative bacteria that cause major diseases and mortality worldwide require the type III secretion system (T3SS) to inject virulence proteins into their hosts and cause infections. A structural component of the T3SS is the needle apparatus, which consists of a base, an external needle, and a tip complex. In Salmonella typhimurium, the external needle is assembled by the polymerization of the needle protein PrgI. On top of this needle sits a tip complex, which is partly formed by the tip protein SipD. How SipD interacts with PrgI during the assembly of the T3SS needle apparatus remains unknown. The central region of PrgI forms an α-helical hairpin, whereas SipD has a long central coiled-coil, which is a defining structural feature of other T3SS tip proteins as well. Using NMR paramagnetic relaxation enhancement, we have identified a specific region on the SipD coiled-coil that interacts directly with PrgI. We present a model of how SipD might dock at the tip of the needle based on our paramagnetic relaxation enhancement results, thus offering new insight about the mechanism of assembly of the T3SS needle apparatus. PMID:21138848

Development of synthetic selfish elements based on modular nucleases in Drosophila melanogaster

PubMed Central

Simoni, Alekos; Siniscalchi, Carla; Chan, Yuk-Sang; Huen, David S.; Russell, Steven; Windbichler, Nikolai; Crisanti, Andrea

2014-01-01

Selfish genes are DNA elements that increase their rate of genetic transmission at the expense of other genes in the genome and can therefore quickly spread within a population. It has been suggested that selfish elements could be exploited to modify the genome of entire populations for medical and ecological applications. Here we report that transcription activator-like effector nuclease (TALEN) and zinc finger nuclease (ZFN) can be engineered into site-specific synthetic selfish elements (SSEs) and demonstrate their transmission of up to 70% in the Drosophila germline. We show here that SSEs can spread via DNA break-induced homologous recombination, a process known as ‘homing’ similar to that observed for homing endonuclease genes (HEGs), despite their fundamentally different modes of DNA binding and cleavage. We observed that TALEN and ZFN have a reduced capability of secondary homing compared to HEG as their repetitive structure had a negative effect on their genetic stability. The modular architecture of ZFNs and TALENs allows for the rapid design of novel SSEs against specific genomic sequences making them potentially suitable for the genetic engineering of wild-type populations of animals and plants, in applications such as gene replacement or population suppression of pest species. PMID:24803674

Patterns of convexal subarachnoid haemorrhage: clinical, radiological and outcome differences between cerebral amyloid angiopathy and other causes.

PubMed

Calviere, Lionel; Raposo, Nicolas; Cuvinciuc, Victor; Cognard, Christophe; Bonneville, Fabrice; Viguier, Alain

2018-01-01

Cerebral amyloid angiopathy (CAA) is a common aetiology of convexal subarachnoid haemorrhage (cSAH) but little is known about its specific characteristics in comparison with cSAH from other causes. In this study we compared patients with CAA vs. non-CAA-related cSAH. Retrospective review of baseline and follow-up data of consecutive patients admitted with a symptomatic acute cSAH. Sixty-two patients were included (mean age 66.2 ± 14.1 years), of whom 31 with probable CAA. CAA patients presented more frequently with transient symptoms (83.9 vs. 19.3%; p < 0.001) usually without headache (19.0 vs. 58.1%; p = 0.002). In CAA, these were essentially positive sensory disturbance that met the criteria of transient focal neurological episodes (TFNE). CAA was more often associated with cortical superficial siderosis (cSS) (80.6 vs. 0%; p < 0.001) and lobar cerebral microbleeds (83.4 vs. 9%; p < 0.001). During a mean of 22 months of follow-up, recurrent symptomatic cSAH occurred in 4/27 (12.9%) CAA patients and in 0/27 non-CAA patients. Among 40 patients with MRI follow-up, cSAH recurrences were observed in 44% of CAA patients vs. 13.3% of other cases (p = 0.08) and extension of cSS was detected only in CAA (60%) (p < 0.001). Acute cSAH evolved to cSS in 96 and 73.3% of CAA and non-CAA patients, respectively (p = 0.06). CAA differs from other cSAH in having TFNE as a frequent clinical presentation, a high prevalence of cSS and an increased risk of recurrent subarachnoid bleeding. However, evolution from acute cSAH to focal cSS may not be specific to CAA.

Computational prediction of secretion systems and secretomes of Brucella: identification of novel type IV effectors and their interaction with the host.

PubMed

Sankarasubramanian, Jagadesan; Vishnu, Udayakumar S; Dinakaran, Vasudevan; Sridhar, Jayavel; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

2016-01-01

Brucella spp. are facultative intracellular pathogens that cause brucellosis in various mammals including humans. Brucella survive inside the host cells by forming vacuoles and subverting host defence systems. This study was aimed to predict the secretion systems and the secretomes of Brucella spp. from 39 complete genome sequences available in the databases. Furthermore, an attempt was made to identify the type IV secretion effectors and their interactions with host proteins. We predicted the secretion systems of Brucella by the KEGG pathway and SecReT4. Brucella secretomes and type IV effectors (T4SEs) were predicted through genome-wide screening using JVirGel and S4TE, respectively. Protein-protein interactions of Brucella T4SEs with their hosts were analyzed by HPIDB 2.0. Genes coding for Sec and Tat pathways of secretion and type I (T1SS), type IV (T4SS) and type V (T5SS) secretion systems were identified and they are conserved in all the species of Brucella. In addition to the well-known VirB operon coding for the type IV secretion system (T4SS), we have identified the presence of additional genes showing homology with T4SS of other organisms. On the whole, 10.26 to 14.94% of total proteomes were found to be either secreted (secretome) or membrane associated (membrane proteome). Approximately, 1.7 to 3.0% of total proteomes were identified as type IV secretion effectors (T4SEs). Prediction of protein-protein interactions showed 29 and 36 host-pathogen specific interactions between Bos taurus (cattle)-B. abortus and Ovis aries (sheep)-B. melitensis, respectively. Functional characterization of the predicted T4SEs and their interactions with their respective hosts may reveal the secrets of host specificity of Brucella.

Adoption of site-specific variable rate sprinkler irrigation systems

USDA-ARS?s Scientific Manuscript database

More than twenty years of private and public research on site-specific variable-rate sprinkler irrigation (SS-VRI) technology has resulted in limited commercial adoption of the technology. Competing patents, liability and proprietary software have affected industry’s willingness to move into a new t...

Design and Assessment of a Real Time Reverse Transcription-PCR Method to Genotype Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae).

EPA Science Inventory

A real-time, reverse transcription-PCR (RT-qPCR) assay was developed to differentiate the four genogroups of male-specific ssRNA coliphages (FRNA) (family Leviviridae). As FRNA display a trend of source-specificity (human sewage or animal waste) at the genogroup level, this assa...

Predictive score of sarcopenia occurrence one year after bariatric surgery in severely obese patients.

PubMed

Voican, Cosmin Sebastian; Lebrun, Amandine; Maitre, Sophie; Lainas, Panagiotis; Lamouri, Karima; Njike-Nakseu, Micheline; Gaillard, Martin; Tranchart, Hadrien; Balian, Axel; Dagher, Ibrahim; Perlemuter, Gabriel; Naveau, Sylvie

2018-01-01

Sarcopenic obesity is a risk factor of morbidity and mortality. The aim of this study was to generate a predictive score of sarcopenia occurrence one year after bariatric surgery. We conducted an observational prospective cohort study on a total of 184 severely obese patients admitted to our institution to undergo sleeve gastrectomy. Skeletal muscle cross-sectional area at the third lumbar vertebrae (SMA, cm2) was measured from the routinely performed computed tomography. The skeletal muscle index (SMI) was calculated as follows: SMA/height2 (cm2/m2). Sarcopenia was defined as an SMI < 38.5 cm2/m2 for women and < 52.4 cm2/m2 for men. Measurements were performed at surgery and one year later. Most of the included patients were female (79%), with a mean age of 42±0.9 years and body mass index of 43.2±0.5 kg/m2. Fifteen patients (8%) had sarcopenia before surgery and 59 (32%) at the one-year follow-up. Male gender (p<0.0001), SMA before surgery (p<0.0001), and SMI before surgery (p<0.0001) significantly correlated with the occurrence of sarcopenia one year after surgery by multivariate analysis. Two predictive sarcopenia occurrence scores were constructed using SMA and gender (SS1 score) or SMI and gender (SS2 score). The area under receiver operating characteristic (AUROC) curve of the SS2 score was significantly greater than that of the SS1 score for the diagnosis of postoperative sarcopenia occurrence (0.95±0.02 versus 0.90±0.02; p<0.01). A cut-off value for the SS2 score of 0.53 had a sensitivity of 90%, a specificity of 91%, a positive predictive value of 83%, and a negative predictive value of 95%. In the group of patients without baseline sarcopenia, the SS2 score had still an excellent AUROC of 0.92±0.02. A cut-off of 0.55 predicted development of sarcopenia one year after sleeve gastrectomy in these patients with a sensitivity of 87%, a specificity of 88%, and negative predictive value of 95%. The SS2 score has excellent predictive value for the occurrence of sarcopenia one year after sleeve gastrectomy. This score can be used to target early intensification of nutritional and dietetic follow-up to the predicted high-risk population.

In Vitro Reconstitution of Functional Type III Protein Export and Insights into Flagellar Assembly.

PubMed

Terashima, Hiroyuki; Kawamoto, Akihiro; Tatsumi, Chinatsu; Namba, Keiichi; Minamino, Tohru; Imada, Katsumi

2018-06-26

The type III secretion system (T3SS) forms the functional core of injectisomes, protein transporters that allow bacteria to deliver virulence factors into their hosts for infection, and flagella, which are critical for many pathogens to reach the site of infection. In spite of intensive genetic and biochemical studies, the T3SS protein export mechanism remains unclear due to the difficulty of accurate measurement of protein export in vivo Here, we developed an in vitro flagellar T3S protein transport assay system using an inverted cytoplasmic membrane vesicle (IMV) for accurate and controlled measurements of flagellar protein export. We show that the flagellar T3SS in the IMV fully retains export activity. The flagellar hook was constructed inside the lumen of the IMV by adding purified component proteins externally to the IMV solution. We reproduced the hook length control and export specificity switch in the IMV consistent with that seen in the native cell. Previous in vivo analyses showed that flagellar protein export is driven by proton motive force (PMF) and facilitated by ATP hydrolysis by FliI, a T3SS-specific ATPase. Our in vitro assay recapitulated these previous in vivo observations but furthermore clearly demonstrated that even ATP hydrolysis by FliI alone can drive flagellar protein export. Moreover, this assay showed that addition of the FliH 2 /FliI complex to the assay solution at a concentration similar to that in the cell dramatically enhanced protein export, confirming that the FliH 2 /FliI complex in the cytoplasm is important for effective protein transport. IMPORTANCE The type III secretion system (T3SS) is the functional core of the injectisome, a bacterial protein transporter used to deliver virulence proteins into host cells, and bacterial flagella, critical for many pathogens. The molecular mechanism of protein transport is still unclear due to difficulties in accurate measurements of protein transport under well-controlled conditions in vivo We succeeded in developing an in vitro transport assay system of the flagellar T3SS using inverted membrane vesicles (IMVs). Flagellar hook formation was reproduced in the IMV, suggesting that the export apparatus in the IMV retains a protein transport activity similar to that in the cell. Using this system, we revealed that ATP hydrolysis by the T3SS ATPase can drive protein export without PMF. Copyright © 2018 Terashima et al.

Efficacy of Epratuzumab, an Anti-CD22 Monoclonal IgG Antibody, in Systemic Lupus Erythematosus Patients With Associated Sjögren's Syndrome: Post Hoc Analyses From the EMBODY Trials.

PubMed

Gottenberg, Jacques-Eric; Dörner, Thomas; Bootsma, Hendrika; Devauchelle-Pensec, Valérie; Bowman, Simon J; Mariette, Xavier; Bartz, Holger; Oortgiesen, Marga; Shock, Anthony; Koetse, Willem; Galateanu, Catrinel; Bongardt, Sabine; Wegener, William A; Goldenberg, David M; Meno-Tetang, Guy; Kosutic, Gordana; Gordon, Caroline

2018-05-01

EMBODY 1 (ClinicalTrials.gov identifier: NCT01262365) and EMBODY 2 (ClinicalTrials.gov identifier: NCT01261793) investigated the efficacy and safety of epratuzumab, a CD22-targeted humanized monoclonal IgG antibody, in patients with systemic lupus erythematosus (SLE). The studies showed no significant difference from placebo in primary or secondary clinical outcome measures but did demonstrate B cell-specific immunologic activity. The aim of this post hoc analysis was to determine whether epratuzumab had a different clinical efficacy profile in SLE patients with versus those without an associated diagnosis of Sjögren's syndrome (SS). The efficacy and safety of epratuzumab were compared between 2 patient subpopulations randomized in EMBODY 1 and 2: SLE patients with and those without a diagnosis of associated SS. British Isles Lupus Assessment Group (BILAG) total score, BILAG-based Combined Lupus Assessment (BICLA) clinical response to treatment, biologic markers (including B cells, IgG, IgM, and IgA), and safety were assessed. A total of 1,584 patients were randomized in the EMBODY 1 and EMBODY 2 trials; 113 patients were anti-SSA positive and had a diagnosis of associated SS, and 1,375 patients (86.8%) had no diagnosis of associated SS (918 patients were randomized to receive epratuzumab and 457 to receive placebo). For patients with associated SS, but not those without associated SS, a higher proportion of patients receiving epratuzumab achieved a BICLA response and a reduction from baseline in BILAG total score. B cell reduction was faster in patients with associated SS. The sensitivity of B cells to epratuzumab as measured by the mean concentration producing 50% of the maximum B cell count depletion was lower for patients with associated SS (9.5 μg/ml) versus the total EMBODY population (87.1 μg/ml). No difference in the frequency of adverse events in those receiving placebo was reported. Patients with SLE and associated SS treated with epratuzumab showed improvement in SLE disease activity, which was associated with bioactivity, such as decreases in B cell number and IgM level. © 2018 The Authors. Arthritis & Rheumatology published by Wiley Periodicals, Inc. on behalf of American College of Rheumatology.

Type VI Secretion System in Pseudomonas aeruginosa

PubMed Central

Hachani, Abderrahman; Lossi, Nadine S.; Hamilton, Alexander; Jones, Cerith; Bleves, Sophie; Albesa-Jové, David; Filloux, Alain

2011-01-01

Pseudomonas aeruginosa is a Gram-negative bacterium causing chronic infections in cystic fibrosis patients. Such infections are associated with an active type VI secretion system (T6SS), which consists of about 15 conserved components, including the AAA+ ATPase, ClpV. The T6SS secretes two categories of proteins, VgrG and Hcp. Hcp is structurally similar to a phage tail tube component, whereas VgrG proteins show similarity to the puncturing device at the tip of the phage tube. In P. aeruginosa, three T6SSs are known. The expression of H1-T6SS genes is controlled by the RetS sensor. Here, 10 vgrG genes were identified in the PAO1 genome, among which three are co-regulated with H1-T6SS, namely vgrG1a/b/c. Whereas VgrG1a and VgrG1c were secreted in a ClpV1-dependent manner, secretion of VgrG1b was ClpV1-independent. We show that VgrG1a and VgrG1c form multimers, which confirmed the VgrG model predicting trimers similar to the tail spike. We demonstrate that Hcp1 secretion requires either VgrG1a or VgrG1c, which may act independently to puncture the bacterial envelope and give Hcp1 access to the surface. VgrG1b is not required for Hcp1 secretion. Thus, VgrG1b does not require H1-T6SS for secretion nor does H1-T6SS require VgrG1b for its function. Finally, we show that VgrG proteins are required for secretion of a genuine H1-T6SS substrate, Tse3. Our results demonstrate that VgrG proteins are not only secreted components but are essential for secretion of other T6SS substrates. Overall, we emphasize variability in behavior of three P. aeruginosa VgrGs, suggesting that, although very similar, distinct VgrGs achieve specific functions. PMID:21325275

Sjögren's syndome and extragonadal sex steroid formation: a clue to a better disease control?

PubMed

Konttinen, Y T; Stegajev, V; Al-Samadi, A; Porola, P; Hietanen, J; Ainola, M

2015-01-01

Sjögren's syndrome (SS) is an autoimmune disease characterized by lymphoplasmacytoid focal adenitis leading to mucosal dryness, with 9:1 female dominance and peak incidence at menopause. Due to autoimmune adenitis it can be speculated that the normal epithelial cell renewal has failed, possibly as a result of local intracrine failure to process dehydroepiandrosterone (DHEA) to dihydrotestosterone (DHT). Local intracrine/-cellular DHT deficiency seems to predispose to SS if estrogens are low, in menopausal women and in men. This intracrine failure could be the initial noxious stimulus, factor X, initiating the development of SS. Abnormal release and presentation of exocrine gland-derived antigens (Ag-epitopes), in a complex with major histocompatibility complex class II (MHC II), by migratory dendritic cells (DC) activates T-cells in the regional lymph nodes. B-cells with the same specificity capture and present self-Ag to Th-cells which provide T-cell help. B-cells transform to plasma cells and start to produce autoantibodies (Ab) against these T-cell-dependent Ag. Ab against SS-A/Ro and SS-B/La ribonucleoproteins occur only in HLA-DQw2.1/DQw6 heterozygous individuals, but hY-RNA and RNA polymerase III transcripts in these Ag may in all SS patients stimulate toll-like receptors (TLR) 7 and 9 of the plasmacytoid DCs, because IFN-α and IFN-signature are produced. CD8+αEβ7+cytotoxic T-cells activated via cross-presentation recirculate to attack intracrine-deficient, apoptotic epithelial cells expressing self-Ag on their surface. Exocrine glands fall into the sphere of mucosal/gut-associated lymphatic tissue. This together with immune complexes spreads the immunological memory/aggression to extra-glandular sites explaining the systemic nature of the syndrome. Secondary SS could be explained by disturbed lymphocyte recirculation. There is no conclusive evidence that SS in those few men affected is more severe than in women, suggesting that sex steroid endo-/intracrinology has its major impact on the target tissue, not on immune modulation. This article is part of a Special Issue entitled 'Essential role of DHEA'. Copyright © 2014 Elsevier Ltd. All rights reserved.

Elevated immunoglobulin G antibodies to the proline-rich amino-terminal region of Epstein-Barr virus nuclear antigen-2 in sera from patients with systemic connective tissue diseases and from a subgroup of Sjögren's syndrome patients with pulmonary involvements.

PubMed

Yamazaki, M; Kitamura, R; Kusano, S; Eda, H; Sato, S; Okawa-Takatsuji, M; Aotsuka, S; Yanagi, K

2005-03-01

Associations of Epstein-Barr virus (EBV) and autoimmune diseases have been hypothesized. We have analysed IgG antibodies to EBV nuclear antigen (EBNA)-2 in sera from Japanese patients with autoimmune systemic connective tissue diseases (CTD), exemplified by systemic lupus erythematosus (SLE), primary Sjogren's syndrome (SS), rheumatoid arthritis (RA), systemic sclerosis (SSc) and secondary SS (classical CTDs complicated with SS). An enzyme-linked immunosorbent assay (ELISA) which uses glutathione-S-transferase polypeptides fused to EBV nuclear antigen (EBNA)-2 and EBNA-1 was developed. Ratios of IgG antibody reactivity to whole IgG concentrations of sera were calculated to normalize EBNA-2 and EBNA-1 antibody levels to the hypergammaglobulinaemia that occurs in CTD. The ELISA optical density OD(450) readings of IgG antibodies to both the amino-terminal aa 1-116 of EBNA-2 and carboxyl-terminal aa 451-641 of EBNA-1 were elevated significantly in patients with SLE, primary SS, RA, SSc and secondary SS when compared to EBNA-1. The OD readings were divided by serum IgG concentrations to normalize for the hypergammaglobulinaemia. The specific levels of IgG antibodies to the amino-terminal region of EBNA-2 were elevated in patients with SLE, primary SS or RA, as well as those with secondary SS complicated with SLE or RA. The EBNA-2 amino-terminal region contains a polyproline tract and a proline-rich sequence and has considerable amino acid sequence homology with many cellular proline-rich proteins. High ratios of EBNA-2 aa 1-116 to EBNA-1 aa 451-641 IgG antibody levels which probably suggest reactivation of EBV latent infection were associated significantly with pulmonary involvement in SS patients. These results are consistent with the hypothesis that the sequence similarity between the amino-terminal region of EBNA-2 and proline-rich cellular proteins is associated with pathogenesis in a subpopulation of CTD patients, possibly by the molecular mimicry-epitope shift mechanism.

The Post-transcriptional Regulator rsmA/csrA Activates T3SS by Stabilizing the 5′ UTR of hrpG, the Master Regulator of hrp/hrc Genes, in Xanthomonas

PubMed Central

Andrade, Maxuel O.; Farah, Chuck S.; Wang, Nian

2014-01-01

The RsmA/CsrA family of the post-transcriptional regulators of bacteria is involved in the regulation of many cellular processes, including pathogenesis. In this study, we demonstrated that rsmA not only is required for the full virulence of the phytopathogenic bacterium Xanthomonas citri subsp. citri (XCC) but also contributes to triggering the hypersensitive response (HR) in non-host plants. Deletion of rsmA resulted in significantly reduced virulence in the host plant sweet orange and a delayed and weakened HR in the non-host plant Nicotiana benthamiana. Microarray, quantitative reverse-transcription PCR, western-blotting, and GUS assays indicated that RsmA regulates the expression of the type 3 secretion system (T3SS) at both transcriptional and post-transcriptional levels. The regulation of T3SS by RsmA is a universal phenomenon in T3SS-containing bacteria, but the specific mechanism seems to depend on the interaction between a particular bacterium and its hosts. For Xanthomonads, the mechanism by which RsmA activates T3SS remains unknown. Here, we show that RsmA activates the expression of T3SS-encoding hrp/hrc genes by directly binding to the 5′ untranslated region (UTR) of hrpG, the master regulator of the hrp/hrc genes in XCC. RsmA stabilizes hrpG mRNA, leading to increased accumulation of HrpG proteins and subsequently, the activation of hrp/hrc genes. The activation of the hrp/hrc genes by RsmA via HrpG was further supported by the observation that ectopic overexpression of hrpG in an rsmA mutant restored its ability to cause disease in host plants and trigger HR in non-host plants. RsmA also stabilizes the transcripts of another T3SS-associated hrpD operon by directly binding to the 5′ UTR region. Taken together, these data revealed that RsmA primarily activates T3SS by acting as a positive regulator of hrpG and that this regulation is critical to the pathogenicity of XCC. PMID:24586158

Identification of target genes of synovial sarcoma-associated fusion oncoprotein using human pluripotent stem cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayakawa, Kazuo; Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto; Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya

2013-03-22

Highlights: ► We tried to identify targets of synovial sarcoma (SS)-associated SYT–SSX fusion gene. ► We established pluripotent stem cell (PSC) lines with inducible SYT–SSX gene. ► SYT–SSX responsive genes were identified by the induction of SYT–SSX in PSC. ► SS-related genes were selected from database by in silico analyses. ► 51 genes were finally identified among SS-related genes as targets of SYT–SSX in PSC. -- Abstract: Synovial sarcoma (SS) is a malignant soft tissue tumor harboring chromosomal translocation t(X; 18)(p11.2; q11.2), which produces SS-specific fusion gene, SYT–SSX. Although precise function of SYT–SSX remains to be investigated, accumulating evidences suggestmore » its role in gene regulation via epigenetic mechanisms, and the product of SYT–SSX target genes may serve as biomarkers of SS. Lack of knowledge about the cell-of-origin of SS, however, has placed obstacle in the way of target identification. Here we report a novel approach to identify SYT–SSX2 target genes using human pluripotent stem cells (hPSCs) containing a doxycycline-inducible SYT–SSX2 gene. SYT–SSX2 was efficiently induced both at mRNA and protein levels within three hours after doxycycline administration, while no morphological change of hPSCs was observed until 24 h. Serial microarray analyses identified genes of which the expression level changed more than twofold within 24 h. Surprisingly, the majority (297/312, 95.2%) were up-regulated genes and a result inconsistent with the current concept of SYT–SSX as a transcriptional repressor. Comparing these genes with SS-related genes which were selected by a series of in silico analyses, 49 and 2 genes were finally identified as candidates of up- and down-regulated target of SYT–SSX, respectively. Association of these genes with SYT–SSX in SS cells was confirmed by knockdown experiments. Expression profiles of SS-related genes in hPSCs and human mesenchymal stem cells (hMSCs) were strikingly different in response to the induction of SYT–SSX, and more than half of SYT–SSX target genes in hPSCs were not induced in hMSCs. These results suggest the importance of cellular context for correct understanding of SYT–SSX function, and demonstrated how our new system will help to overcome this issue.« less

Analysis of the Pelvic Functional Orientation in the Sagittal Plane: A Radiographic Study With EOS 2D/3D Technology.

PubMed

Loppini, Mattia; Longo, Umile Giuseppe; Ragucci, Pasquala; Trenti, Nicoletta; Balzarini, Luca; Grappiolo, Guido

2017-03-01

We investigated the relationship between pelvic incidence (PI) with anterior pelvic plane angle (APPA), pelvic tilt (PT) angle, and sacral slope (SS) in standing and sitting positions to identify the best parameter expressing the pelvic functional orientation in the sagittal plane. We enrolled 109 consecutive patients (M:F = 43:66) eligible for a primary total hip arthroplasty (THA) with an average age of 63.4 years (15-85). EOS 2D/3D radiography was performed in standing and sitting positions before THA to evaluate the functional pelvic orientation. 3D images took into account the patient-specific sagittal balance measuring APPA, PT, SS, and PI. In standing position, functional parameters measured 5° ± 7.1 for APPA, 11° ± 8.3 for PT, 43° ± 8.5 for SS, and 53° ± 10.9 for PI. In sitting position, they were -18° ± 10.4 for APPA, 34° ± 11.8 for PT, 20° ± 12.6 for SS, and 54° ± 10.9 for PI. There was no significant difference between men and women in terms of the functional parameters in both positions. No relationship was found between APPA and PI in both positions. SS correlated with PI in standing (r = 0.66; P < .0001; R 2  = 0.44) and sitting (r = 0.51; P < .0001; R 2  = 0.26). PT correlated with PI in standing (r = 0.65; P < .0001; R 2  = 0.42) and sitting (r = 0.38; P < .0001; R 2  = 0.14). SS shows the highest correlation with functional pelvic tilt. The study suggests that adjustments in acetabular anteversion during primary THA should be based on SS. Copyright © 2016 Elsevier Inc. All rights reserved.

Characterization of systemic disease in primary Sjögren's syndrome: EULAR-SS Task Force recommendations for articular, cutaneous, pulmonary and renal involvements.

PubMed

Ramos-Casals, Manuel; Brito-Zerón, Pilar; Seror, Raphaèle; Bootsma, Hendrika; Bowman, Simon J; Dörner, Thomas; Gottenberg, Jacques-Eric; Mariette, Xavier; Theander, Elke; Bombardieri, Stefano; De Vita, Salvatore; Mandl, Thomas; Ng, Wan-Fai; Kruize, Aike; Tzioufas, Athanasios; Vitali, Claudio

2015-12-01

To reach a European consensus on the definition and characterization of the main organ-specific extraglandular manifestations in primary SS. The EULAR-SS Task Force Group steering committee agreed to approach SS-related systemic involvement according to the EULAR SS Disease Activity Index (ESSDAI) classification and proposed the preparation of four separate manuscripts: articular, cutaneous, pulmonary and renal ESSDAI involvement; muscular, peripheral nervous system, CNS and haematological ESSDAI involvement; organs not included in the ESSDAI classification; and lymphoproliferative disease. Currently available evidence was obtained by a systematic literature review focused on SS-related systemic features. The following information was summarized for articular, cutaneous, pulmonary and renal involvement: a clear, consensual definition of the clinical feature, a brief epidemiological description including an estimate of the prevalence reported in the main clinical series and a brief list of the key clinical and diagnostic features that could help physicians clearly identify these features. Unfortunately we found that the body of evidence relied predominantly on information retrieved from individual cases, and the scientific information provided was heterogeneous. The analysis of types of involvement was biased due to the unbalanced reporting of severe cases over non-severe cases, although the main sources of bias were the heterogeneous definitions of organ involvement (or even the lack of definition in some studies) and the heterogeneous diagnostic approach used in studies to investigate involvment of each organ. The proposals included in this article are a first step to developing an optimal diagnostic approach to systemic involvement in primary SS and may pave the way for further development of evidence-based diagnostic and therapeutic guidelines. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Sickle erythrocytes and platelets augment lung leukotriene synthesis with downregulation of anti-inflammatory proteins: relevance in the pathology of the acute chest syndrome

PubMed Central

Opene, Michael; Kurantsin-Mills, Joseph; Husain, Sumair

2014-01-01

Abstract Initiation, progression, and resolution of vaso-occlusive pain episodes in sickle cell disease (SCD) have been recognized as reperfusion injury, which provokes an inflammatory response in the pulmonary circulation. Some 5-lipoxygenase (5-lox) metabolites are potent vasoconstrictors in the pulmonary circulation. We studied stimulation of production of the inflammatory eicosanoids leukotrienes (LTs) and prostaglandin E2 (PGE2) by isolated rat lungs perfused with sickle (HbSS) erythrocytes. Our hypothesis is that HbSS erythrocytes produce more LTs than normal (HbAA) erythrocytes, which can induce vaso-occlusive episodes in SCD patients. Lung perfusates were collected at specific time points and purified by high-pressure liquid chromatography, and LTC4 and PGE2 contents were measured by enzyme-linked immunosorbent assay (ELISA). Rat lung explants were also cultured with purified HbAA and HbSS peptides, and 5-lox, cyclooxygenase 1/2, and platelet-activating factor receptor (PAFR) proteins were measured by Western blotting, while prostacyclin and LTs produced by cultured lung explants were measured by ELISA. Lung weight gain and blood gas data were not different among the groups. HbSS-perfused lungs produced more LTC4 and PGE2 than HbAA-perfused lungs: 10.40 ± 0.62 versus 0.92 ± 0.2 ng/g dry lung weight (mean ± SEM; P = 0.0001) for LTC4. Inclusion of autologous platelets (platelet-rich plasma) elevated LTC4 production to 12.6 ± 0.96 and 7 ± 0.60 ng/g dry lung weight in HbSS and HbAA perfusates, respectively. HbSS lungs also expressed more 5-lox and PAFR. The data suggest that HbSS erythrocytes and activated platelets in patient’s pulmonary microcirculation will enhance the synthesis and release of the proinflammatory mediators LTC4 and PGE2, both of which may contribute to onset of the acute chest syndrome in SCD. PMID:25621162

Differences in muscarinic acetylcholine receptor subtypes in the central nervous system of long sleep and short sleep mice. [Ethanol effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watson, M.; Ming, X.; McArdle, J.J.

Differences in voluntary ethanol consumption have been noted in various inbred strains of mice and pharmacogenetic approaches have been used to study the mechanisms of action of many drugs such as ethanol. Long-sleep (LS) and short-sleep (SS) mice, selectively bred for differences in ethanol induced narcosis, provide a method by which a relationship between the differential responsiveness of these geno-types and muscarinic acetylcholine receptors (mAChR) may be evaluated. Sleep times after injection of 3ml ethanol/kg (i.p.) verified the higher sensitivity of LS vs. SS. Mean body weights of LS (26.5g) vs. SS (22g) were also significantly (p<.01) greater. Binding assaysmore » for ({sup 3}H)(-) quinuclidinylbenzilate (({sup 3}H)(-)QNB), a specific but nonsubtype selective mAChR antagonist, ({sup 3}H)pirenzepine (({sup 3}H)PZ), a specific M1 mAChR antagonist and ({sup 3}H)11-2-((2-((diethylamino) methyl)-1-piperidinyl) acetyl)-5,11-dihydro-6H-pyrido (2,3-b) (1,4) benzodiazepine-6-one, (({sup 3}H)AF-DX 116), an M2 selective antagonist were performed to determine mAChR affinity (K{sub d}) and density (B{sub max}) in CNS regions such as the cerebral cortex, hippocampus, corpus striatum and other areas. Significantly lower (30-40%) ({sup 3}H)(-)QNB binding suggests that SS have fewer mAChR's than LS in many areas. These differences may relate to their differential ethanol sensitivity.« less

Determination of trace glucose and forecast of human diseases by affinity adsorption solid substrate room temperature phosphorimetry based on Triticum valgaris lectin labeled with 4.0-generation dendrimers

NASA Astrophysics Data System (ADS)

Li, Zhiming; Zhu, Guohui; Liu, Jiaming; Lu, Qiaomei; Yang, Minlan; Wu, Hong; Shi, Xiumei; Chen, Xinhua

2007-08-01

A new phosphorescence labeling reagent Triton-100X-4.0G-D (4.0G-D refers to 4.0-generation dendrimers) was found. Quantitative specific affinity adsorption (AA) reaction between Triton-100X-4.0G-D-WGA and glucose (G) was carried out on the surface of nitrocellulose membrane (NCM), and the Δ Ip of the product of AA reaction was linear correlation to the content of G. Based on the facts above, a new method for the determination of trace G was established by WGA labeled with Triton-100X-4.0G-D affinity adsorption solid substrate room temperature phosphorimetry (Triton-100X-4.0G-D-WGA-AA-SS-RTP). This research showed that AA-SS-RTP for either direct method or sandwich method could combine very well the characteristics of both the high sensitivity of SS-RTP and the specificity of the AA reaction. Detection limits (LD) were 0.24 fg spot -1 for direct method and 0.18 fg spot -1 for sandwich method, indicating both of them were of high sensitivity. The method has been applied to the determination of the content of G in human serum, and the results were coincided with those obtained by glucose oxidize enzyme method. It can also be applied to forecast accurately some human diseases, such as primary hepatic carcinoma, cirrhosis, acute and chronic hepatitis, transfer hepatocellular, etc. Meanwhile, the mechanism for the determination of G with AA-SS-RTP was discussed.

Validation of a Low-Cost Paper-Based Screening Test for Sickle Cell Anemia

PubMed Central

Piety, Nathaniel Z.; Yang, Xiaoxi; Kanter, Julie; Vignes, Seth M.; George, Alex; Shevkoplyas, Sergey S.

2016-01-01

Background The high childhood mortality and life-long complications associated with sickle cell anemia (SCA) in developing countries could be significantly reduced with effective prophylaxis and education if SCA is diagnosed early in life. However, conventional laboratory methods used for diagnosing SCA remain prohibitively expensive and impractical in this setting. This study describes the clinical validation of a low-cost paper-based test for SCA that can accurately identify sickle trait carriers (HbAS) and individuals with SCA (HbSS) among adults and children over 1 year of age. Methods and Findings In a population of healthy volunteers and SCA patients in the United States (n = 55) the test identified individuals whose blood contained any HbS (HbAS and HbSS) with 100% sensitivity and 100% specificity for both visual evaluation and automated analysis, and detected SCA (HbSS) with 93% sensitivity and 94% specificity for visual evaluation and 100% sensitivity and 97% specificity for automated analysis. In a population of post-partum women (with a previously unknown SCA status) at a primary obstetric hospital in Cabinda, Angola (n = 226) the test identified sickle cell trait carriers with 94% sensitivity and 97% specificity using visual evaluation (none of the women had SCA). Notably, our test permits instrument- and electricity-free visual diagnostics, requires minimal training to be performed, can be completed within 30 minutes, and costs about $0.07 in test-specific consumable materials. Conclusions Our results validate the paper-based SCA test as a useful low-cost tool for screening adults and children for sickle trait and disease and demonstrate its practicality in resource-limited clinical settings. PMID:26735691

Cascaded bidirectional recurrent neural networks for protein secondary structure prediction.

PubMed

Chen, Jinmiao; Chaudhari, Narendra

2007-01-01

Protein secondary structure (PSS) prediction is an important topic in bioinformatics. Our study on a large set of non-homologous proteins shows that long-range interactions commonly exist and negatively affect PSS prediction. Besides, we also reveal strong correlations between secondary structure (SS) elements. In order to take into account the long-range interactions and SS-SS correlations, we propose a novel prediction system based on cascaded bidirectional recurrent neural network (BRNN). We compare the cascaded BRNN against another two BRNN architectures, namely the original BRNN architecture used for speech recognition as well as Pollastri's BRNN that was proposed for PSS prediction. Our cascaded BRNN achieves an overall three state accuracy Q3 of 74.38\\%, and reaches a high Segment OVerlap (SOV) of 66.0455. It outperforms the original BRNN and Pollastri's BRNN in both Q3 and SOV. Specifically, it improves the SOV score by 4-6%.

Use of on-section immunolabeling and cryosubstitution for studies of bacterial DNA distribution.

PubMed Central

Hobot, J A; Bjornsti, M A; Kellenberger, E

1987-01-01

Escherichia coli cells were very rapidly frozen and substituted at a low temperature with 3% glutaraldehyde in acetone. Infiltration and embedding with Lowicryl K4M were carried out at -35 degrees C. This procedure resulted in good structural preservation of both the nucleoid morphology and its DNA plasm, such that immunolabeling with the protein-A gold technique could be carried out. With antibodies specific for either double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA), it was shown that dsDNA was present throughout the nucleoid but that ssDNA was located on the nucleoid periphery. Chloramphenicol-treated cells, in which protein synthesis but not DNA replication is stopped, produced a characteristic ringlike nucleoid shape and had both dsDNA and ssDNA present throughout the annular section of the DNA plasm. The relationship between metabolically active DNA and overall bacterial genome organization is discussed. Images PMID:3553155

Knowledge insufficient: the management of haemoglobin SC disease.

PubMed

Pecker, Lydia H; Schaefer, Beverly A; Luchtman-Jones, Lori

2017-02-01

Although haemoglobin SC (HbSC) accounts for 30% of sickle cell disease (SCD) in the United States and United Kingdom, evidence-based guidelines for genotype specific management are lacking. The unique pathology of HbSC disease is complex, characterized by erythrocyte dehydration, intracellular sickling and increased blood viscosity. The evaluation and treatment of patients with HbSC is largely inferred from studies of SCD consisting mostly of haemoglobin SS (HbSS) patients. These studies are underpowered to allow definitive conclusions about HbSC. We review the pathophysiology of HbSC disease, including known and potential differences between HbSS and HbSC, and highlight knowledge gaps in HbSC disease management. Clinical and translational research is needed to develop targeted treatments and to validate management recommendations for efficacy, safety and impact on quality of life for people with HbSC. © 2016 John Wiley & Sons Ltd.

BLM and RMI1 alleviate RPA inhibition of TopoIIIα decatenase activity.

PubMed

Yang, Jay; Bachrati, Csanad Z; Hickson, Ian D; Brown, Grant W

2012-01-01

RPA is a single-stranded DNA binding protein that physically associates with the BLM complex. RPA stimulates BLM helicase activity as well as the double Holliday junction dissolution activity of the BLM-topoisomerase IIIα complex. We investigated the effect of RPA on the ssDNA decatenase activity of topoisomerase IIIα. We found that RPA and other ssDNA binding proteins inhibit decatenation by topoisomerase IIIα. Complex formation between BLM, TopoIIIα, and RMI1 ablates inhibition of decatenation by ssDNA binding proteins. Together, these data indicate that inhibition by RPA does not involve species-specific interactions between RPA and BLM-TopoIIIα-RMI1, which contrasts with RPA modulation of double Holliday junction dissolution. We propose that topoisomerase IIIα and RPA compete to bind to single-stranded regions of catenanes. Interactions with BLM and RMI1 enhance toposiomerase IIIα activity, promoting decatenation in the presence of RPA.

High-throughput illumina strand-specific RNA sequencing library preparation

USDA-ARS?s Scientific Manuscript database

Conventional Illumina RNA-Seq does not have the resolution to decode the complex eukaryote transcriptome due to the lack of RNA polarity information. Strand-specific RNA sequencing (ssRNA-Seq) can overcome these limitations and as such is better suited for genome annotation, de novo transcriptome as...

SU-E-I-30: Image Analysis in Ultrasonography for Diagnosis of Sjoegren's Syndrome Using Dual-Tree Complex Wavelet Transform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsui, T; Ohki, M; Nakamura, T

Purpose: Sjoegren's syndrome (SS) is an autoimmune disease invading mainly salivary and lacrimal glands. Ultrasonography is used for an initial and non-invasive examination of this disease. However, the ultrasonography diagnosis tends to lack in objectivity and depends on the operator's skills. The purpose of this study is to propose a computer-aided diagnosis (CAD) system for SS based on a dual-tree complex wavelet transform (DT-CWT) and machine learning. Methods: The subjects of this study were 174 patients suspected of having SS at Nagasaki University Hospital and examined with ultrasonography of the parotid glands. Out of these patients, 77 patients were diagnosedmore » with SS by sialography. A region of interest (ROI) of 128 × 128 pixels was set within the parotid gland that was indicated by a dental radiologist. The DT-CWT was applied to the images in the ROI and every image was decomposed into 72 sub-images of the real and imaginary components in six different resolution levels and six orientations. The statistical features of the sub-image were calculated and used as data input for the support vector machine (SVM) classifier for the detection of SS. A ten-fold cross-validation was employed to verify the Resultof SVM. The accuracy of diagnosis was compared by a CAD system with a human observer performance. Results: The sensitivity, specificity, and accuracy in the detection of SS were 95%, 86%, and 91% through our CAD system respectively, while those by a human observer were 84%, 81%, and 83% respectively. Conclusion: The proposed computer-aided diagnosis system for Sjoegren's syndrome in ultrasonography based on dual-tree complex wavelet transform had a better performance than a human observer.« less

Effects of low-alkalinity binders on stabilization/solidification of geogenic As-containing soils: Spectroscopic investigation and leaching tests.

PubMed

Li, Jiang-Shan; Wang, Lei; Cui, Jin-Li; Poon, Chi Sun; Beiyuan, Jingzi; Tsang, Daniel C W; Li, Xiang-Dong

2018-08-01

The low-alkalinity stabilization/solidification (S/S) treatment of the soil containing high concentrations of geogenic As by physical encapsulation is considered as a proper management before land development; however, the choice of an effective binder and the leaching potential of As remain uncertain. In this study, the influence of S/S binders (cement blended with fuel ash (FA), furnace bottom ash (FBA), or ground granulated blast furnace slag (GGBS)) on the speciation and leaching characteristics of geogenic As was studied. The results of X-ray diffractometer (XRD) and X-ray photoelectron spectroscopy (XPS) showed the reduced amount of calcium silicate hydrate phase and the decrease in oxidation state of As(V)-O on the surface of Fe(III) oxides/hydroxides in the low-alkalinity S/S treated soils. This might be due to the binder incorporation and change in pH conditions, which slightly affected the As-Fe interaction and increased the non-specifically sorbed species of As. Therefore, the S/S treatment increased the leachability and bioaccessibility of geogenic As to varying degree but decreased the phyto-extractable As. The S/S treatment by cement incorporating 25% of class C fly ash (O4C1) could achieve comparable or better performance, while reducing the risk assessment code (RAC) to a greater extent compared to that of using cement only. This study illustrates the effectiveness and limitations of low-alkalinity binders (e.g., O4C1) for geogenic As immobilization and encapsulation, which provides a new insight for determining the appropriate S/S binder in soil remediation. Copyright © 2018 Elsevier B.V. All rights reserved.

GTPase Ran strongly accumulates at the kinetochores of somatic chromosomes in the spermatogonial mitoses of Acricotopus lucidus (Diptera, Chironomidae).

PubMed

Staiber, Wolfgang

2014-07-01

Unequal chromosome segregation and spindle formation occurs in the last gonial mitosis in the germ line of the chironomid Acricotopus lucidus. During this differential mitosis, all germ line-limited chromosomes (=Ks) migrate undivided to only one pole of the cell, while the somatic chromosomes (=Ss) first remain in the metaphase plane, and with the arrival of the Ks at the pole, they then separate equally. The evolutionarily conserved GTPase Ran plays a crucial role in many cellular processes. This includes the regulation of microtubule nucleation and stabilisation at kinetochores and of spindle assembly during mitosis, which is promoted by a RanGTP concentration gradient that forms around the mitotic chromosomes (Kalab et al. in Science 295:2452-2456, 2002, Nature 440:697-701, 2006). In the present study, a strong accumulation of Ran was detected by immunofluorescence at the kinetochores of the Ss in normal gonial and differential gonial mitoses of males of A. lucidus. In contrast, no Ran accumulation was observed at the kinetochores of the Ss in the metaphases of brain ganglia mitoses or of aberrant spermatocytes or in metaphases I and II of spermatocyte meiotic divisions. Likewise, there was no accumulation at the kinetochores of Drosophila melanogaster mitotic chromosomes from larval brains. The specific accumulation of Ran at the kinetochores of the Ss in differential gonial mitoses of A. lucidus strongly suggests that Ran is involved in a mechanism acting in this exceptional mitosis, which retains the Ss at the metaphase plane and prevents a premature separation and unequal segregation of the Ss during monopolar migration of the Ks.

Oral Fluid Cocaine and Benzoylecgonine Concentrations Following Controlled Intravenous Cocaine Administration

PubMed Central

Ellefsen, Kayla N.; Concheiro, Marta; Pirard, Sandrine; Gorelick, David A.; Huestis, Marilyn A.

2016-01-01

Limited oral fluid (OF) pharmacokinetic data collected with commercially available collection devices after controlled cocaine administration hinder OF result interpretations. Ten cocaine-using adults provided OF, collected with Oral-Eze® (OE) and StatSure Saliva Sampler™ (SS) devices, an hour prior to and up to 69 h after 25 mg intravenous (IV) cocaine administration. Cocaine and benzoylecgonine (BE) were quantified by a validated 2D-GC-MS method. Large inter-subject variability was observed. Cocaine was detected in OF in the first 0.17 h sample after IV administration, with much more rapid elimination than BE. OE median observed Cmax (range) was 932 (394–1,574) μg/L for cocaine and 248 (96.9–953) μg/L for BE. SS median (range) observed cocaine and BE Cmax trended lower at 732 (83.3–1,892) μg/L and 360 (77.2–836) μg/L, respectively. OE and SS cocaine OF detection times were 12.5 and 6.5 h and for BE 30.5 and 28.0 h, respectively at 1 μg/L. There were no significant pharmacokinetic differences between OE and SS OF collection devices, except cocaine half-life was significantly shorter in SS OF specimens. This difference could be attributed to differences in stabilizing buffers present in OF collection devices, which may affect cocaine stability in OF specimens, or decreased recovery from collection pads. Both OE and SS OF collection devices were effective in monitoring cocaine and metabolite concentrations with similar detection windows. Furthermore, we demonstrated that different confirmatory OF cutoffs can be selected to produce shorter or longer cocaine and metabolite detection windows to address specific needs of clinical and forensic drug testing programs. PMID:26851651

An investigation into the prevalence of sleep disturbances in primary Sjögren’s syndrome: a systematic review of the literature

PubMed Central

Gotts, Zoe M.; Ellis, Jason; Deary, Vincent; Rapley, Tim; Ng, Wan-Fai; Newton, Julia L.; Deane, Katherine H. O.

2017-01-01

Abstract Objectives. To identify whether sleep disturbances are more prevalent in primary SS (pSS) patients compared with the general population and to recognize which specific sleep symptoms are particularly problematic in this population. Methods. Electronic searches of the literature were conducted in PubMed, Medline (Ovid), Embase (Ovid), PsychINFO (Ovid) and Web of Science and the search strategy registered a priori. Titles and abstracts were reviewed by two authors independently against a set of prespecified inclusion/exclusion criteria, reference lists were examined and a narrative synthesis of the included articles was conducted. Results. Eight whole-text papers containing nine separate studies met the inclusion criteria and were included in the narrative analysis. Few of these studies met all of the quality assessment criteria. The studies used a range of self-reported measures and objective measures, including polysomnography. Mixed evidence was obtained for some of the individual sleep outcomes, but overall compared with controls, pSS patients reported greater subjective sleep disturbances and daytime somnolence and demonstrated more night awakenings and pre-existing obstructive sleep apnoea. Conclusions. A range of sleep disturbances are commonly reported in pSS patients. Further polysomnography studies are recommended to confirm the increased prevalence of night awakenings and obstructive sleep apnoea in this patient group. pSS patients with excessive daytime somnolence should be screened for co-morbid sleep disorders and treated appropriately. Interventions targeted at sleep difficulties in pSS, such as cognitive behavioural therapy for insomnia and nocturnal humidification devices, have the potential to improve quality of life in this patient group and warrant further investigation. PMID:28013207

An investigation into the prevalence of sleep disturbances in primary Sjögren's syndrome: a systematic review of the literature.

PubMed

Hackett, Katie L; Gotts, Zoe M; Ellis, Jason; Deary, Vincent; Rapley, Tim; Ng, Wan-Fai; Newton, Julia L; Deane, Katherine H O

2017-04-01

To identify whether sleep disturbances are more prevalent in primary SS (pSS) patients compared with the general population and to recognize which specific sleep symptoms are particularly problematic in this population. Electronic searches of the literature were conducted in PubMed, Medline (Ovid), Embase (Ovid), PsychINFO (Ovid) and Web of Science and the search strategy registered a priori . Titles and abstracts were reviewed by two authors independently against a set of prespecified inclusion/exclusion criteria, reference lists were examined and a narrative synthesis of the included articles was conducted. Eight whole-text papers containing nine separate studies met the inclusion criteria and were included in the narrative analysis. Few of these studies met all of the quality assessment criteria. The studies used a range of self-reported measures and objective measures, including polysomnography. Mixed evidence was obtained for some of the individual sleep outcomes, but overall compared with controls, pSS patients reported greater subjective sleep disturbances and daytime somnolence and demonstrated more night awakenings and pre-existing obstructive sleep apnoea. A range of sleep disturbances are commonly reported in pSS patients. Further polysomnography studies are recommended to confirm the increased prevalence of night awakenings and obstructive sleep apnoea in this patient group. pSS patients with excessive daytime somnolence should be screened for co-morbid sleep disorders and treated appropriately. Interventions targeted at sleep difficulties in pSS, such as cognitive behavioural therapy for insomnia and nocturnal humidification devices, have the potential to improve quality of life in this patient group and warrant further investigation. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaffer, Richard, E-mail: rickyshaffer@yahoo.co.u; Department of Clinical Oncology, Imperial College London National Health Service Trust, London; Pickles, Tom

Purpose: Prior studies have derived low values of alpha-beta ratio (a/ss) for prostate cancer of approximately 1-2 Gy. These studies used poorly matched groups, differing definitions of biochemical failure, and insufficient follow-up. Methods and Materials: National Comprehensive Cancer Network low- or low-intermediate risk prostate cancer patients, treated with external beam radiotherapy or permanent prostate brachytherapy, were matched for prostate-specific antigen, Gleason score, T-stage, percentage of positive cores, androgen deprivation therapy, and era, yielding 118 patient pairs. The Phoenix definition of biochemical failure was used. The best-fitting value for a/ss was found for up to 90-month follow-up using maximum likelihood analysis,more » and the 95% confidence interval using the profile likelihood method. Linear quadratic formalism was applied with the radiobiological parameters of relative biological effectiveness = 1.0, potential doubling time = 45 days, and repair half-time = 1 hour. Bootstrap analysis was performed to estimate uncertainties in outcomes, and hence in a/ss. Sensitivity analysis was performed by varying the values of the radiobiological parameters to extreme values. Results: The value of a/ss best fitting the outcomes data was >30 Gy, with lower 95% confidence limit of 5.2 Gy. This was confirmed on bootstrap analysis. Varying parameters to extreme values still yielded best-fit a/ss of >30 Gy, although the lower 95% confidence interval limit was reduced to 0.6 Gy. Conclusions: Using carefully matched groups, long follow-up, the Phoenix definition of biochemical failure, and well-established statistical methods, the best estimate of a/ss for low and low-tier intermediate-risk prostate cancer is likely to be higher than that of normal tissues, although a low value cannot be excluded.« less

Fatigue in primary Sjögren's syndrome is associated with lower levels of proinflammatory cytokines.

PubMed

Howard Tripp, Nadia; Tarn, Jessica; Natasari, Andini; Gillespie, Colin; Mitchell, Sheryl; Hackett, Katie L; Bowman, Simon J; Price, Elizabeth; Pease, Colin T; Emery, Paul; Lanyon, Peter; Hunter, John; Gupta, Monica; Bombardieri, Michele; Sutcliffe, Nurhan; Pitzalis, Costantino; McLaren, John; Cooper, Annie; Regan, Marian; Giles, Ian; Isenberg, David A; Saravanan, Vadivelu; Coady, David; Dasgupta, Bhaskar; McHugh, Neil; Young-Min, Steven; Moots, Robert; Gendi, Nagui; Akil, Mohammed; Griffiths, Bridget; Lendrem, Dennis W; Ng, Wan-Fai

2016-01-01

This article reports relationships between serum cytokine levels and patient-reported levels of fatigue, in the chronic immunological condition primary Sjögren's syndrome (pSS). Blood levels of 24 cytokines were measured in 159 patients with pSS from the United Kingdom Primary Sjögren's Syndrome Registry and 28 healthy non-fatigued controls. Differences between cytokines in cases and controls were evaluated using Wilcoxon test. Patient-reported scores for fatigue were evaluated, classified according to severity and compared with cytokine levels using analysis of variance. Logistic regression was used to determine the most important predictors of fatigue levels. 14 cytokines were significantly higher in patients with pSS (n=159) compared to non-fatigued healthy controls (n=28). While serum levels were elevated in patients with pSS compared to healthy controls, unexpectedly, the levels of 4 proinflammatory cytokines-interferon-γ-induced protein-10 (IP-10) (p=0.019), tumour necrosis factor-α (p=0.046), lymphotoxin-α (p=0.034) and interferon-γ (IFN-γ) (p=0.022)-were inversely related to patient-reported levels of fatigue. A regression model predicting fatigue levels in pSS based on cytokine levels, disease-specific and clinical parameters, as well as anxiety, pain and depression, revealed IP-10, IFN-γ (both inversely), pain and depression (both positively) as the most important predictors of fatigue. This model correctly predicts fatigue levels with reasonable (67%) accuracy. Cytokines, pain and depression appear to be the most powerful predictors of fatigue in pSS. Our data challenge the notion that proinflammatory cytokines directly mediate fatigue in chronic immunological conditions. Instead, we hypothesise that mechanisms regulating inflammatory responses may be important.

Fatigue in primary Sjögren's syndrome is associated with lower levels of proinflammatory cytokines

PubMed Central

Howard Tripp, Nadia; Tarn, Jessica; Natasari, Andini; Gillespie, Colin; Mitchell, Sheryl; Hackett, Katie L; Bowman, Simon J; Price, Elizabeth; Pease, Colin T; Emery, Paul; Lanyon, Peter; Hunter, John; Gupta, Monica; Bombardieri, Michele; Sutcliffe, Nurhan; Pitzalis, Costantino; McLaren, John; Cooper, Annie; Regan, Marian; Giles, Ian; Isenberg, David A; Saravanan, Vadivelu; Coady, David; Dasgupta, Bhaskar; McHugh, Neil; Young-Min, Steven; Moots, Robert; Gendi, Nagui; Akil, Mohammed; Griffiths, Bridget; Lendrem, Dennis W; Ng, Wan-Fai

2016-01-01

Objectives This article reports relationships between serum cytokine levels and patient-reported levels of fatigue, in the chronic immunological condition primary Sjögren's syndrome (pSS). Methods Blood levels of 24 cytokines were measured in 159 patients with pSS from the United Kingdom Primary Sjögren's Syndrome Registry and 28 healthy non-fatigued controls. Differences between cytokines in cases and controls were evaluated using Wilcoxon test. Patient-reported scores for fatigue were evaluated, classified according to severity and compared with cytokine levels using analysis of variance. Logistic regression was used to determine the most important predictors of fatigue levels. Results 14 cytokines were significantly higher in patients with pSS (n=159) compared to non-fatigued healthy controls (n=28). While serum levels were elevated in patients with pSS compared to healthy controls, unexpectedly, the levels of 4 proinflammatory cytokines—interferon-γ-induced protein-10 (IP-10) (p=0.019), tumour necrosis factor-α (p=0.046), lymphotoxin-α (p=0.034) and interferon-γ (IFN-γ) (p=0.022)—were inversely related to patient-reported levels of fatigue. A regression model predicting fatigue levels in pSS based on cytokine levels, disease-specific and clinical parameters, as well as anxiety, pain and depression, revealed IP-10, IFN-γ (both inversely), pain and depression (both positively) as the most important predictors of fatigue. This model correctly predicts fatigue levels with reasonable (67%) accuracy. Conclusions Cytokines, pain and depression appear to be the most powerful predictors of fatigue in pSS. Our data challenge the notion that proinflammatory cytokines directly mediate fatigue in chronic immunological conditions. Instead, we hypothesise that mechanisms regulating inflammatory responses may be important. PMID:27493792

Regulation of the Yersinia type III secretion system: traffic control

PubMed Central

Dewoody, Rebecca S.; Merritt, Peter M.; Marketon, Melanie M.

2013-01-01

Yersinia species, as well as many other Gram-negative pathogens, use a type III secretion system (T3SS) to translocate effector proteins from the bacterial cytoplasm to the host cytosol. This T3SS resembles a molecular syringe, with a needle-like shaft connected to a basal body structure, which spans the inner and outer bacterial membranes. The basal body of the injectisome shares a high degree of homology with the bacterial flagellum. Extending from the T3SS basal body is the needle, which is a polymer of a single protein, YscF. The distal end of the needle serves as a platform for the assembly of a tip complex composed of LcrV. Though never directly observed, prevailing models assume that LcrV assists in the insertion of the pore-forming proteins YopB and YopD into the host cell membrane. This completes a bridge between the bacterium and host cell to provide a continuous channel through which effectors are delivered. Significant effort has gone into understanding how the T3SS is assembled, how its substrates are recognized and how substrate delivery is controlled. Arguably the latter topic is the least understood; however, recent advances have provided new insight, and therefore, this review will focus primarily on summarizing the current state of knowledge regarding the control of substrate delivery by the T3SS. Specifically, we will discuss the roles of YopK, as well as YopN and YopE, which have long been linked to regulation of translocation. We also propose models whereby the YopK regulator communicates with the basal body of the T3SS to control translocation. PMID:23390616

A Transcriptional Regulatory Mechanism Finely Tunes the Firing of Type VI Secretion System in Response to Bacterial Enemies

PubMed Central

Lazzaro, Martina; Feldman, Mario F.

2017-01-01

ABSTRACT The ability to detect and measure danger from an environmental signal is paramount for bacteria to respond accordingly, deploying strategies that halt or counteract potential cellular injury and maximize survival chances. Type VI secretion systems (T6SSs) are complex bacterial contractile nanomachines able to target toxic effectors into neighboring bacteria competing for the same colonization niche. Previous studies support the concept that either T6SSs are constitutively active or they fire effectors in response to various stimuli, such as high bacterial density, cell-cell contact, nutrient depletion, or components from dead sibling cells. For Serratia marcescens, it has been proposed that its T6SS is stochastically expressed, with no distinction between harmless or aggressive competitors. In contrast, we demonstrate that the Rcs regulatory system is responsible for finely tuning Serratia T6SS expression levels, behaving as a transcriptional rheostat. When confronted with harmless bacteria, basal T6SS expression levels suffice for Serratia to eliminate the competitor. A moderate T6SS upregulation is triggered when, according to the aggressor-prey ratio, an unbalanced interplay between homologous and heterologous effectors and immunity proteins takes place. Higher T6SS expression levels are achieved when Serratia is challenged by a contender like Acinetobacter, which indiscriminately fires heterologous effectors able to exert lethal cellular harm, threatening the survival of the Serratia population. We also demonstrate that Serratia’s RcsB-dependent T6SS regulatory mechanism responds not to general stress signals but to the action of specific effectors from competitors, displaying an exquisite strategy to weigh risks and keep the balance between energy expenditure and fitness costs. PMID:28830939

Primary Sjögren's syndrome accompanied by pleural effusion: a case report and literature review.

PubMed

Ma, Dedong; Lu, Hongxiu; Qu, Yiqing; Wang, Shanshan; Ying, Yangyang; Xiao, Wei

2015-01-01

Sjögren's syndrome (SS) is a systemic autoimmune disease characterized by the infiltration of lymphocytes in exocrine glands, specifically the salivary and lacrimal glands, resulting in the typical symptoms of xerophthalmia and xerostomia. SS may be accompanied by pleural effusion when the lung is involved, but this occurrence has been reported in only 10 cases in the literature. We report the case of a 42 year-old woman with severe bilateral pleural effusion for eight years. Primary Sjögren's Syndrome was finally diagnosed based on the presence of xerophthalmia and xerostomia, biopsy of the minor salivary glands, and positive anti-SS-A antibody in the serum and pleural effusion. Biopsy of the parietal pleura through video-assisted thoracoscopy revealed infiltration of lymphocytes. The patient had a long history of pleural effusion without clear etiology. Malignant disease was first suspected because of abnormal density lesion on the left lung and malignant cells found on cytology, but PET-CT revealed no malignant lesion. Examinations did not support infection, malignant tumor, pulmonary sarcoidosis, or other connective tissue diseases. This data could be useful for the future study of pleural effusion in SS.

Microdiversity of Echinococcus granulosus sensu stricto in Australia.

PubMed

Alvarez Rojas, C A; Ebi, D; Gauci, C G; Scheerlinck, J P; Wassermann, M; Jenkins, D J; Lightowlers, M W; Romig, T

2016-07-01

Echinococcus granulosus (sensu lato) is now recognized as an assemblage of cryptic species, which differ considerably in morphology, development, host specificity (including infectivity/pathogenicity for humans) and other aspects. One of these species, E. granulosus sensu stricto (s.s.), is now clearly identified as the principal agent causing cystic echinococcosis in humans. Previous studies of a small section of the cox1 and nadh1 genes identified two variants of E. granulosus s.s. to be present in Australia; however, no further work has been carried out to characterize the microdiversity of the parasite in its territory. We have analysed the sequence of the full length of the cox1 gene (1609 bp) from 37 isolates of E. granulosus from different hosts and geographic regions of Australia. The analysis shows that seven haplotypes of E. granulosus s.s. not previously described were found, together with five haplotypes known to be present in other parts of the world, including the haplotype EG01 which is widespread and present in all endemic regions. These data extend knowledge related to the geographical spread and host range of E. granulosus s.s. in a country such as Australia in which the parasite established around 200 years ago.

Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs

PubMed Central

Cléry, Antoine; Allain, Frédéric H-T

2017-01-01

Abstract RNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode. The different binding modes are: canonical binding to the β-sheet surface; canonical binding with involvement of N- and C-termini; binding to conserved loops; and binding to an α-helix. Our results identify enthalpy as the sole and general force driving association at physiological temperatures. Also, networks of weak interactions are a general feature regulating stability of the different RRM–ssRNA complexes. In agreement, non-polyelectrolyte effects contributed between ∼75 and 90% of the overall free energy of binding in the considered complexes. The various RNA binding modes also displayed enormous heat capacity differences, that upon dissection revealed large differential changes in hydration, conformations and dynamics upon binding RNA. Altogether, different modes employed by RRMs to bind cognate ssRNAs utilize various thermodynamics strategies during the association process. PMID:28334819

Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model

PubMed Central

2012-01-01

Background Starch serves as a temporal storage of carbohydrates in plant leaves during day/night cycles. To study transcriptional regulatory modules of this dynamic metabolic process, we conducted gene regulation network analysis based on small-sample inference of graphical Gaussian model (GGM). Results Time-series significant analysis was applied for Arabidopsis leaf transcriptome data to obtain a set of genes that are highly regulated under a diurnal cycle. A total of 1,480 diurnally regulated genes included 21 starch metabolic enzymes, 6 clock-associated genes, and 106 transcription factors (TF). A starch-clock-TF gene regulation network comprising 117 nodes and 266 edges was constructed by GGM from these 133 significant genes that are potentially related to the diurnal control of starch metabolism. From this network, we found that β-amylase 3 (b-amy3: At4g17090), which participates in starch degradation in chloroplast, is the most frequently connected gene (a hub gene). The robustness of gene-to-gene regulatory network was further analyzed by TF binding site prediction and by evaluating global co-expression of TFs and target starch metabolic enzymes. As a result, two TFs, indeterminate domain 5 (AtIDD5: At2g02070) and constans-like (COL: At2g21320), were identified as positive regulators of starch synthase 4 (SS4: At4g18240). The inference model of AtIDD5-dependent positive regulation of SS4 gene expression was experimentally supported by decreased SS4 mRNA accumulation in Atidd5 mutant plants during the light period of both short and long day conditions. COL was also shown to positively control SS4 mRNA accumulation. Furthermore, the knockout of AtIDD5 and COL led to deformation of chloroplast and its contained starch granules. This deformity also affected the number of starch granules per chloroplast, which increased significantly in both knockout mutant lines. Conclusions In this study, we utilized a systematic approach of microarray analysis to discover the transcriptional regulatory network of starch metabolism in Arabidopsis leaves. With this inference method, the starch regulatory network of Arabidopsis was found to be strongly associated with clock genes and TFs, of which AtIDD5 and COL were evidenced to control SS4 gene expression and starch granule formation in chloroplasts. PMID:22898356

Cross-cultural adaptation and initial validation of the Stroke-Specific Quality of Life Scale into the Yoruba language.

PubMed

Akinpelu, Aderonke O; Odetunde, Marufat O; Odole, Adesola C

2012-12-01

Stroke-Specific Quality of Life 2.0 (SS-QoL 2.0) scale is used widely and has been cross-culturally adapted to many languages. This study aimed at the cross-cultural adaptation of SS-QoL 2.0 to Yoruba, the indigenous language of south-western Nigeria, and to carry out an initial investigation on its validity. English SS-QoL 2.0 was first adapted to Yoruba language by including Yoruba culture-specific examples in items SC4, UE2 and UE6. The adapted English version (AEV) was independently translated into Yoruba by two language experts who later agreed on a consensus translation, which was then back translated, subjected to an expert committee review and pretested; a cognitive debriefing interview was also carried out to generate the Yoruba translated version (YTV). Thirty-five stroke survivors completed the AEV and Yoruba version (YV) in English and Yoruba. The order of administration was randomized. Data were analysed using Spearman's rank order correlation and Wilcoxon's signed-rank test at a P value less than 0.05. The mean age of the participants (23 men, 12 women) was 58.5±11.3 years. The domain scores of the participants on AEV and YV did not differ significantly, except in the work/productivity domain. In both versions, the mean domain score of the participants was the highest in the language domain [22.6±3.8 (AEV) and 22.7±3.4 (YV)] and the lowest in the work domain [9.0±3.7 (AEV) and 8.0±3.3 (YTV)]. Domain scores on both versions correlated significantly (P<0.05). Participants' ratings of their current state and prestroke state correlated significantly (P<0.01) in all the general areas, except energy and mood. The YTV of SS-QoL 2.0 fulfilled the initial criteria for validity.

Influence of contamination on bonding to zirconia ceramic.

PubMed

Yang, Bin; Scharnberg, Michael; Wolfart, Stefan; Quaas, Anne C; Ludwig, Klaus; Adelung, Rainer; Kern, Matthias

2007-05-01

The purpose of this study was to investigate the influences of contaminations and cleaning methods on bonding to dental zirconia ceramic. After saliva immersion and using silicone disclosing agent, airborne-particle abraded ceramic specimens were cleaned with isopropanol (AL), acetone (AC), 37% phosphoric acid (PA), additional airborne-particle abrasion (AA), or only with water rinsing (SS). Airborne-particle abraded specimens without contaminations (CL) were used as control group. For chemical analysis specimens of all groups were examined with X-ray photoelectron spectroscopy (XPS). Plexiglas tubes filled with composite resin were bonded to ceramic specimens using a phosphate-monomer containing composite luting resin. After 3-day water storage, tensile bond strengths (TBS) were tested. XPS analysis of group SS showed the presence of saliva and silicone (Si) contamination on the surface. The ratios of carbon/zirconium and oxygen/zirconium for groups PA and AA were comparable to those ratios obtained for group CL, indicating the removal of the organic saliva contamination. Airborne-particle abrasion and acetone completely removed Si contamination from ceramic surfaces. Isopropanol had little cleaning effect on the two contaminants. TBS (median +/- standard deviation) in MPa of the groups SS (11.6 +/- 3.1), AL (10.0 +/- 2.9), and AC (13.0 +/- 2.8) were statistically lower than those of groups PA (33.6 +/- 5.5), AA (40.1 +/- 3.6), and CL (47.0 +/- 8.1) (p < 0.001), while no differences were found in TBS between groups AA and CL (p > 0.5). Contamination significantly reduced bond strengths to zirconia ceramic. Airborne-particle abrasion was the most effective cleaning method.

Hydraulic properties of the Madison aquifer system in the western Rapid City area, South Dakota

USGS Publications Warehouse

Greene, Earl A.

1993-01-01

Available information on hydrogeology, data from borehole geophysical logs, and aquifer tests were used to determine the hydraulic properties of the Madison aquifer. From aquifer-test analysis, transmissivity and storage coefficient were determined for the Minnelusa and Madison aquifers, and vertical hydraulic conductivity (Kv') along with specific storage (Ss') for the Minnelusa confining bed. Borehole geophysical well logs were used to determine the thickness and location of the Minnelusa aquifer, the lower Minnelusa confining bed, and the Madison aquifer within the Madison Limestone. Porosity values determined from quantitative analysis of borehole geophysical well logs were used in analyzing the aquifer-test data. The average porosity at the two aquifer-test sites is about 10 percent in the Minnelusa aquifer, 5 percent in the lower Minnelusa confining bed, and 35 percent in the Madison aquifer. The first aquifer test, which was conducted at Rapid City production well #6, produced measured drawdown in the Minnelusa and Madison aquifers. Neuman and Witherspoon's method of determining the hydraulic properties of leaky two-aquifer systems was used to evaluate the aquifer-test data by assuming the fracture and solution-opening network is equivalent to a porous media. Analysis of the aquifer test for the Minnelusa aquifer yielded a transmissivity value of 12,000 feet squared per day and a storage coefficient of 3 x 10-3. The specific storage of the Minnelusa confining bed was 2 x 10-7 per foot, and its vertical hydraulic conductivity was 0.3 foot per day. The transmissivity of the Madison aquifer at this site was 17,000 feet squared per day, and the storage coefficient was 2 x 10-3. The second aquifer test, which was conducted at Rapid City production well #5 (RC-5) produced measured drawdown only in the Madison aquifer. Hantush and Jacob's method of determining the hydraulic properties of leaky confined aquifers with no storage in the confining bed was used to evaluate the aquifer-test data by assuming the fracture and solution-opening network is equivalent to a porous media. The analysis of data from the RC-5 aquifer test showed that transmissivity was not equal in all directions. Hantush's method was used to determine the direction of radial anisotropy and magnitude of the major and minor axes of transmissivity. The major axis of transmissivity is at an angle of 42? east of north, and the transmissivity along this axis is about 56,000 feet squared per day. The minor axis of transmissivity is at an angle of 48? west of north, and the transmissivity along this axis is about 1,300 feet squared per day. The major axis of transmissivity intersects Cleghorn Springs, a large resurgent spring on the west edge of Rapid City. The shape of the potentiometric contours of the Madison aquifer near RC-5 agree with the orientation of the transmissivity ellipse. The average value of the storage coefficient from the isotropic analysis of the aquifer-test data was 3.5 x 10-4, and the average vertical hydraulic conductivity of the lower Minnelusa confining bed was 9.6 x 10-3 foot per day.

Analysis of tear cytokines and clinical correlations in Sjögren syndrome dry eye patients and non-Sjögren syndrome dry eye patients.

PubMed

Lee, Sang Yeop; Han, Soo Jung; Nam, Sang Min; Yoon, Sang Chul; Ahn, Ji Min; Kim, Tae-Im; Kim, Eung Kweon; Seo, Kyoung Yul

2013-08-01

To compare concentrations of tear cytokines in 3 groups composed of Sjögren syndrome (SS) dry eye, non-Sjögren syndrome (non-SS) dry eye, and normal subjects. Correlations between ocular surface parameters and tear cytokines were also investigated. Prospective cross-sectional study. SS dry eye patients (n = 24; 40 eyes) were diagnosed with primary SS according to the criteria set by the American-European Consensus Group. Non-SS dry eye patients (n = 25; 40 eyes) and normal subjects (n = 21; 35 eyes) were also enrolled. Tear concentrations of interleukin (IL)-17, IL-6, IL-10, IL-4, IL-2, interferon γ (IFN-γ), and tumor necrosis factor α (TNF-α) were measured by a multiplex immunobead assay. Ocular Surface Disease Index (OSDI), tear film breakup time (TBUT), Schirmer I test, and fluorescein staining scores were obtained from dry eye patients. All cytokine levels except for IL-2 were highest in the SS group, followed by non-SS dry eye group and control subjects. Concentrations of IL-17, TNF-α, and IL-6 were significantly different among the 3 groups (IL-17: SS > control P < .001, non-SS > control P = .042, SS > non-SS P < .001; TNF-α: SS > control P = .006, non-SS > control P = .034, SS > non-SS P = .029; IL-6: SS > control P = .002, non-SS > control P = .032, SS > non-SS P = .002). IL-17 was significantly correlated with TBUT (R = -0.22, P = .012) and Schirmer I test (R = -0.36, P = .027) scores in the SS group. IL-6 was significantly correlated only with TBUT (R = -0.38, P = .02) in the non-SS group. Differences in tear cytokine levels and correlation patterns between SS dry eye and non-SS dry eye patients suggest the involvement of different inflammatory processes as causes of dry eye syndrome. Copyright © 2013 Elsevier Inc. All rights reserved.

Immobilization free electrochemical biosensor for folate receptor in cancer cells based on terminal protection.

PubMed

Ni, Jiancong; Wang, Qingxiang; Yang, Weiqiang; Zhao, Mengmeng; Zhang, Ying; Guo, Longhua; Qiu, Bin; Lin, Zhenyu; Yang, Huang-Hao

2016-12-15

The determination of folate receptor (FR) that over expressed in vast quantity of cancerous cells frequently is significant for the clinical diagnosis and treatment of cancers. Many DNA-based electrochemical biosensors have been developed for FR detection with high selectivity and sensitivity, but most of them need complicated immobilization of DNA on the electrode surface firstly, which is tedious and therefore results in the poor reproducibility. In this study, a simple, sensitive, and selective electrochemical FR biosensor in cancer cells has been proposed, which combines the advantages of the convenient immobilization-free homogeneous indium tin oxide (ITO)-based electrochemical detection strategy and the high selectivity of the terminal protection of small molecule linked DNA. The small molecule of folic acid (FA) and an electroactive molecule of ferrocence (Fc) were tethered to 3'- and 5'-end of an arbitrary single-stranded DNA (ssDNA), respectively, forming the FA-ssDNA-Fc complex. In the absence of the target FR, the FA-ssDNA-Fc was degraded by exonuclease I (Exo I) from 3'-end and produced a free Fc, diffusing freely to the ITO electrode surface and resulting in strong electrochemical signal. When the target FR was present, the FA-ssDNA-Fc was bound to FR through specific interaction with FA anchored at the 3'-end, effectively protecting the ssDNA strand from hydrolysis by Exo I. The FR-FA-ssDNA-Fc could not diffuse easily to the negatively charged ITO electrode surface due to the electrostatic repulsion between the DNA strand and the negatively charged ITO electrode, so electrochemical signal reduced. The decreased electrochemical signal has a linear relationship with the logarithm of FR concentration in range of 10fM to 10nM with a detection limit of 3.8fM (S/N=3). The proposed biosensor has been applied to detect FR in HeLa cancer cells, and the decreased electrochemical signal has a linear relationship with the logarithm of cell concentration ranging from 100-10000cell/mL. Compared with the traditional heterogeneous electrochemical FR biosensors, the proposed biosensor owns the merits of the simplicity and high specificity, presenting the great potential application in the area of early diagnosis of cancers. Copyright © 2016 Elsevier B.V. All rights reserved.

Down-regulation of increased TRAF6 expression in the peripheral mononuclear cells of patients with primary Sjögren's syndrome by an EBV-EBER1-specific synthetic single-stranded complementary DNA molecule.

PubMed

Sipka, Sándor; Zilahi, Erika; Papp, Gábor; Chen, Ji-Qing; Nagy, Andrea; Hegyi, Katalin; Kónya, József; Zeher, Margit

2017-05-01

We described earlier a simultaneously increased that the increased expression of miRNA-146a/b was accompanied by an increase in the expression of and TRAF6 and a decrease in the expression of IRAK1 genes in the peripheral mononuclear cells (PBMCs) of patients with primary Sjogren's syndrome (pSS) patients. Recently, the expression of EBV encoded. RNA (EBER) was published in the B cells of salivary glands of in pSS. In the present study, we applied an EBV-EBER1 specific synthetic single stranded complementary DNA molecule (EBV-EBER1-cDNA) to test whether any EBER1 related effect exists also in PBMCs of pSS patients. In the PBMCs of pSS patients and healthy controls, we investigated in vitro the effects of a synthetic single stranded EBV-EBER1-cDNA molecule, synthetic double-stranded (ds)RNA polyinosinic-polycytidylic acid [poly (I:C)] and polyadenylic acid potassium salt poly-adenylic acid [poly-(A)] on the expression of TRAF6 gene tested by qRTPCR. The release of interferon -α was detected by ELISA. EBV-EBER1-cDNA resulted in a significant reduction in the expression of TRAF6 in the cells of patients, but in the healthy controls not, whereas the treatments with poly (I:C) and poly-(A) could not reduce the TRAF6 over-expression. No release of EBER1 could be observed in the culture supernatants of patients with pSS. Only the treatment with poly (I:C) resulted in a significant increase of interferon -α release, and only in the heathy controls. No release of EBER1 molecules took place during the culturing of cells. EBV-EBER- cDNA acted functionally on the cells of patients only. These findings give a further evidence of the linkage between EBV and pSS, furthermore, they show the possible role of EBV-EBER1 in the induction of increased TRAF6 expression in the peripheral B cells of Sjögren's patients. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

Meibomian Gland Dysfunction in Primary and Secondary Sjögren Syndrome.

PubMed

Sullivan, David A; Dana, Reza; Sullivan, Rose M; Krenzer, Kathleen L; Sahin, Afsun; Arica, Beril; Liu, Yang; Kam, Wendy R; Papas, Athena S; Cermak, Jennifer M

2018-01-01

We hypothesized that women with primary (pSS) and secondary Sjögren syndrome (sSS; with systemic lupus erythematosus [SLE] or rheumatoid arthritis [RA]) have meibomian gland dysfunction (MGD). We sought to test our hypothesis. Subjects with pSS, sSS + SLE, sSS + RA, and non-SS-related MGD were recruited from the Sjögren's Syndrome Foundation or outpatient clinics at Tufts University School of Dental Medicine or Brigham and Women's Hospital. The control population was recruited from the Greater Boston area. After providing written informed consent, the subjects underwent an eye examination and/or completed two questionnaires that assess symptoms of dry eye disease (DED). Our results demonstrate that pSS and sSS patients have MGD. These subjects had meibomian gland orifice metaplasia, an increased number of occluded meibomian gland orifices, and a reduced quality of meibomian gland secretions. Further, patients with pSS, sSS + SLE, sSS + RA, and MGD had significant alterations in their tear film, lid margin, cornea, and conjunctiva. Symptoms of DED were increased ∼10-fold in all pSS, sSS, and MGD groups relative to controls. Our findings support our hypothesis and show that individuals with pSS, sSS + SLE, and sSS + RA have MGD. In addition, our study indicates that patients with pSS and sSS have both aqueous-deficient and evaporative DED. © 2018 S. Karger AG, Basel.

Effects of in ovo injection with selenium on immune and antioxidant responses during experimental necrotic enteritis in broiler chickens.

PubMed

Lee, S H; Lillehoj, H S; Jang, S I; Jeong, M S; Xu, S Z; Kim, J B; Park, H J; Kim, H R; Lillehoj, E P; Bravo, D M

2014-05-01

This study was conducted to investigate the effects of in ovo injection of Se on modulating the immune system and antioxidant responses in broiler chickens with experimental necrotic enteritis. Broiler eggs were injected at 18 d of embryo age with either 100 μL of PBS alone or sodium selenite (Na2SeO3) in PBS, providing 0 (SS0), 10 (SS10), or 20 (SS20) μg of Se/egg. At 14 d posthatch, PBS-treated and uninfected chickens were kept as the control group, whereas the remaining chickens were orally infected with 1.0 × 10(4) sporulated oocysts of Eimeria maxima (SS0, SS10, SS20). At 18 d posthatch, E. maxima-infected chickens were orally infected with 1.0 × 10(9) cfu of Clostridium perfringens. Infected control SS0 group showed significantly decreased BW compared with the uninfected control. However, SS20 group showed significantly increased BW compared with the infected control SS0 group, whereas the BW were similar among uninfected control and infected SS10 and SS20 groups. The SS10 group showed significantly lower intestinal lesions compared with the SS0 group, and oocyst production was decreased in both SS10 and SS20 groups. Serum malondialdehyde level and catalase activity were also decreased in both SS10 and SS20 groups, whereas the superoxide dismutase level was significantly lower in the SS10 group compared with the SS0 group. The SS20 group showed significantly higher levels of transcripts for IL-1β and IL-6 in intestine, and SS10 and SS20 groups had higher levels of transcripts for IL-8 and inducible nitric oxide synthase expression and decreased glutathione peroxidase 7 mRNA levels compared with the SS0 group. The SS10 and SS20 groups also showed increased serum antibody levels to C. perfringens α-toxin and NetB toxin compared with the SS0 group. These collective results suggest that the injection of Se into the amniotic cavity of developing eggs may be beneficial for enhancing immune and antioxidant responses in the hatched chickens exposed to the necrotic enteritis-causing pathogens.

Male song quality modulates c-Fos expression in the auditory forebrain of the female canary

PubMed Central

Monbureau, Marie; Barker, Jennifer M.; Leboucher, Gérard; Balthazart, Jacques

2015-01-01

In canaries, specific phrases of male song (sexy songs, SS) that are difficult to produce are especially attractive for females. Females exposed to SS produce more copulation displays and deposit more testosterone into their eggs than females exposed to non-sexy songs (NS). Increased expression of the immediate early genes c-Fos or zenk (a.k.a. egr-1) has been observed in the auditory forebrain of female songbirds hearing attractive songs. C-Fos immunoreactive (Fos-ir) cell numbers were quantified here in the brain of female canaries that had been collected 30 min after they had been exposed for 60 min to the playback of SS or NS or control white noise. Fos-ir cell numbers increased in the caudomedial mesopallium (CMM) and caudomedial nidopallium (NCM) of SS birds as compared to controls. Song playback (pooled SS and NS) also tended to increase average Fos-ir cell numbers in the mediobasal hypothalamus (MBH) but this effect did not reach full statistical significance. At the individual level, Fos expression in CMM was correlated with its expression in NCM and in MBH but also with the frequency of calls that females produced in response to the playbacks. These data thus indicate that male songs of different qualities induce a differential metabolic activation of NCM and CMM. The correlation between activation of auditory regions and of the MBH might reflect the link between auditory stimulation and changes in behavior and reproductive physiology. PMID:25846435

Mitochondrial proteomic analysis reveals deficiencies in oxygen utilization in medullary thick ascending limb of Henle in the Dahl salt-sensitive rat

PubMed Central

Zheleznova, Nadezhda N.; Yang, Chun; Ryan, Robert P.; Halligan, Brian D.; Liang, Mingyu; Greene, Andrew S.

2012-01-01

The renal medullary thick ascending limb (mTAL) of the Dahl salt-sensitive (SS) rat is the site of enhanced NaCl reabsorption and excess superoxide production. In the present studies we isolated mitochondria from mTAL of SS and salt-resistant control strain SS.13BN rats on 0.4 and 8% salt diet for 7 days and performed a proteomic analysis. Purity of mTAL and mitochondria isolations exceeded 93.6 and 55%, respectively. Using LC/MS spectral analysis techniques we identified 96 mitochondrial proteins in four biological mTAL mitochondria samples, run in duplicate, as defined by proteins with a false discovery rate <5% and scan count ≥2. Seven of these 96 proteins, including IDH2, ACADM, SCOT, Hsp60, ATPA, EFTu, and VDAC2 were differentially expressed between the two rat strains. Oxygen consumption and high-resolution respirometry analyses showed that mTAL cells and the mitochondria in the outer medulla of SS rats fed high-salt diet exhibited lower rates of oxygen utilization compared with those from SS.13BN rats. These studies advance the conventional proteomic paradigm of focusing exclusively upon whole tissue homogenates to a focus upon a single cell type and specific subcellular organelle. The results reveal the importance of a largely unexplored role for deficiencies of mTAL mitochondrial metabolism and oxygen utilization in salt-induced hypertension and renal medullary oxidative stress. PMID:22805345

Engineering increased thermostability in the thermostable GH-11 xylanase from Thermobacillus xylanilyticus.

PubMed

Paës, Gabriel; O'Donohue, Michael J

2006-09-18

Enzymatic hydrolysis constitutes an attractive strategy for biorefining of abundant, low-cost agricultural by-products such as wheat bran and straw. However, to adopt such an approach, efficient enzymes are required, in particular xylanases. To promote heat-induced disorganization of the complex cell wall network in wheat bran and thus increase enzymatic hydrolysis, we have attempted to improve the thermoresistance of a GH-11 xylanase that is already moderately thermostable. Using a previously described engineering strategy that involves the introduction of disulphide bridges, a mutant (Tx-xyl-SS3) displaying enhanced thermostability and thermoactivity was obtained. The half life at 70 degrees C (180 min) of Tx-xyl-SS3 is 10-fold greater than that of the wild type enzyme and its specific activity is almost doubled (3500 IU mg(-1)). Despite these improvements, Tx-xyl-SS3 was unsuitable for use at significantly higher reaction temperatures (i.e. 85-95 degrees C) and thus the initial objective of this study remained unaccomplished. However, unexpectedly even at the normal hydrolytic temperature (60 degrees C), Tx-xyl-SS3 was able to solubilize 50% of the wheat bran arabinoxylans, 10 points more than the wild type enzyme in parallel reactions. The data presented here show that this improvement is not directly linked to the increase in thermostability and/or thermoactivity, but rather to other unidentified changes to physico-chemical properties that may allow Tx-xyl-SS3 to better penetrate the cell wall network in wheat bran.

Design and Validation Testing of TruckScan to Assay Large Sacks of Fukushima Radioactive Debris on a Truck

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suzuki, Atsuo; Bronson, Frazier

As a result of the March 2011 earthquake and resulting tsunami in Japan, there was a serious accident at the Fukushima Dai-ichi Nuclear Power Plant. This accident has contaminated soil and vegetation in a wide area around the plant. Decontamination projects over the last 4 years have resulted in large numbers of 1 cubic meter canvas bags of debris, commonly called Super Sacks [SS]. These are currently stored nearby where they were generated, but starting in 2015, they will be moved to various Interim Storage Facilities [ISF]. Trucks will typically carry 8-20 of these SSs. When the trucks arrive atmore » the ISF they need to be rapidly sorted into groups according to radioactivity level, for efficient subsequent processing. Canberra Industries, Inc. [CI] has designed a new truck monitoring system 'TruckScan' for use at these ISFs. The TruckScan system must measure the entire truck loaded with multiple closely packed SSs, and generate a nuclide specific assay report showing the radioactivity in each individual SS. The Canberra-Japan office, along with Obayashi Corporation have performed validation testing to demonstrate to the regulatory authorities that the proposed technique was sufficiently accurate. These validation tests were conducted at a temporary storage area in Fukushima prefecture. Decontaminated waste of various representative types and of various levels of radioactivity was gathered and mixed to create homogeneous volumes. These volumes were sampled multiple times and assayed with laboratory HPGe detectors to determine the reference concentration of each pile. Multiple SSs were loaded from each pile. Some of the SSs were filled 50% full, others 75% full, and others 100% full, to represent the typical loading configuration of the existing SSs in the field. The content of the SSs are either sand, soil, or vegetation with densities ranging from 0.3 g/cc - 1.6 g/cc. These SSs with known concentrations of Cs-134 and Cs-137 were then loaded onto trucks in a variety of configurations, typical of how they might be on the real trucks. A partial system was installed at the site and used to assay these trucks with the various loading configurations. Whereas the full system will have 8 collimated 3 x 3'' NaI detectors, the test system only had two detectors; therefore the truck was moved and counted 4 times. The data were acquired and analyzed with the Canberra Genie software to determine the peak counts for both Cesium nuclides. That data was then analyzed with a prototype version of a Maximum Entropy algorithm, to determine the individual SS activity. The goal of the validation tests was to demonstrate that the system could detect 1000 Bq/kg in 15 seconds, and to determine how accurately it could quantify individual SSs. The validation tests demonstrated that the product would perform as predicted. The TruckScan results were consistent with the sample assay results [y = 1.0029 x, R{sup 2} = 0.914]. The Total Propagated Uncertainty, including both uncertainties from these tests and others that were estimated but not tested was 16.6% percent. (authors)« less

Molecular analysis of vector genome structures after liver transduction by conventional and self-complementary adeno-associated viral serotype vectors in murine and nonhuman primate models.

PubMed

Sun, Xun; Lu, You; Bish, Lawrence T; Calcedo, Roberto; Wilson, James M; Gao, Guangping

2010-06-01

Vectors based on several new adeno-associated viral (AAV) serotypes demonstrated strong hepatocyte tropism and transduction efficiency in both small- and large-animal models for liver-directed gene transfer. Efficiency of liver transduction by AAV vectors can be further improved in both murine and nonhuman primate (NHP) animals when the vector genomes are packaged in a self-complementary (sc) format. In an attempt to understand potential molecular mechanism(s) responsible for enhanced transduction efficiency of the sc vector in liver, we performed extensive molecular studies of genome structures of conventional single-stranded (ss) and sc AAV vectors from liver after AAV gene transfer in both mice and NHPs. These included treatment with exonucleases with specific substrate preferences, single-cutter restriction enzyme digestion and polarity-specific hybridization-based vector genome mapping, and bacteriophage phi29 DNA polymerase-mediated and double-stranded circular template-specific rescue of persisted circular genomes. In mouse liver, vector genomes of both genome formats seemed to persist primarily as episomal circular forms, but sc vectors converted into circular forms more rapidly and efficiently. However, the overall differences in vector genome abundance and structure in the liver between ss and sc vectors could not account for the remarkable differences in transduction. Molecular structures of persistent genomes of both ss and sc vectors were significantly more heterogeneous in macaque liver, with noticeable structural rearrangements that warrant further characterizations.

Molecular Analysis of Vector Genome Structures After Liver Transduction by Conventional and Self-Complementary Adeno-Associated Viral Serotype Vectors in Murine and Nonhuman Primate Models

PubMed Central

Sun, Xun; Lu, You; Bish, Lawrence T.; Calcedo, Roberto; Wilson, James M.

2010-01-01

Abstract Vectors based on several new adeno-associated viral (AAV) serotypes demonstrated strong hepatocyte tropism and transduction efficiency in both small- and large-animal models for liver-directed gene transfer. Efficiency of liver transduction by AAV vectors can be further improved in both murine and nonhuman primate (NHP) animals when the vector genomes are packaged in a self-complementary (sc) format. In an attempt to understand potential molecular mechanism(s) responsible for enhanced transduction efficiency of the sc vector in liver, we performed extensive molecular studies of genome structures of conventional single-stranded (ss) and sc AAV vectors from liver after AAV gene transfer in both mice and NHPs. These included treatment with exonucleases with specific substrate preferences, single-cutter restriction enzyme digestion and polarity-specific hybridization-based vector genome mapping, and bacteriophage ϕ29 DNA polymerase-mediated and double-stranded circular template-specific rescue of persisted circular genomes. In mouse liver, vector genomes of both genome formats seemed to persist primarily as episomal circular forms, but sc vectors converted into circular forms more rapidly and efficiently. However, the overall differences in vector genome abundance and structure in the liver between ss and sc vectors could not account for the remarkable differences in transduction. Molecular structures of persistent genomes of both ss and sc vectors were significantly more heterogeneous in macaque liver, with noticeable structural rearrangements that warrant further characterizations. PMID:20113166

Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions.

PubMed

Silvas, Tania V; Hou, Shurong; Myint, Wazo; Nalivaika, Ellen; Somasundaran, Mohan; Kelch, Brian A; Matsuo, Hiroshi; Kurt Yilmaz, Nese; Schiffer, Celia A

2018-05-14

The APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, secondary structure, and solution pH. We identified the A3A ssDNA binding motif as (T/C)TC(A/G), which correlated with enzymatic activity. We also validated that A3A binds RNA in a sequence specific manner. A3A bound tighter to substrate binding motif within a hairpin loop compared to linear oligonucleotide, suggesting A3A affinity is modulated by substrate structure. Based on these findings and previously published A3A-ssDNA co-crystal structures, we propose a new model with intra-DNA interactions for the molecular mechanism underlying A3A sequence preference. Overall, the sequence and structural preferences identified for A3A leads to a new paradigm for identifying A3A's involvement in mutation of endogenous or exogenous DNA.

The DNA-recognition mode shared by archaeal feast/famine-regulatory proteins revealed by the DNA-binding specificities of TvFL3, FL10, FL11 and Ss-LrpB

PubMed Central

Yokoyama, Katsushi; Nogami, Hideki; Kabasawa, Mamiko; Ebihara, Sonomi; Shimowasa, Ai; Hashimoto, Keiko; Kawashima, Tsuyoshi; Ishijima, Sanae A.; Suzuki, Masashi

2009-01-01

The DNA-binding mode of archaeal feast/famine-regulatory proteins (FFRPs), i.e. paralogs of the Esherichia coli leucine-responsive regulatory protein (Lrp), was studied. Using the method of systematic evolution of ligands by exponential enrichment (SELEX), optimal DNA duplexes for interacting with TvFL3, FL10, FL11 and Ss-LrpB were identified as TACGA[AAT/ATT]TCGTA, GTTCGA[AAT/ATT]TCGAAC, CCGAAA[AAT/ATT]TTTCGG and TTGCAA[AAT/ATT]TTGCAA, respectively, all fitting into the form abcdeWWWedcba. Here W is A or T, and e.g. a and a are bases complementary to each other. Apparent equilibrium binding constants of the FFRPs and various DNA duplexes were determined, thereby confirming the DNA-binding specificities of the FFRPs. It is likely that these FFRPs recognize DNA in essentially the same way, since their DNA-binding specificities were all explained by the same pattern of relationship between amino-acid positions and base positions to form chemical interactions. As predicted from this relationship, when Gly36 of TvFL3 was replaced by Thr, the b base in the optimal DNA duplex changed from A to T, and, when Thr36 of FL10 was replaced by Ser, the b base changed from T to G/A. DNA-binding characteristics of other archaeal FFRPs, Ptr1, Ptr2, Ss-Lrp and LysM, are also consistent with the relationship. PMID:19468044

Cargo Movement Operations System (CMOS). Requirements Traceability Matrix Increment II

DTIC Science & Technology

1990-05-17

NO [ ] COMMENT DISPOSITION: ACCEPT [ ] REJECT [ ] COMMENT STATUS: OPEN [ ] CLOSED [ ] Cmnt Page Paragraph No. No. Number Comment 1. C-i SS0-3 Change "workstation" to "processor". 2. C-2 SS0009 Change "workstation" to "processor". SS0016 3. C-6 SS0032 Change "workstation" to "processor". SS0035 4. C-9 SS0063 Add comma after "e.g." 5. C-i SS0082 Change "workstation" to "processor". 6. C-17 SS0131 Change "workstation" to "processor". SS0132 7. C-28 SS0242 Change "workstation"

Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae)

EPA Science Inventory

Male-specific ssRNA (FRNA) coliphages belong to the family Leviviridae. Two genera subdivided into four genogroups (Levivirus, genogroups I and II and Allolevivirus, genogroups III and IV) comprise the lower taxonomic levels. Strains isolated from several continents have been p...

Impact of 10-Minute Interval Roller Massage on Performance and Active Range of Motion.

PubMed

Hodgson, D D; Quigley, P J; Whitten, J H D; Reid, J C; Behm, David G

2017-11-16

Hodgson, DD, Quigley, PJ, Whitten, JHD, Reid, JC, and Behm, DG. Impact of 10-minute interval roller massage on performance and active range of motion. J Strength Cond Res XX(X): 000-000, 2017-Roller massage (RM) has been shown to increase range of motion (ROM) without subsequent performance deficits. However, prolonged static stretching (SS) can induce performance impairments. The objective of this study was to examine the effects of combining SS and RM with and without subsequent RM on ROM and neuromuscular performance. Subjects (n = 12) participated in 5 sessions: (a) SS only (SS_rest), (b) SS + RM (SS + RM_rest), (c) SS with RM at 10 and 20 minutes after stretch (SS_RM), (d) SS + RM with RM at 10 and 20 minutes after stretch (SS + RM_RM), and (e) control. For the SS conditions, the quadriceps and hamstrings received passive SS for 2 × 30 seconds each. For the SS + RM conditions, SS was applied to the quadriceps and hamstrings for 30 seconds each, and RM was performed for 30 seconds per muscle. SS_RM and SS + RM_RM conditions received an additional 30-second RM at 10 and 20 minutes after warm-up, whereas sessions without additional RM rested for the same duration. Testing measures included hip flexion (HF) and knee flexion (KF) active and passive ROM, hurdle jump height and contact time, countermovement jump height, and maximal voluntary isometric contraction force. Initial KF and HF ROM improvements provided by SS_RM and SS + RM_RM were sustained up to 30 minutes after intervention. Furthermore, SS_RM exhibited greater ROM compared with sessions lacking additional RM in active and passive HF as well as active and passive KF. Similarly, SS + RM_RM elicited greater KF and HF ROM improvements than SS_rest. In conclusion, active KF and HF ROM improvements were prolonged by additional RM, whereas neuromuscular performance remained relatively unaffected.

[Isolation and identification of the temperate bacteriophage from isolated strains of Streptococcus suis serotype 2].

PubMed

Ma, Yuling; Lu, Chengping; Fan, Hongjie

2008-04-01

A PCR assay was developed to study the distributional characteristics of phage integrase gene in Streptococcus suis serotype 2 (SS2). A 323bp distinct DNA target can be amplified in 25 strains of virulent SS2, while can not be amplified in avirulent strain T15, 5 strains of other serotypes (SS1, SS7, SS9) and strains of group C Streptococcus strains from pigs, which suggested that the phage integrase gene may be related to the pathogenicity of SS2 and can be consider as a detection factor of the virulent gene of SS2. The sequencing and restriction endonuclease analysis of the PCR products were also done. Comparisons between the sequences of phage integrase gene with that of SS2 strain, showed a high homology with SS2 China strains 98HAH33, 05ZYH33 and North American strain 89-1591. Complete cell lysis was observed with SS2 virulent strains but not with avirulent strain T15 after the induction by mitomycin C. Electron microscopy analysis of the lysate from SS2 virulent strains HA9801 and ZY05719 revealed the presence of phage particles. The induced phage, named SS2-HA and SS2-ZY, both have a small isometric nucleocapsid approximately 50 nm in diameter and have no tail and is therefore a member of the Tectiviridae family. The phage integrase gene sequence of phage SS2-HA and SS2-ZY shared high homologue identities with virulent SS2 strains, which suggested that the phage integrase gene of SS2 has high specify. The temperate phage and phage integrase gene can only detected from SS2 virulent strains but not from avirulent strain, and the detection of phage integrase gene was related to the virulence-associate factors of SS2, such as the muramidase-released protein gene (mrp), which suggested that the temperate phage of SS2 may be related to the pathogenicity of SS2.

Engineering issues for hand-held sensing devices, with examples

NASA Astrophysics Data System (ADS)

Freiwald, David A.; Freiwald, Joyce

1994-03-01

It is now U.S. defense policy that there will be no new platform starts. The emphasis for platforms will be on O&M cost reduction, life-extension improvements, and force-multiplier- device upgrades. There is also an increasing emphasis on hand-held force-multiplier devices for individuals, which is the focus of this paper. Engineering issues include operations analysis, weight, cube, cost, prime power, ease of use, data storage, reliability, fault tolerance, data communications and human factors. Two examples of hand-held devices are given. Applications include USMC, Army, SOCOM, DEA, FBI, SS, Border Patrol and others. Barriers to adoption of such technology are also discussed.

Development of synthetic selfish elements based on modular nucleases in Drosophila melanogaster.

PubMed

Simoni, Alekos; Siniscalchi, Carla; Chan, Yuk-Sang; Huen, David S; Russell, Steven; Windbichler, Nikolai; Crisanti, Andrea

2014-06-01

Selfish genes are DNA elements that increase their rate of genetic transmission at the expense of other genes in the genome and can therefore quickly spread within a population. It has been suggested that selfish elements could be exploited to modify the genome of entire populations for medical and ecological applications. Here we report that transcription activator-like effector nuclease (TALEN) and zinc finger nuclease (ZFN) can be engineered into site-specific synthetic selfish elements (SSEs) and demonstrate their transmission of up to 70% in the Drosophila germline. We show here that SSEs can spread via DNA break-induced homologous recombination, a process known as 'homing' similar to that observed for homing endonuclease genes (HEGs), despite their fundamentally different modes of DNA binding and cleavage. We observed that TALEN and ZFN have a reduced capability of secondary homing compared to HEG as their repetitive structure had a negative effect on their genetic stability. The modular architecture of ZFNs and TALENs allows for the rapid design of novel SSEs against specific genomic sequences making them potentially suitable for the genetic engineering of wild-type populations of animals and plants, in applications such as gene replacement or population suppression of pest species. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Evidence for two distinct KiSS genes in non-placental vertebrates that encode kisspeptins with different gonadotropin-releasing activities in fish and mammals.

PubMed

Felip, Alicia; Zanuy, Silvia; Pineda, Rafael; Pinilla, Leonor; Carrillo, Manuel; Tena-Sempere, Manuel; Gómez, Ana

2009-11-27

Kisspeptins, the products of KiSS-1 gene, have recently emerged as fundamental regulators of reproductive function in different mammalian and, presumably, non-mammalian species. To date, a single form of KiSS-1 has been described in mammals, and recently, in several fish species and Xenopus. We report herein the cloning and characterization of two distinct KiSS-like genes, namely, KiSS-1 and KiSS-2, in the teleost sea bass. While KiSS-1 encodes a peptide identical to rodent kisspeptin-10, the predicted KiSS-2 decapeptide diverges at 4 amino acids (FNFNPFGLRF). Genome database searches showed that both genes are present in non-placental vertebrate genomes. Indeed, phylogenetic and genome mapping analyses suggest that KiSS-1 and KiSS-2 are paralogous genes that originated by duplication of an ancestral gene, although KiSS-2 is lost in placental mammals. KiSS-1 and KiSS-2 mRNAs are present in brain and gonads of sea bass, medaka and zebrafish. Comparative functional studies demonstrated that KiSS-2 decapeptide was significantly more potent than KiSS-1 peptide in inducing LH and FSH secretion in sea bass. In contrast, KiSS-2 decapeptide only weakly elicited LH secretion in rats, whereas KiSS-1 peptide was maximally effective. Our data are the first to provide conclusive evidence for the existence of a second KiSS gene, KiSS-2, in non-placental vertebrates, whose product is likely to play a dominant stimulatory role in the regulation of the gonadotropic axis at least in teleosts.

Manifestation of meibomian gland dysfunction in patients with Sjögren's syndrome, non-Sjögren's dry eye, and non-dry eye controls.

PubMed

Kang, Yeon Soo; Lee, Hyo Seok; Li, Ying; Choi, Won; Yoon, Kyung Chul

2018-06-01

To evaluate the manifestation of meibomian gland dysfunction in patients with Sjögren's syndrome (SS), non-Sjögren's syndrome dry eye (non-SS) patients, and non-dry eye controls. We recruited 31 participants with SS dry eye, 30 participants with non-SS dry eye, and 35 healthy controls without dry eye symptoms. Noninvasive tear breakup time (NITBUT) and meibomian gland dropout score (meiboscore) were measured using the Oculus Keratograph 5 M. Meibomian gland expressibility and secretion quality were evaluated via slit lamp biomicroscopy. The correlation between measurements was analyzed. NITBUT was lower, and the meiboscore, meibomian gland expressibility, and secretion quality scores were significantly higher in the SS and non-SS groups than in the control group (p < 0.001). NITBUT was lower, and the meiboscore and meibomian gland expressibility were higher in the SS group than in the non-SS group. NITBUT correlated negatively with the meiboscore in both SS and non-SS groups and with meibomian gland expressibility in the SS group. A positive correlation was obtained between meiboscore and meibomian gland expressibility in both the SS and the non-SS groups. Patients in both SS and non-SS groups exhibited greater impairment in meibomian gland function than the non-dry eye controls. SS patients had more severe meibomian gland dysfunction with poorer mean meiboscore and meibomian gland expressibility than non-SS patients.

Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bao, Junwei Lucas; Zheng, Jingjing; Truhlar, Donald G.

Here, pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry. We employ a new calibration procedure for quantum Rice–Ramsperger–Kassel (QRRK) unimolecular rate theory within a chemical activation mechanism to calculate the pressure-falloff effect of a radical association with an aromatic ring. The new theoretical framework is applied to the reaction of H with toluene, which is a prototypical reaction in the combustion chemistry of aromatic hydrocarbons present in most fuels. Both the hydrogen abstraction reactions and the hydrogen addition reactions are calculated. Our system-specific (SS) QRRK approach is adjusted with SS parameters to agree with multistructural canonical variational transition statemore » theory with multidimensional tunneling (MS-CVT/SCT) at the high-pressure limit. The new method avoids the need for the usual empirical estimations of the QRRK parameters, and it eliminates the need for variational transition state theory calculations as a function of energy, although in this first application we do validate the falloff curves by comparing SS-QRRK results without tunneling to multistructural microcanonical variational transition state theory (MS-μVT) rate constants without tunneling. At low temperatures, the two approaches agree well with each other, but at high temperatures, SS-QRRK tends to overestimate falloff slightly. We also show that the variational effect is important in computing the energy-resolved rate constants. Multiple-structure anharmonicity, torsional–potential anharmonicity, and high-frequency-mode vibrational anharmonicity are all included in the rate computations, and torsional anharmonicity effects on the density of states are investigated. Branching fractions, which are both temperature- and pressure-dependent (and for which only limited data is available from experiment), are predicted as a function of pressure.« less

Acute effects of static and dynamic stretching on jump performance after 15 min of reconditioning shooting phase in basketball players.

PubMed

Annino, Giuseppe; Ruscello, Bruno; Lebone, Pietro; Palazzo, Francesco; Lombardo, Mauro; Padua, Elvira; Verdecchia, Luca; Tancredi, Virginia; Iellamo, Ferdinando

2017-04-01

The aim of this study was to assess the effects of static (SS) and dynamic stretching (DS) on vertical jump performance executed before, immediately after and at the end of the shooting phase (i.e., 15 min later), as to simulate the actual conditions preceding a match, in professional basketball players. Ten elite basketball players (age: 29±6.73 years, height: 194.67±7.75 cm, weight: 91±8.17 kg and BMI 23.8±7.91 kg.m-2) participated to the study. SS and DS protocols were administered during the first training session of the week, 48 hours after the championship match. Stretching protocols consisted in ~7 minutes of general warm-up phase followed by ~8 minutes of SS and DS, performed with a cross-over design., and ~15 minutes of a specific warm-up shooting phase (SP). Vertical jump tests consisted in counter movement jump (CMJ) and CMJ with arm swings (CMJas) and were performed immediately after the end of each stretching phase (preS, postS, postSP). A significant decrease (P=0.05; η2partial=0.29) in jumping tests height occurred in CMJas, when performed after the SS (i.e., PostS). However, no significant differences in jumping performances, occurred after the general warm phase and the specific warm-up shooting phase, between the two stretching protocols. These results would indicate that, overall, stretching routines either dynamic or static, performed before a basketball match are transient and affect only marginally leg muscles performance. Stretching routines, particularly the dynamic ones, may be useful to maintain muscle performance before a competition, provided that this latter begins shortly after.

Single-stranded DNA Binding by the Helix-Hairpin-Helix Domain of XPF Protein Contributes to the Substrate Specificity of the ERCC1-XPF Protein Complex*

PubMed Central

Das, Devashish; Faridounnia, Maryam; Kovacic, Lidija; Kaptein, Robert; Boelens, Rolf; Folkers, Gert E.

2017-01-01

The nucleotide excision repair protein complex ERCC1-XPF is required for incision of DNA upstream of DNA damage. Functional studies have provided insights into the binding of ERCC1-XPF to various DNA substrates. However, because no structure for the ERCC1-XPF-DNA complex has been determined, the mechanism of substrate recognition remains elusive. Here we biochemically characterize the substrate preferences of the helix-hairpin-helix (HhH) domains of XPF and ERCC-XPF and show that the binding to single-stranded DNA (ssDNA)/dsDNA junctions is dependent on joint binding to the DNA binding domain of ERCC1 and XPF. We reveal that the homodimeric XPF is able to bind various ssDNA sequences but with a clear preference for guanine-containing substrates. NMR titration experiments and in vitro DNA binding assays also show that, within the heterodimeric ERCC1-XPF complex, XPF specifically recognizes ssDNA. On the other hand, the HhH domain of ERCC1 preferentially binds dsDNA through the hairpin region. The two separate non-overlapping DNA binding domains in the ERCC1-XPF heterodimer jointly bind to an ssDNA/dsDNA substrate and, thereby, at least partially dictate the incision position during damage removal. Based on structural models, NMR titrations, DNA-binding studies, site-directed mutagenesis, charge distribution, and sequence conservation, we propose that the HhH domain of ERCC1 binds to dsDNA upstream of the damage, and XPF binds to the non-damaged strand within a repair bubble. PMID:28028171

Comparison of CHROMagar Salmonella Medium and Xylose-Lysine-Desoxycholate and Salmonella-Shigella Agars for Isolation of Salmonella Strains from Stool Samples

PubMed Central

Maddocks, Susan; Olma, Tom; Chen, Sharon

2002-01-01

The growth and appearance of 115 stock Salmonella isolates on a new formulation of CHROMagar Salmonella (CAS) medium were compared to those on xylose-lysine-desoxycholate agar (XLD), Salmonella-Shigella agar (SS), and Hektoen enteric agar (HEA) media. CAS medium was then compared prospectively to XLD and SS for the detection and presumptive identification of Salmonella strains in 500 consecutive clinical stool samples. All stock Salmonella isolates produced typical mauve colonies on CAS medium. Nine Salmonella strains were isolated from clinical specimens. The sensitivities for the detection of salmonellae after primary plating on CAS medium and the combination of XLD and SS after enrichment were 100%. The specificity for the detection of salmonellae after primary plating on CAS medium (83%) was significantly (P < 0.0001) higher than that after primary plating on the combination of SS and XLD media (55%) (a 28% difference in rates; 95% confidence interval, 23.0 to 34%). Twenty-nine non-Salmonella organisms produced mauve colonies on CAS medium, including 17 Candida spp. (59%) and 8 Pseudomonas spp. (28%). These were easily excluded as salmonellae by colony morphology, microscopic examination of a wet preparation, or oxidase testing. One biochemically inert Escherichia coli isolate required further identification to differentiate it from Salmonella spp. The use of plating on CAS medium demonstrated high levels of sensitivity and specificity and reduced the time to final identification of Salmonella spp., resulting in substantial cost savings. It can be recommended for use for the primary isolation of Salmonella spp. from stool specimens. Other media (e.g., XLD) are required to detect Shigella spp. concurrently. PMID:12149365

Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory

DOE PAGES

Bao, Junwei Lucas; Zheng, Jingjing; Truhlar, Donald G.

2016-02-03

Here, pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry. We employ a new calibration procedure for quantum Rice–Ramsperger–Kassel (QRRK) unimolecular rate theory within a chemical activation mechanism to calculate the pressure-falloff effect of a radical association with an aromatic ring. The new theoretical framework is applied to the reaction of H with toluene, which is a prototypical reaction in the combustion chemistry of aromatic hydrocarbons present in most fuels. Both the hydrogen abstraction reactions and the hydrogen addition reactions are calculated. Our system-specific (SS) QRRK approach is adjusted with SS parameters to agree with multistructural canonical variational transition statemore » theory with multidimensional tunneling (MS-CVT/SCT) at the high-pressure limit. The new method avoids the need for the usual empirical estimations of the QRRK parameters, and it eliminates the need for variational transition state theory calculations as a function of energy, although in this first application we do validate the falloff curves by comparing SS-QRRK results without tunneling to multistructural microcanonical variational transition state theory (MS-μVT) rate constants without tunneling. At low temperatures, the two approaches agree well with each other, but at high temperatures, SS-QRRK tends to overestimate falloff slightly. We also show that the variational effect is important in computing the energy-resolved rate constants. Multiple-structure anharmonicity, torsional–potential anharmonicity, and high-frequency-mode vibrational anharmonicity are all included in the rate computations, and torsional anharmonicity effects on the density of states are investigated. Branching fractions, which are both temperature- and pressure-dependent (and for which only limited data is available from experiment), are predicted as a function of pressure.« less

Borrelia species in Ixodes affinis and Ixodes scapularis ticks collected from the coastal plain of North Carolina.

PubMed

Maggi, Ricardo G; Reichelt, Sara; Toliver, Marcée; Engber, Barry

2010-12-01

Ixodes affinis and I. scapularis are tick species that are widely distributed in the coastal plain region of North Carolina. Both tick species are considered enzootic vectors for spirochetal bacteria of the genus Borrelia and specifically for B. burgdorferi s.s., the pathogen most often attributed as the cause of Lyme disease in the USA. Laboratory testing of individual I. affinis and I. scapularis ticks for the presence of Borrelia DNA was accomplished by PCR, targeting 2 regions of the 16S-23S intergenic spacer. In I. affinis, Borrelia DNA was detected in 63.2% of 155 individual ticks. B. burgdorferi s.s. and B. bissettii were identified by DNA sequencing in 33.5% and 27.9% I. affinis, respectively. Statistical differences were found for sex distribution of Borrelia DNA between I. affinis females (76.8%) and I. affinis males (55.6%) where B. burgdorferi s.s. was more prevalent in females (44.6%) than in males (27.3%). In I. scapularis, 298 individually tested ticks yielded no Borrelia PCR-positive results. This study found a higher incidence of Borrelia spp. in I. affinis collected in coastal North Carolina as compared to previous reports for this tick species in other Southern states, highlighting the potential importance of I. affinis in the maintenance of the enzootic transmission cycle of B. burgdorferi s.l. in North Carolina. The lack of Borrelia DNA in I. scapularis highlights the need for additional studies to better define the transmission cycle for B. burgdorferi s.s. in the southeastern USA and specifically in the state of North Carolina. Copyright © 2010 Elsevier GmbH. All rights reserved.

Do the EULAR Sjögren's syndrome outcome measures correlate with health status in primary Sjögren's syndrome?

PubMed

Lendrem, Dennis; Mitchell, Sheryl; McMeekin, Peter; Gompels, Luke; Hackett, Katie; Bowman, Simon; Price, Elizabeth; Pease, Colin T; Emery, Paul; Andrews, Jacqueline; Lanyon, Peter; Hunter, John; Gupta, Monica; Bombardieri, Michele; Sutcliffe, Nurhan; Pitzalis, Costantino; McLaren, John; Cooper, Annie; Regan, Marian; Giles, Ian; Isenberg, David; Saravanan, Vadivelu; Coady, David; Dasgupta, Bhaskar; McHugh, Neil; Young-Min, Steven; Moots, Robert; Gendi, Nagui; Akil, Mohammed; Griffiths, Bridget; Ng, Wan-Fai

2015-04-01

This study sets out to investigate the relationship between health status [EuroQol five-dimensions questionnaire (EQ-5D)] in primary SS and three of the European League Against Rheumatism (EULAR) SS outcome measures-the disease activity index (ESSDAI), the patient reported index (ESSPRI) and the sicca score. In particular, the goal was to establish whether there is a relationship between the EULAR outcome measures and quality of life. Health status was evaluated using a standardized measure developed by the EuroQol Group-the EQ5D. This permits calculation of two measures of health status: time trade-off (TTO) values and the EQ-5D visual analogue scale (VAS) scores. We used Spearman's rank correlation analysis to investigate the strength of association between health status and three EULAR measures of physician- and patient-reported disease activity in 639 patients from the UK primary SS registry (UKPSSR) cohort. This study demonstrates that the EULAR SS disease-specific outcome measures are significantly correlated with health outcome values (P < 0.001). Higher scores on the ESSDAI, EULAR sicca score and ESSPRI are associated with poorer health states-i.e. lower TTO values and lower VAS scores. While all three are significantly correlated with TTO values and EQ-5D VAS scores, the effect is strongest for the ESSPRI. This study provides further evidence supporting the use of ESSDAI, EULAR sicca score and ESSPRI measures in the clinic. We also discuss the need for disease-specific measures of health status and their comparison with standardized health outcome measures. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Functionalization of quantum rods with oligonucleotides for programmable assembly with DNA origami

NASA Astrophysics Data System (ADS)

Doane, Tennyson L.; Alam, Rabeka; Maye, Mathew M.

2015-02-01

The DNA-mediated self-assembly of CdSe/CdS quantum rods (QRs) onto DNA origami is described. Two QR types with unique optical emission and high polarization were synthesized, and then functionalized with oligonucleotides (ssDNA) using a novel protection-deprotection approach, which harnessed ssDNA's tailorable rigidity and denaturation temperature to increase DNA coverage by reducing non-specific coordination and wrapping. The QR assembly was programmable, and occurred at two different assembly zones that had capture strands in parallel alignment. QRs with different optical properties were assembled, opening up future studies on orientation dependent QR FRET. The QR-origami conjugates could be purified via gel electrophoresis and sucrose gradient ultracentrifugation. Assembly yields, QR stoichiometry and orientation, as well as energy transfer implications were studied in light of QR distances, origami flexibility, and conditions.The DNA-mediated self-assembly of CdSe/CdS quantum rods (QRs) onto DNA origami is described. Two QR types with unique optical emission and high polarization were synthesized, and then functionalized with oligonucleotides (ssDNA) using a novel protection-deprotection approach, which harnessed ssDNA's tailorable rigidity and denaturation temperature to increase DNA coverage by reducing non-specific coordination and wrapping. The QR assembly was programmable, and occurred at two different assembly zones that had capture strands in parallel alignment. QRs with different optical properties were assembled, opening up future studies on orientation dependent QR FRET. The QR-origami conjugates could be purified via gel electrophoresis and sucrose gradient ultracentrifugation. Assembly yields, QR stoichiometry and orientation, as well as energy transfer implications were studied in light of QR distances, origami flexibility, and conditions. Electronic supplementary information (ESI) available: Experimental conditions, DNA origami blueprint and sequences, FRET calculations. Additional Fig. S1-S13. See DOI: 10.1039/c4nr07662a

Evaluating the use of in-situ turbidity measurements to quantify fluvial sediment and phosphorus concentrations and fluxes in agricultural streams.

PubMed

Stutter, Marc; Dawson, Julian J C; Glendell, Miriam; Napier, Fiona; Potts, Jacqueline M; Sample, James; Vinten, Andrew; Watson, Helen

2017-12-31

Accurate quantification of suspended sediments (SS) and particulate phosphorus (PP) concentrations and loads is complex due to episodic delivery associated with storms and management activities often missed by infrequent sampling. Surrogate measurements such as turbidity can improve understanding of pollutant behaviour, providing calibrations can be made cost-effectively and with quantified uncertainties. Here, we compared fortnightly and storm intensive water quality sampling with semi-continuous turbidity monitoring calibrated against spot samples as three potential methods for determining SS and PP concentrations and loads in an agricultural catchment over two-years. In the second year of sampling we evaluated the transferability of turbidity calibration relationships to an adjacent catchment with similar soils and land cover. When data from nine storm events were pooled, both SS and PP concentrations (all in log space) were better related to turbidity than they were to discharge. Developing separate calibration relationship for the rising and falling limbs of the hydrograph provided further improvement. However, the ability to transfer calibrations between adjacent catchments was not evident as the relationships of both SS and PP with turbidity differed both in gradient and intercept on the rising limb of the hydrograph between the two catchments. We conclude that the reduced uncertainty in load estimation derived from the use of turbidity as a proxy for specific water quality parameters in long-term regulatory monitoring programmes, must be considered alongside the increased capital and maintenance costs of turbidity equipment, potentially noisy turbidity data and the need for site-specific prolonged storm calibration periods. Copyright © 2017 Elsevier B.V. All rights reserved.

Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory.

PubMed

Bao, Junwei Lucas; Zheng, Jingjing; Truhlar, Donald G

2016-03-02

Pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry. We employ a new calibration procedure for quantum Rice-Ramsperger-Kassel (QRRK) unimolecular rate theory within a chemical activation mechanism to calculate the pressure-falloff effect of a radical association with an aromatic ring. The new theoretical framework is applied to the reaction of H with toluene, which is a prototypical reaction in the combustion chemistry of aromatic hydrocarbons present in most fuels. Both the hydrogen abstraction reactions and the hydrogen addition reactions are calculated. Our system-specific (SS) QRRK approach is adjusted with SS parameters to agree with multistructural canonical variational transition state theory with multidimensional tunneling (MS-CVT/SCT) at the high-pressure limit. The new method avoids the need for the usual empirical estimations of the QRRK parameters, and it eliminates the need for variational transition state theory calculations as a function of energy, although in this first application we do validate the falloff curves by comparing SS-QRRK results without tunneling to multistructural microcanonical variational transition state theory (MS-μVT) rate constants without tunneling. At low temperatures, the two approaches agree well with each other, but at high temperatures, SS-QRRK tends to overestimate falloff slightly. We also show that the variational effect is important in computing the energy-resolved rate constants. Multiple-structure anharmonicity, torsional-potential anharmonicity, and high-frequency-mode vibrational anharmonicity are all included in the rate computations, and torsional anharmonicity effects on the density of states are investigated. Branching fractions, which are both temperature- and pressure-dependent (and for which only limited data is available from experiment), are predicted as a function of pressure.

Hydrogel based QCM aptasensor for detection of avian influenza virus.

PubMed

Wang, Ronghui; Li, Yanbin

2013-04-15

The objective of this study was to develop a quartz crystal microbalance (QCM) aptasensor based on ssDNA crosslinked polymeric hydrogel for rapid, sensitive and specific detection of avian influenza virus (AIV) H5N1. A selected aptamer with high affinity and specificity against AIV H5N1 surface protein was used, and hybridization between the aptamer and ssDNA formed the crosslinker in the polymer hydrogel. The aptamer hydrogel was immobilized on the gold surface of QCM sensor using a self-assembled monolayer method. The hydrogel remained in the state of shrink if no H5N1 virus was present in the sample because of the crosslinking between the aptamer and ssDNA in the polymer network. When it exposed to target virus, the binding reaction between the aptamer and H5N1 virus caused the dissolution of the linkage between the aptamer and ssDNA, resulting in the abrupt swelling of the hydrogel. The swollen hydrogel was monitored by the QCM sensor in terms of decreased frequency. Three polymeric hydrogels with different ratio (100:1 hydrogel I, 10:1 hydrogel II, 1:1 hydrogel III) of acrylamide and the aptamer monomer were synthesized, respectively, and then were used as the QCM sensor coating material. The results showed that the developed hydrogel QCM aptasensor was capable of detecting target H5N1 virus, and among the three developed aptamer hydrogels, hydrogel III coated QCM aptasensor achieved the highest sensitivity with the detection limit of 0.0128 HAU (HA unit). The total detection time from sampling to detection was only 30 min. In comparison with the anti-H5 antibody coated QCM immunosensor, the hydrogel QCM aptasensor lowered the detection limit and reduced the detection time. Copyright © 2012 Elsevier B.V. All rights reserved.

Specificity in suppression of SOS expression by recA4162 and uvrD303

PubMed Central

Massoni, Shawn C.; Sandler, Steven J.

2013-01-01

Detection and repair of DNA damage is essential in all organisms and depends on the ability of proteins recognizing and processing specific DNA substrates. In E. coli, the RecA protein forms a filament on single-stranded DNA (ssDNA) produced by DNA damage and induces the SOS response. Previous work has shown that one type of recA mutation (e.g., recA4162 (I298V)) and one type of uvrD mutation (e.g., uvrD303 (D403A, D404A)) can differentially decrease SOS expression depending on the type of inducing treatments (UV damage versus RecA mutants that constitutively express SOS). Here it is tested using other SOS inducing conditions if there is a general feature of ssDNA generated during these treatments that allows recA4162 and uvrD303 to decrease SOS expression. The SOS inducing conditions tested include growing cells containing temperature-sensitive DNA replication mutations (dnaE486, dnaG2903, dnaN159, dnaZ2016 (at 37°C)), a del(polA)501 mutation and induction of Double-Strand Breaks (DSBs). uvrD303 could decrease SOS expression under all conditions, while recA4162 could decrease SOS expression under all conditions except in the polA strain or when DSBs occur. It is hypothesized that recA4162 suppresses SOS expression best when the ssDNA occurs at a gap and that uvrD303 is able to decrease SOS expression when the ssDNA is either at a gap or when it is generated at a DSB (but does so better at a gap). PMID:24084169

Specificity in suppression of SOS expression by recA4162 and uvrD303.

PubMed

Massoni, Shawn C; Sandler, Steven J

2013-12-01

Detection and repair of DNA damage is essential in all organisms and depends on the ability of proteins recognizing and processing specific DNA substrates. In E. coli, the RecA protein forms a filament on single-stranded DNA (ssDNA) produced by DNA damage and induces the SOS response. Previous work has shown that one type of recA mutation (e.g., recA4162 (I298V)) and one type of uvrD mutation (e.g., uvrD303 (D403A, D404A)) can differentially decrease SOS expression depending on the type of inducing treatments (UV damage versus RecA mutants that constitutively express SOS). Here it is tested using other SOS inducing conditions if there is a general feature of ssDNA generated during these treatments that allows recA4162 and uvrD303 to decrease SOS expression. The SOS inducing conditions tested include growing cells containing temperature-sensitive DNA replication mutations (dnaE486, dnaG2903, dnaN159, dnaZ2016 (at 37°C)), a del(polA)501 mutation and induction of Double-Strand Breaks (DSBs). uvrD303 could decrease SOS expression under all conditions, while recA4162 could decrease SOS expression under all conditions except in the polA strain or when DSBs occur. It is hypothesized that recA4162 suppresses SOS expression best when the ssDNA occurs at a gap and that uvrD303 is able to decrease SOS expression when the ssDNA is either at a gap or when it is generated at a DSB (but does so better at a gap). Copyright © 2013 Elsevier B.V. All rights reserved.

RNA binding specificity of Ebola virus transcription factor VP30.

PubMed

Schlereth, Julia; Grünweller, Arnold; Biedenkopf, Nadine; Becker, Stephan; Hartmann, Roland K

2016-09-01

The transcription factor VP30 of the non-segmented RNA negative strand Ebola virus balances viral transcription and replication. Here, we comprehensively studied RNA binding by VP30. Using a novel VP30:RNA electrophoretic mobility shift assay, we tested truncated variants of 2 potential natural RNA substrates of VP30 - the genomic Ebola viral 3'-leader region and its complementary antigenomic counterpart (each ∼155 nt in length) - and a series of other non-viral RNAs. Based on oligonucleotide interference, the major VP30 binding region on the genomic 3'-leader substrate was assigned to the internal expanded single-stranded region (∼ nt 125-80). Best binding to VP30 was obtained with ssRNAs of optimally ∼ 40 nt and mixed base composition; underrepresentation of purines or pyrimidines was tolerated, but homopolymeric sequences impaired binding. A stem-loop structure, particularly at the 3'-end or positioned internally, supports stable binding to VP30. In contrast, dsRNA or RNAs exposing large internal loops flanked by entirely helical arms on both sides are not bound. Introduction of a 5´-Cap(0) structure impaired VP30 binding. Also, ssDNAs bind substantially weaker than isosequential ssRNAs and heparin competes with RNA for binding to VP30, indicating that ribose 2'-hydroxyls and electrostatic contacts of the phosphate groups contribute to the formation of VP30:RNA complexes. Our results indicate a rather relaxed RNA binding specificity of filoviral VP30, which largely differs from that of the functionally related transcription factor of the Paramyxoviridae which binds to ssRNAs as short as 13 nt with a preference for oligo(A) sequences.

Burnout syndrome among dental students: a short version of the "Burnout Clinical Subtype Questionnaire" adapted for students (BCSQ-12-SS).

PubMed

Montero-Marin, Jesus; Monticelli, Francesca; Casas, Marina; Roman, Amparo; Tomas, Inmaculada; Gili, Margarita; Garcia-Campayo, Javier

2011-12-12

Burnout has been traditionally defined in relation to the dimensions of "exhaustion", "cynicism", and "inefficiency". More recently, the Burnout Clinical Subtype Questionnaire (BCSQ-12) further established three different subtypes of burnout: the "frenetic" subtype (related to "overload"), the "under-challenged" subtype (related to "lack of development"), and the "worn-out" subtype (related to "neglect"). However, to date, these definitions have not been applied to students. The aims of this research were (1) to adapt a Spanish version of the BCSQ-12 for use with students, (2) to test its factorial validity, internal consistency, convergent and discriminant validity, and (3) to assess potential socio-demographic and occupational risk factors associated with the development of the subtypes. We used a cross-sectional design on a sample of dental students (n = 314) from Santiago and Huesca universities (Spain). Participants completed the Burnout Clinical Subtype Questionnaire Student Survey (BCSQ-12-SS), the Maslach Burnout Inventory Student Survey (MBI-SS), and a series of socio-demographic and occupational questions formulated for the specific purpose of this study. Data were subjected to exploratory factor analysis (EFA) using the principal component method with varimax orthogonal rotation. To assess the relations with the criterion, we calculated the Pearson correlation coefficient (r), multiple correlation coefficient (R(y.123)), and the coefficient of determination (R(2)(y.123)). To assess the association between the subtypes and the socio-demographic variables, we examined the adjusted odds ratio (OR) obtained from multivariate logistic regression models. Factorial analyses supported the theoretical proposition of the BCSQ-12-SS, with α-values exceeding 0.80 for all dimensions. The "overload-exhaustion" relation was r = 0.59 (p < 0.001), "lack of development"-"cynicism", r = 0.49 (p < 0.001), "neglect"-"inefficiency", r = 0.47 (p < 0.001). The "overload"-"lack of development" relation was r = 0.21 (p < 0.001), "overload"-"neglect", r = 0.20 (p < 0.001), and "lack of development"-"neglect", r = 0.38 (p < 0.001). The BCSQ-12-SS explained 38.44% of the variability in "exhaustion", (R(y.123) = 0.62), 30.25% in "cynicism" (R(y.123) = 0.55), and 26.01% in "inefficiency" (R(y.123) = 0.51). "Hours spent on studying" was found to be associated with "overload" (p = 0.001), "campus" with "lack of development" (p = 0.013), and "failed subjects" with "neglect" (p = 0.011). The results support the definition of burnout as established by the BCSQ-12-SS. As such, the BCSQ-12-SS can be used for the recognition of clinical profiles and for the suggestion of potential intervention strategies specific to the characteristics of each particular case.

Burnout syndrome among dental students: a short version of the "Burnout Clinical Subtype Questionnaire" adapted for students (BCSQ-12-SS)

PubMed Central

2011-01-01

Background Burnout has been traditionally defined in relation to the dimensions of "exhaustion", "cynicism", and "inefficiency". More recently, the Burnout Clinical Subtype Questionnaire (BCSQ-12) further established three different subtypes of burnout: the "frenetic" subtype (related to "overload"), the "under-challenged" subtype (related to "lack of development"), and the "worn-out" subtype (related to "neglect"). However, to date, these definitions have not been applied to students. The aims of this research were (1) to adapt a Spanish version of the BCSQ-12 for use with students, (2) to test its factorial validity, internal consistency, convergent and discriminant validity, and (3) to assess potential socio-demographic and occupational risk factors associated with the development of the subtypes. Method We used a cross-sectional design on a sample of dental students (n = 314) from Santiago and Huesca universities (Spain). Participants completed the Burnout Clinical Subtype Questionnaire Student Survey (BCSQ-12-SS), the Maslach Burnout Inventory Student Survey (MBI-SS), and a series of socio-demographic and occupational questions formulated for the specific purpose of this study. Data were subjected to exploratory factor analysis (EFA) using the principal component method with varimax orthogonal rotation. To assess the relations with the criterion, we calculated the Pearson correlation coefficient (r), multiple correlation coefficient (Ry.123), and the coefficient of determination (R2y.123). To assess the association between the subtypes and the socio-demographic variables, we examined the adjusted odds ratio (OR) obtained from multivariate logistic regression models. Results Factorial analyses supported the theoretical proposition of the BCSQ-12-SS, with α-values exceeding 0.80 for all dimensions. The "overload-exhaustion" relation was r = 0.59 (p < 0.001), "lack of development"-"cynicism", r = 0.49 (p < 0.001), "neglect"-"inefficiency", r = 0.47 (p < 0.001). The "overload"-"lack of development" relation was r = 0.21 (p < 0.001), "overload"-"neglect", r = 0.20 (p < 0.001), and "lack of development"-"neglect", r = 0.38 (p < 0.001). The BCSQ-12-SS explained 38.44% of the variability in "exhaustion", (Ry.123 = 0.62), 30.25% in "cynicism" (Ry.123 = 0.55), and 26.01% in "inefficiency" (Ry.123 = 0.51). "Hours spent on studying" was found to be associated with "overload" (p = 0.001), "campus" with "lack of development" (p = 0.013), and ""failed subjects" with "neglect" (p = 0.011). Conclusions The results support the definition of burnout as established by the BCSQ-12-SS. As such, the BCSQ-12-SS can be used for the recognition of clinical profiles and for the suggestion of potential intervention strategies specific to the characteristics of each particular case. PMID:22151576

Downregulation of SS18-SSX1 expression in synovial sarcoma by small interfering RNA enhances the focal adhesion pathway and inhibits anchorage-independent growth in vitro and tumor growth in vivo.

PubMed

Takenaka, Satoshi; Naka, Norifumi; Araki, Nobuhito; Hashimoto, Nobuyuki; Ueda, Takafumi; Yoshioka, Kiyoko; Yoshikawa, Hideki; Itoh, Kazuyuki

2010-04-01

Synovial sarcoma (SS) is an aggressive soft-tissue malignancy characterized by a unique t(X;18) translocation resulting in expression of SS18-SSX fusion protein. In order to investigate the biological function of this fusion protein and to develop a novel therapeutic option, we examined downregulation of SS18-SSX1 expression by small interfering RNA targeting SS18-SSX1 in three human SS cell lines. Microarray analysis comparing SS18-SSX1-silenced cells with control cells in three SS cell lines showed that SS18-SSX1 mainly affected the focal adhesion pathway. In accord with the array data, silencing of SS18-SSX1 enhances adhesion to the extracellular matrix through the induction of expression of myosin light-chain kinase. Furthermore, the silencing of SS18-SSX1 inhibits anchorage-independent growth in vitro and systemic delivery of siRNA against SS18-SSX1 using a nanoparticle system inhibited tumor growth in a nude mouse xenograft model. Our results demonstrate that siRNA targeting of SS18-SSX1 has therapeutic potential for the treatment of SS.

Myth and reality: practical test system for the measurement of anti-DNA antibodies in the diagnosis of systemic lupus erythematosus (SLE).

PubMed

McCloskey, Laura J; Christner, Paul; Jacobs-Kosmin, Dana; Jaskowski, Troy D; Hill, Harry R; Lakos, Gabriella; Teodorescu, Marius

2010-01-01

The myth persists that only the labor intensive Farr radioimmunoassay and Crithidia luciliae immunofluorescence (CL-IFA) are systemic lupus erythematosus (SLE)-specific tests. We compared them to ELISA with bacteriophage lambda DNA (EL-dsDNA) and denatured calf thymus DNA (EL-ssDNA). By percentile ranking, the specificity cut-off level was set both out of clinical context (SOCC) on 100 blood bank donors, and in clinical context (SICC) on 100 patients with either rheumatoid arthritis or scleroderma (50/50). Clinical sensitivity was calculated on 100 random SLE patients. At 95% SICC, the sensitivity of Farr, CL-IFA, EL-dsDNA, and EL-ssDNA was similar (95%CI): 76% (66-84), 76% (66-84), 63% (53-72), and 75% (65-83), respectively; 87% of the patients were positive by at least one method and 55%by all methods. At 99% SICC, the sensitivity was also similar (95% CI): 57% (47-67), 47% (37-57), 58% (47-67), and 43% (33-53), respectively. The areas under ROC curve were similar (95% CI) when patients were used as controls for specificity. At 99% SOCC, EL-ssDNA identified 89% positive, 2 negative but positive by another method at 95% SICC, and 9 negative (i.e. 89/2/9), followed by CL-IFA (80/6/14), Farr (76/12/12), and EL-dsDNA (64/23/13). Thus, at relatively low cost and easy automation, under the same conditions of specificity, the two ELISA tests combined were at least as good, if not superior, to CL-IFA or Farr: they showed similar clinical sensitivity and also identified more patients with anti-DNA antibodies. (c) 2010 Wiley-Liss, Inc.

Rapid and label-free electrochemical DNA biosensor for detecting hepatitis A virus.

PubMed

Manzano, Marisa; Viezzi, Sara; Mazerat, Sandra; Marks, Robert S; Vidic, Jasmina

2018-02-15

Diagnostic systems that can deliver highly specific and sensitive detection of hepatitis A virus (HAV) in food and water are of particular interest in many fields including food safety, biosecurity and control of outbreaks. Our aim was the development of an electrochemical method based on DNA hybridization to detect HAV. A ssDNA probe specific for HAV (capture probe) was designed and tested on DNAs from various viral and bacterial samples using Nested-Reverse Transcription Polymerase Chain Reaction (nRT-PCR). To develop the electrochemical device, a disposable gold electrode was functionalized with the specific capture probe and tested on complementary ssDNA and on HAV cDNA. The DNA hybridization on the electrode was measured through the monitoring of the oxidative peak potential of the indicator tripropylamine by cyclic voltammetry. To prevent non-specific binding the gold surface was treated with 3% BSA before detection. High resolution atomic force microscopy (AFM) confirmed the efficiency of electrode functionalization and on-electrode hybridization. The proposed device showed a limit of detection of 0.65pM for the complementary ssDNA and 6.94fg/µL for viral cDNA. For a comparison, nRT-PCR quantified the target HAV cDNA with a limit of detection of 6.4fg/µL. The DNA-sensor developed can be adapted to a portable format to be adopted as an easy-to- use and low cost method for screening HAV in contaminated food and water. In addition, it can be useful for rapid control of HAV infections as it takes only a few minutes to provide the results. Copyright © 2017. Published by Elsevier B.V.

Testosterone-dependent sex differences in red blood cell hemolysis in storage, stress, and disease.

PubMed

Kanias, Tamir; Sinchar, Derek; Osei-Hwedieh, David; Baust, Jeffrey J; Jordan, Andrew; Zimring, James C; Waterman, Hayley R; de Wolski, Karen S; Acker, Jason P; Gladwin, Mark T

2016-10-01

Red blood cell (RBC) hemolysis represents an intrinsic mechanism for human vascular disease. Intravascular hemolysis releases hemoglobin and other metabolites that inhibit nitric oxide signaling and drive oxidative and inflammatory stress. Although these pathways are important in disease pathogenesis, genetic and population modifiers of hemolysis, including sex, have not been established. We studied sex differences in storage or stress-induced hemolysis in RBC units from the United States and Canada in 22 inbred mouse strains and in patients with sickle cell disease (SCD) using measures of hemolysis in 315 patients who had homozygous SS hemoglobin from the Walk-PHASST cohort. A mouse model also was used to evaluate posttransfusion recovery of stored RBCs, and gonadectomy was used to determine the mechanisms related to sex hormones. An analysis of predisposition to hemolysis based on sex revealed that male RBCs consistently exhibit increased susceptibility to hemolysis compared with females in response to routine cold storage, under osmotic or oxidative stress, after transfusion in mice, and in patients with SCD. The sex difference is intrinsic to the RBC and is not mediated by plasmatic factors or female sex hormones. Importantly, orchiectomy in mice improves RBC storage stability and posttransfusion recovery, whereas testosterone repletion therapy exacerbates hemolytic response to osmotic or oxidative stress. Our findings suggest that testosterone increases susceptibility to hemolysis across human diseases, suggesting that male sex may modulate clinical outcomes in blood storage and SCD and establishing a role for donor genetic variables in the viability of stored RBCs and in human hemolytic diseases. © 2016 AABB.

Thermal Storage Applications Workshop. Volume 2: Contributed Papers

NASA Technical Reports Server (NTRS)

1979-01-01

The solar thermal and the thermal and thermochemical energy storage programs are described as well as the technology requirements for both external (electrical) and internal (thermal, chemical) modes for energy storage in solar power plants. Specific technical issues addressed include thermal storage criteria for solar power plants interfacing with utility systems; optimal dispatch of storage for solar plants in a conventional electric grid; thermal storage/temperature tradeoffs for solar total energy systems; the value of energy storage for direct-replacement solar thermal power plants; systems analysis of storage in specific solar thermal power applications; the value of seasonal storage of solar energy; criteria for selection of the thermal storage system for a 10 MW(2) solar power plant; and the need for specific requirements by storage system development teams.

Primary Sjögren syndrome: an update on current pharmacotherapy options and future directions.

PubMed

Brito-Zerón, Pilar; Sisó-Almirall, Antoni; Bové, Albert; Kostov, Belchin A; Ramos-Casals, Manuel

2013-02-01

Primary Sjögren syndrome (SS) is a chronic systemic autoimmune disease characterized by sicca features and systemic manifestations, and requires a multidisciplinary therapeutic approach. Treatment of sicca manifestations is symptomatic and is based on the administration of topical therapies (saliva substitutes and preservative-free artificial tears). In severe cases of keratoconjunctivitis sicca, topical cyclosporine A may be used. For patients with residual salivary gland function, stimulation of salivary flow with a sialogogue (pilocarpine or cevimeline) is the treatment of choice. The management of extraglandular features must be tailored to the specific organ(s) involved. Hydroxychloroquine may be appropriate for patients with fatigue, arthralgia and myalgia, while glucocorticoids and immunosuppressive agents should be reserved for severe systemic involvement (although no controlled trials in primary SS guide their use). RCTs have demonstrated the lack of efficacy of antitumor necrosis factor agents and promising results for B-cell depleting agents. The overall low level of evidence in therapeutic studies in primary SS suggests that much larger trials of the most promising therapies are necessary. The use of drugs targeting molecules and receptors involved in the etiopathogenesis of primary SS may open up a new era in the therapeutic management of the disease, but the potential risks and benefits of these agents must be weighed carefully.

Nonalcoholic fatty liver disease is associated with dysbiosis independent of body mass index and insulin resistance.

PubMed

Da Silva, Hannah E; Teterina, Anastasia; Comelli, Elena M; Taibi, Amel; Arendt, Bianca M; Fischer, Sandra E; Lou, Wendy; Allard, Johane P

2018-01-23

This study aimed to determine if there is an association between dysbiosis and nonalcoholic fatty liver disease (NAFLD) independent of obesity and insulin resistance (IR). This is a prospective cross-sectional study assessing the intestinal microbiome (IM) of 39 adults with biopsy-proven NAFLD (15 simple steatosis [SS]; 24 nonalcoholic steatohepatitis [NASH]) and 28 healthy controls (HC). IM composition (llumina MiSeq Platform) in NAFLD patients compared to HC were identified by two statistical methods (Metastats, Wilcoxon). Selected taxa was validated using quantitative PCR (qPCR). Metabolites in feces and serum were also analyzed. In NAFLD, 8 operational taxonomic units, 6 genera, 6 families and 2 phyla (Bacteroidetes, Firmicutes) were less abundant and; 1 genus (Lactobacillus) and 1 family (Lactobacillaceae) were more abundant compared to HC. Lower abundance in both NASH and SS patients compared to HC were confirmed by qPCR for Ruminococcus, Faecalibacterium prausnitzii and Coprococcus. No difference was found between NASH and SS. This lower abundance in NAFLD (NASH+SS) was independent of BMI and IR. NAFLD patients had higher concentrations of fecal propionate and isobutyric acid and serum 2-hydroxybutyrate and L-lactic acid. These findings suggest a potential role for a specific IM community and functional profile in the pathogenesis of NAFLD.

TIMES-SS--recent refinements resulting from an industrial skin sensitisation consortium.

PubMed

Patlewicz, G; Kuseva, C; Mehmed, A; Popova, Y; Dimitrova, G; Ellis, G; Hunziker, R; Kern, P; Low, L; Ringeissen, S; Roberts, D W; Mekenyan, O

2014-01-01

The TImes MEtabolism Simulator platform for predicting Skin Sensitisation (TIMES-SS) is a hybrid expert system, first developed at Bourgas University using funding and data from a consortium of industry and regulators. TIMES-SS encodes structure-toxicity and structure-skin metabolism relationships through a number of transformations, some of which are underpinned by mechanistic 3D QSARs. The model estimates semi-quantitative skin sensitisation potency classes and has been developed with the aim of minimising animal testing, and also to be scientifically valid in accordance with the OECD principles for (Q)SAR validation. In 2007 an external validation exercise was undertaken to fully address these principles. In 2010, a new industry consortium was established to coordinate research efforts in three specific areas: refinement of abiotic reactions in the skin (namely autoxidation) in the skin, refinement of the manner in which chemical reactivity was captured in terms of structure-toxicity rules (inclusion of alert reliability parameters) and defining the domain based on the underlying experimental data (study of discrepancies between local lymph node assay Local Lymph Node Assay (LLNA) and Guinea Pig Maximisation Test (GPMT)). The present paper summarises the progress of these activities and explains how the insights derived have been translated into refinements, resulting in increased confidence and transparency in the robustness of the TIMES-SS predictions.

The Ardennes Campaign Simulation Data Base (ACSDB). Volume 1. Volume 2

DTIC Science & Technology

1990-02-07

Railway Artillery Battalion RRArtBt Railway Artillery Battery SS Schutzstaffeln (indicates combat elements of SS -- Waffen SS) SSArtBN SS Artillery...34 Rocket Launcher) Battalion VWBty Volkswerfer ("People’s" Rocket Launcher) Battery VTB Volga Tartar Battalion Note: SS = Waffen SS (Schutz Staffeln

Associations of Personality with Alcohol Use Behaviour and Alcohol Problems in Adolescents Receiving Child Welfare Services

ERIC Educational Resources Information Center

Stewart, Sherry Heather; McGonnell, Melissa; Wekerle, Christine; Adlaf, Ed

2011-01-01

Four specific personality factors have been theorized to put adolescents at risk for alcohol abuse: hopelessness (HOP), anxiety sensitivity (AS), sensation seeking (SS), and impulsivity (IMP). We examined relations of these personality factors to various alcohol-related indices in a sample at high risk for alcohol problems--specifically, a child…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Damian, Luminita, E-mail: luminitadamian@microcal.eu.com; Universite de Toulouse, UPS, IPBS, F-31077 Toulouse; IUB, School of Engineering and Science, D-28727 Bremen

Is single-strand DNA translatable? Since the 60s, the question still remains whether or not DNA could be directly translated into protein. Some discrepancies in the results were reported about functional translation of single-strand DNA but all results converged on a similar behavior of RNA and ssDNA in the initiation step. Isothermal Titration Calorimetry method was used to determine thermodynamic constants of interaction between single-strand DNA and S30 extract of Escherichia coli. Our results showed that the binding was not affected by the nature of the template tested and the dissociation constants were in the same range when ssDNA (K{sub d}more » = 3.62 {+-} 2.1 x 10{sup -8} M) or the RNA corresponding sequence (K{sub d} = 2.7 {+-} 0.82 x 10{sup -8} M) bearing SD/ATG sequences were used. The binding specificity was confirmed by antibiotic interferences which block the initiation complex formation. These results suggest that the limiting step in translation of ssDNA is the elongation process.« less

Metal-organic frameworks for precise inclusion of single-stranded DNA and transfection in immune cells.

PubMed

Peng, Shuang; Bie, Binglin; Sun, Yangzesheng; Liu, Min; Cong, Hengjiang; Zhou, Wentao; Xia, Yucong; Tang, Heng; Deng, Hexiang; Zhou, Xiang

2018-04-03

Effective transfection of genetic molecules such as DNA usually relies on vectors that can reversibly uptake and release these molecules, and protect them from digestion by nuclease. Non-viral vectors meeting these requirements are rare due to the lack of specific interactions with DNA. Here, we design a series of four isoreticular metal-organic frameworks (Ni-IRMOF-74-II to -V) with progressively tuned pore size from 2.2 to 4.2 nm to precisely include single-stranded DNA (ssDNA, 11-53 nt), and to achieve reversible interaction between MOFs and ssDNA. The entire nucleic acid chain is completely confined inside the pores providing excellent protection, and the geometric distribution of the confined ssDNA is visualized by X-ray diffraction. Two MOFs in this series exhibit excellent transfection efficiency in mammalian immune cells, 92% in the primary mouse immune cells (CD4+ T cell) and 30% in human immune cells (THP-1 cell), unrivaled by the commercialized agents (Lipo and Neofect).

Validation of the early childhood attitude toward women in science scale (ECWiSS): A pilot administration

NASA Astrophysics Data System (ADS)

Mulkey, Lynn M.

The intention of this research was to measure attitudes of young children toward women scientists. A 27-item instrument, the Early Childhood Women in Science Scale (ECWiSS) was validated in a test case of the proposition that differential socialization predicts entry into the scientific talent pool. Estimates of internal consistency indicated that the scale is highly reliable. Known groups and correlates procedures, employed to determine the validity of the instrument, revealed that the scale is able to discriminate significant differences between groups and distinguishes three dimensions of attitude (role-specific self-concept, home-related sex-role conflict, and work-related sex-role conflict). Results of the analyses also confirmed the anticipated pattern of correlations with measures of another construct. The findings suggest the utility of the ECWiSS for measurement of early childhood attitudes in models of the ascriptive and/or meritocratic processes affecting recruitment to science and more generally in program and curriculum evaluation where attitude toward women in science is the construct of interest.

Multicomponent polymeric nanoparticles enhancing intracellular drug release in cancer cells.

PubMed

Ahmed, Arsalan; Liu, Sen; Pan, Yutong; Yuan, Shanmei; He, Jian; Hu, Yong

2014-12-10

Three kinds of amphiphilic copolymer, that is, poly(ε-caprolactone)-SS-poly(ethylene glycol) (PCL-SS-PEG), poly(ε-caprolactone)-polyethylenimine (PCL-PEI), and poly(ε-caprolactone)-polyethylenimine-folate (PCL-PEI-Fol) were synthesized and self-assembled into surface engineered hybrid nanoparticles (NPs). Morphological studies elucidated the stable, spherical, and uniform sandwich structure of the NPs. PCL-PEI and PCL-SS-PEG segments have introduced pH and reduction responsive characteristics in these NPs, while PCL-PEI-FA copolymers could provide specific targeting capability to cancer cells. The stimuli responsive capabilities of these NPs were carried out. Negative-to-positive charge reversible property, in response to the pH change, was investigated by zeta potential and nuclear magnetic resonance (NMR) measurements. The structure cleavage, due to redox gradient, was studied by dynamic light scattering (DLS) and transmission electron microscopy (TEM). These NPs showed controlled degradation, better drug release, less toxicity, and effective uptake in MCF-7 breast cancer cells. These multifunctional NPs showed promising potential in the treatment of cancer.

Biomass hydrolysis inhibition at high hydrogen partial pressure in solid-state anaerobic digestion.

PubMed

Cazier, E A; Trably, E; Steyer, J P; Escudie, R

2015-08-01

In solid-state anaerobic digestion, so-called ss-AD, biogas production is inhibited at high total solids contents. Such inhibition is likely caused by a slow diffusion of dissolved reaction intermediates that locally accumulate. In this study, we investigated the effect of H2 and CO2 partial pressure on ss-AD. Partial pressure of H2 and/or CO2 was artificially fixed, from 0 to 1 557mbars for H2 and from 0 to 427mbars for CO2. High partial pressure of H2 showed a significant effect on methanogenesis, while CO2 had no impact. At high [Formula: see text] , the overall substrate degradation decreased with no accumulation of metabolites from acidogenic bacteria, indicating that the hydrolytic activity was specifically impacted. Interestingly, such inhibition did not occur when CO2 was added with H2. This result suggests that CO2 gas transfer is probably a key factor in ss-AD from biomass. Copyright © 2015 Elsevier Ltd. All rights reserved.

Periodic Assembly of Nanospecies on Repetitive DNA Sequences Generated on Gold Nanoparticles by Rolling Circle Amplification

NASA Astrophysics Data System (ADS)

Zhao, Weian; Brook, Michael A.; Li, Yingfu

Periodical assembly of nanospecies is desirable for the construction of nanodevices. We provide a protocol for the preparation of a gold nanoparticle (AuNP)/DNA scaffold on which nanospecies can be assembled in a periodical manner. AuNP/DNA scaffold is prepared by growing long single-stranded DNA (ssDNA) molecules (typically hundreds of nanometers to a few microns in length) on AuNPs via rolling circle amplification (RCA). Since these long ssDNA molecules contain many repetitive sequence units, complementary DNA-attached nanospecies can be assembled through specific hybridization in a controllable and periodical manner.

Electronic excitation of molecules in solution calculated using the symmetry-adapted cluster–configuration interaction method in the polarizable continuum model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukuda, Ryoichi, E-mail: fukuda@ims.ac.jp; Ehara, Masahiro; Elements Strategy Initiative for Catalysts and Batteries

2015-12-31

The effects from solvent environment are specific to the electronic states; therefore, a computational scheme for solvent effects consistent with the electronic states is necessary to discuss electronic excitation of molecules in solution. The PCM (polarizable continuum model) SAC (symmetry-adapted cluster) and SAC-CI (configuration interaction) methods are developed for such purposes. The PCM SAC-CI adopts the state-specific (SS) solvation scheme where solvent effects are self-consistently considered for every ground and excited states. For efficient computations of many excited states, we develop a perturbative approximation for the PCM SAC-CI method, which is called corrected linear response (cLR) scheme. Our test calculationsmore » show that the cLR PCM SAC-CI is a very good approximation of the SS PCM SAC-CI method for polar and nonpolar solvents.« less

Deep-sea vent phage DNA polymerase specifically initiates DNA synthesis in the absence of primers.

PubMed

Zhu, Bin; Wang, Longfei; Mitsunobu, Hitoshi; Lu, Xueling; Hernandez, Alfredo J; Yoshida-Takashima, Yukari; Nunoura, Takuro; Tabor, Stanley; Richardson, Charles C

2017-03-21

A DNA polymerase is encoded by the deep-sea vent phage NrS-1. NrS-1 has a unique genome organization containing genes that are predicted to encode a helicase and a single-stranded DNA (ssDNA)-binding protein. The gene for an unknown protein shares weak homology with the bifunctional primase-polymerases (prim-pols) from archaeal plasmids but is missing the zinc-binding domain typically found in primases. We show that this gene product has efficient DNA polymerase activity and is processive in DNA synthesis in the presence of the NrS-1 helicase and ssDNA-binding protein. Remarkably, this NrS-1 DNA polymerase initiates DNA synthesis from a specific template DNA sequence in the absence of any primer. The de novo DNA polymerase activity resides in the N-terminal domain of the protein, whereas the C-terminal domain enhances DNA binding.

Unexplained cough: it is time to rule out Sjogren's syndrome.

PubMed

Koslow, Matthew; Kivity, Shaye; Vishnevskia-Dai, Vicktoria; Ben-Dov, Issahar

2018-05-01

Sjogren's syndrome is associated with chronic cough, but sicca symptoms are missing from cough evaluation guidelines. We evaluated patients with unexplained cough for undiagnosed Sjogren's syndrome. Patients referred to our pulmonary clinic (Sheba Medical Center, 2009 to 2012) with unexplained cough and concomitant dry eyes were selected for evaluation. Unexplained cough was defined as chronic cough of unknown etiology despite algorithm-based evaluation and treatment. Patients were evaluated in a dedicated clinic by a pulmonologist, rheumatologist, and ophthalmologist specializing in autoimmune disease. Patients completed the Leicester Cough Questionnaire, spirometry, antibody testing for anti Ro/La, ophthalmologic examination with visual acuity, eyelid, ocular surface fluorescein staining, tear break-up time and Schirmer's test, full slit lamp, and fundus examinations. Four-year follow-up was conducted by telephone questionnaire. We identified 24 patients among which 22 (21 females) agreed for evaluation. Eight patients (36%), seven initially, and one during follow-up were diagnosed with Sjogren's syndrome (SS) (six secondary and two primary SS). At 4-year follow-up, cough tended to persist and improve in only 37% with SS. These include 2 (Scl and RA) who received rituximab and 1 (stage 1 sarcoidosis) with spontaneous improvement. In contrast, cough improved in most (64%) patients without SS; the majority (eight/nine) report intensified disease-specific treatment (five allergic and three GERD). We describe patients in whom unexplained chronic cough was associated with dry eyes. Focused workup revealed undiagnosed Sjogren's syndrome in 36%. Dry eyes, with or without SS, is under-recognized and should be added to diagnostic algorithms for unexplained cough.

RNA-LIM: a novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure.

PubMed

Hall, Damien; Li, Songling; Yamashita, Kazuo; Azuma, Ryuzo; Carver, John A; Standley, Daron M

2015-03-01

RNA-LIM is a procedure that can analyze various pseudo-potentials describing the affinity between single-stranded RNA (ssRNA) ribonucleotides and surface amino acids to produce a coarse-grained estimate of the structure of the ssRNA at the protein interface. The search algorithm works by evolving an ssRNA chain, of known sequence, as a series of walks between fixed sites on a protein surface. Optimal routes are found by application of a set of minimal "limiting" restraints derived jointly from (i) selective sampling of the ribonucleotide amino acid affinity pseudo-potential data, (ii) limited surface path exploration by prior determination of surface arc lengths, and (iii) RNA structural specification obtained from a statistical potential gathered from a library of experimentally determined ssRNA structures. We describe the general approach using a NAST (Nucleic Acid Simulation Tool)-like approximation of the ssRNA chain and a generalized pseudo-potential reflecting the location of nucleic acid binding residues. Minimum and maximum performance indicators of the methodology are established using both synthetic data, for which the pseudo-potential defining nucleic acid binding affinity is systematically degraded, and a representative real case, where the RNA binding sites are predicted by the amplified antisense RNA (aaRNA) method. Some potential uses and extensions of the routine are discussed. RNA-LIM analysis programs along with detailed instructions for their use are available on request from the authors. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

The Differential Diagnosis of Dry Eyes, Dry Mouth, and Parotidomegaly: A Comprehensive Review.

PubMed

Cornec, Divi; Saraux, Alain; Jousse-Joulin, Sandrine; Pers, Jacques-Olivier; Boisramé-Gastrin, Sylvie; Renaudineau, Yves; Gauvin, Yves; Roguedas-Contios, Anne-Marie; Genestet, Steeve; Chastaing, Myriam; Cochener, Béatrice; Devauchelle-Pensec, Valérie

2015-12-01

Primary Sjögren's syndrome (pSS) is a frequent autoimmune systemic disease, clinically characterized by eyes and mouth dryness in all patients, salivary gland swelling or extraglandular systemic manifestations in half of the patients, and development of lymphoma in 5 to 10 % of the patients. However, patients presenting with sicca symptoms or salivary gland swelling may have a variety of conditions that may require very different investigations, treatments, or follow-up. Eye and/or mouth dryness is a frequent complaint in clinical setting, and its frequency increases with age. When evaluating a patient with suspected pSS, the first step is to rule out its differential diagnoses, before looking for positive arguments for the disease. Knowledge of normal and abnormal lachrymal and salivary gland physiology allows the clinician to prescribe the most adapted procedures for evaluating their function and structure. New tests have been developed in recent years for evaluating these patients, notably new ocular surface staining scores or salivary gland ultrasonography. We describe the different diagnoses performed in our monocentric cohort of 240 patients with suspected pSS. The most frequent diagnoses are pSS, other systemic autoimmune diseases, idiopathic sicca syndrome and drug-induced sicca syndrome. However, other diseases are important to rule out due to their specific management, such as sarcoidosis, granulomatosis with polyangeitis, IgG4-related disease, chronic hepatitis C virus or human immunodeficiency virus infections, graft-versus-host disease, and head and neck radiation therapy. At the light of these data, we propose a core of minimal investigations to be performed when evaluating a patient with suspected pSS.

The use of whole saliva in the differential diagnosis of Sjögren's syndrome.

PubMed

Sreebny, L M; Zhu, W X

1996-04-01

Sjögren's Syndrome (SS) is a chronic, multisystem, autoimmune disorder. It is characterized by (1) generalized exocrine gland dysfunction, (2) serologic abnormalities, and (3) organ-system changes. Oral changes are a prominent feature of this disease. Among these are xerostomia and hypofunction of the salivary glands. Given the intimate relationship between SS and the salivary glands, it is reasonable to postulate that whole saliva (WS) contains the stigmata associated with the presence of this disease. But few studies have been conducted on this secretion. Indeed, WS has largely been neglected and ignored by physicians, dentists, and scientists. Objections to its use have included the fact that it is "impure", that it does not adequately represent what is present in the salivary glands, that no standards have been established for its rate of flow, and that findings based on it lack specificity. Yet, it is this secretion which coats and protects the hard and soft oral tissues, enables us to prepare our food for digestion, and assists our speech. This review will demonstrate that there is a uniqueness and constancy to whole saliva and that it may be used to diagnose the presence of SS. "Screening tests", which include several simple-to-perform sialometric, chemical, and microbiologic procedures, may be conducted in doctors' offices to establish the "profile" of an SS patient. Electrophoretic studies may be used to study the nature of the salivary proteins, and an immunologic test, which is performed on WS and utilizes Western Blot Autoantibody Strips (ImmunoVision, Springdale, AR), may be used to establish the definitive diagnosis of SS.

Investigation of Local Structures in Cation-ordered Microwave Dielectric A Solid-state NMR and First Principle Calculation Study

NASA Astrophysics Data System (ADS)

Kalfarisi, Rony G.

Solid-state Nuclear Magnetic Resonance (ssNMR) spectroscopy has proven to be a powerful method to probe the local structure and dynamics of a system. In powdered solids, the nuclear spins experience various anisotropic interactions which depend on the molecular orientation. These anisotropic interactions make ssNMR very useful as they give a specific appearance to the resonance lines of the spectra. The position and shape of these resonance lines can be related to local structure and dynamics of the system under study. My research interest has focused around studying local structures and dynamics of quadrupolar nuclei in materials using ssNMR spectroscopy. 7Li and 93Nb ssNMR magic angle spinning (MAS) spectra, acquired at 17.6 and 7.06 T, have been used to evaluate the structural and dynamical properties of cation-ordered microwave dielectric materials. Microwave dielectric materials are essential in the application of wireless telecommunication, biomedical engineering, and other scientific and industrial implementations that use radio and microwave signals. The study of the local environment with respect to average structure, such as X-ray diffraction study, is essential for the better understanding of the correlations between structures and properties of these materials. The investigation for short and medium range can be performed with the use of ssNMR techniques. Even though XRD results show cationic ordering at the B-site (third coordination sphere), NMR spectra show a presence of disorder materials. This was indicated by the observation of a distribution in NMR parameters derived from experimental . {93}Nb NMR spectraand supported by theoretical calculations.

Microzooplankton grazing and phytoplankton growth in marine mesocosms with increased CO2 levels

NASA Astrophysics Data System (ADS)

Suffrian, K.; Simonelli, P.; Nejstgaard, J. C.; Putzeys, S.; Carotenuto, Y.; Antia, A. N.

2008-01-01

Microzooplankton grazing and algae growth responses to increasing pCO2 levels (350, 700 and 1050 μatm) were investigated in nitrate and phosphate fertilized mesocosms during the PeECE III experiment 2005. Grazing and growth rates were estimated by the dilution technique combined with taxon specific HPLC pigment analysis. Phytoplankton and microzooplankton composition were determined by light microscopy. Despite a range up to 3 times the present CO2 levels, there were no clear differences in any measured parameter between the different CO2 treatments. Thus, during the first 9 days of the experiment the algae community standing stock (SS), measured as chlorophyll a (Chl a), showed the highest instantaneous grow rates (0.02-0.99 d-1) and increased from ca 2-3 to 6-12 μg l-1, in all mesocosms. Afterwards the phytoplankton SS decreased in all mesocosms until the end of the experiment. The microzooplankton SS, that was mainly dinoflagellates and ciliates varied between 23 and 130 μg C l-1, peaking on day 13-15, apparently responding to the phytoplankton development. Instantaneous Chl a growth rates were generally higher than the grazing rates, indicating only a limited overall effect of microzooplankton grazing on the most dominant phytoplankton. Diatoms and prymnesiophytes were significantly grazed (14-43% of the SS d-1) only in the pre-bloom phase when they were in low numbers and in the post-bloom phase when they were already limited by low nutrients and/or virus lysis. The cyanobacteria populations appeared more effected by microzooplankton grazing, generally removing 20-65% of the SS d-1.

Peach water relations, gas exchange, growth and shoot mortality under water deficit in semi-arid weather conditions.

PubMed

Rahmati, Mitra; Davarynejad, Gholam Hossein; Génard, Michel; Bannayan, Mohammad; Azizi, Majid; Vercambre, Gilles

2015-01-01

In this study the sensitivity of peach tree (Prunus persica L.) to three water stress levels from mid-pit hardening until harvest was assessed. Seasonal patterns of shoot and fruit growth, gas exchange (leaf photosynthesis, stomatal conductance and transpiration) as well as carbon (C) storage/mobilization were evaluated in relation to plant water status. A simple C balance model was also developed to investigate sink-source relationship in relation to plant water status at the tree level. The C source was estimated through the leaf area dynamics and leaf photosynthesis rate along the season. The C sink was estimated for maintenance respiration and growth of shoots and fruits. Water stress significantly reduced gas exchange, and fruit, and shoot growth, but increased fruit dry matter concentration. Growth was more affected by water deficit than photosynthesis, and shoot growth was more sensitive to water deficit than fruit growth. Reduction of shoot growth was associated with a decrease of shoot elongation, emergence, and high shoot mortality. Water scarcity affected tree C assimilation due to two interacting factors: (i) reduction in leaf photosynthesis (-23% and -50% under moderate (MS) and severe (SS) water stress compared to low (LS) stress during growth season) and (ii) reduction in total leaf area (-57% and -79% under MS and SS compared to LS at harvest). Our field data analysis suggested a Ψstem threshold of -1.5 MPa below which daily net C gain became negative, i.e. C assimilation became lower than C needed for respiration and growth. Negative C balance under MS and SS associated with decline of trunk carbohydrate reserves--may have led to drought-induced vegetative mortality.

Peach Water Relations, Gas Exchange, Growth and Shoot Mortality under Water Deficit in Semi-Arid Weather Conditions

PubMed Central

Rahmati, Mitra; Davarynejad, Gholam Hossein; Génard, Michel; Bannayan, Mohammad; Azizi, Majid; Vercambre, Gilles

2015-01-01

In this study the sensitivity of peach tree (Prunus persica L.) to three water stress levels from mid-pit hardening until harvest was assessed. Seasonal patterns of shoot and fruit growth, gas exchange (leaf photosynthesis, stomatal conductance and transpiration) as well as carbon (C) storage/mobilization were evaluated in relation to plant water status. A simple C balance model was also developed to investigate sink-source relationship in relation to plant water status at the tree level. The C source was estimated through the leaf area dynamics and leaf photosynthesis rate along the season. The C sink was estimated for maintenance respiration and growth of shoots and fruits. Water stress significantly reduced gas exchange, and fruit, and shoot growth, but increased fruit dry matter concentration. Growth was more affected by water deficit than photosynthesis, and shoot growth was more sensitive to water deficit than fruit growth. Reduction of shoot growth was associated with a decrease of shoot elongation, emergence, and high shoot mortality. Water scarcity affected tree C assimilation due to two interacting factors: (i) reduction in leaf photosynthesis (-23% and -50% under moderate (MS) and severe (SS) water stress compared to low (LS) stress during growth season) and (ii) reduction in total leaf area (-57% and -79% under MS and SS compared to LS at harvest). Our field data analysis suggested a Ψstem threshold of -1.5 MPa below which daily net C gain became negative, i.e. C assimilation became lower than C needed for respiration and growth. Negative C balance under MS and SS associated with decline of trunk carbohydrate reserves – may have led to drought-induced vegetative mortality. PMID:25830350

Production of silk sericin/silk fibroin blend nanofibers

NASA Astrophysics Data System (ADS)

Zhang, Xianhua; Tsukada, Masuhiro; Morikawa, Hideaki; Aojima, Kazuki; Zhang, Guangyu; Miura, Mikihiko

2011-08-01

Silk sericin (SS)/silk fibroin (SF) blend nanofibers have been produced by electrospinning in a binary SS/SF trifluoroacetic acid (TFA) solution system, which was prepared by mixing 20 wt.% SS TFA solution and 10 wt.% SF TFA solution to give different compositions. The diameters of the SS/SF nanofibers ranged from 33 to 837 nm, and they showed a round cross section. The surface of the SS/SF nanofibers was smooth, and the fibers possessed a bead-free structure. The average diameters of the SS/SF (75/25, 50/50, and 25/75) blend nanofibers were much thicker than that of SS and SF nanofibers. The SS/SF (100/0, 75/25, and 50/50) blend nanofibers were easily dissolved in water, while the SS/SF (25/75 and 0/100) blend nanofibers could not be completely dissolved in water. The SS/SF blend nanofibers could not be completely dissolved in methanol. The SS/SF blend nanofibers were characterized by Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry, and differential thermal analysis. FTIR showed that the SS/SF blend nanofibers possessed a random coil conformation and ß-sheet structure.

Halophilic Bacteria of Lunsu Produce an Array of Industrially Important Enzymes with Salt Tolerant Activity.

PubMed

Gupta, Sonika; Sharma, Parul; Dev, Kamal; Sourirajan, Anuradha

2016-01-01

The halophilic bacterial isolates SS1, SS2, SS3, SS5, and SS8 were characterized for production of industrially important enzymes like amylase, protease, lipase, and glutaminase. Halophilic bacterial isolates SS1 and SS3 exhibited salt dependent extracellular amylase and protease activities. Both the halophilic isolates SS1 and SS3 exhibited maximum amylase and protease activities in the presence of 1.5 and 1.0 M NaCl, respectively, with the optimum pH 8 and temperature 40°C. SS2 showed maximum extracellular protease and lipase activities in the presence of 0.75 M NaCl, at optimum pH of 7, and temperature 37°C. The glutaminase activity of SS3 increased with increase in concentration of NaCl up to 2.5 M. The optimum pH and temperature for L-glutaminase activity of SS3 was 8 and 40°C, respectively. The combined hydrolytic activities of these halophilic bacterial isolates can be used for bioconversion of organic materials to useful products.

Halophilic Bacteria of Lunsu Produce an Array of Industrially Important Enzymes with Salt Tolerant Activity

PubMed Central

Gupta, Sonika; Sharma, Parul; Dev, Kamal; Sourirajan, Anuradha

2016-01-01

The halophilic bacterial isolates SS1, SS2, SS3, SS5, and SS8 were characterized for production of industrially important enzymes like amylase, protease, lipase, and glutaminase. Halophilic bacterial isolates SS1 and SS3 exhibited salt dependent extracellular amylase and protease activities. Both the halophilic isolates SS1 and SS3 exhibited maximum amylase and protease activities in the presence of 1.5 and 1.0 M NaCl, respectively, with the optimum pH 8 and temperature 40°C. SS2 showed maximum extracellular protease and lipase activities in the presence of 0.75 M NaCl, at optimum pH of 7, and temperature 37°C. The glutaminase activity of SS3 increased with increase in concentration of NaCl up to 2.5 M. The optimum pH and temperature for L-glutaminase activity of SS3 was 8 and 40°C, respectively. The combined hydrolytic activities of these halophilic bacterial isolates can be used for bioconversion of organic materials to useful products. PMID:26885394

Construction, characterization and evaluation of the protective efficacy of the Streptococcus suis double mutant strain ΔSsPep/ΔSsPspC as a live vaccine candidate in mice.

PubMed

Hu, Jin; You, Wujin; Wang, Bin; Hu, Xueying; Tan, Chen; Liu, Jinlin; Chen, Huanchun; Bei, Weicheng

2015-01-01

Streptococcus suis serotype 2 (S. suis 2) causes sepsis and meningitis in piglets and humans, and results in one of the most serious bacterial diseases affecting the production of commercial pigs around the world. Due to the failure of the current inactivated vaccine to protect against the disease, development of a new attenuated live vaccine against S. suis 2 by deleting essential virulence factors is urgently needed. We have previously reported the construction and characterization of an SsPep single gene deletion mutant strain ΔSsPep based on S. suis 2. Our previous results have shown that SsPep plays a critical role in the pathogenesis of S. suis 2. In this study, a precisely defined double-deletion mutant ΔSsPep/ΔSsPspC of S. suis 2 without antibiotic-resistance markers was constructed based on ΔSsPep, and the levels of virulence of the wild-type (WT) and ΔSsPep/ΔSsPspC were compared in a mouse experimental infection model. We demonstrated that the double mutant ΔSsPep/ΔSsPspC was less virulent than the WT, and could induce a noticeable antibody response. Analysis of IgG subclasses (IgG1 and IgG2a) indicated that both Th1 and Th2 responses were induced by ΔSsPep/ΔSsPspC, although the IgG2a (Th1) response predominated over the IgG1 (Th2) response. Moreover, ΔSsPep/ΔSsPspC could confer 90% protective efficacy against challenge with a lethal dose of fully virulent S. suis 2. Taken together, these data demonstrate that ΔSsPep/ΔSsPspC can be used as an effective live vaccine and provide a novel strategy against infection of S. suis 2. Copyright © 2014 Elsevier GmbH. All rights reserved.

Korean Solar Salt Ameliorates Colon Carcinogenesis in an AOM/DSS-Induced C57BL/6 Mouse Model.

PubMed

Ju, Jaehyun; Kim, Yeung-Ju; Park, Eui Seong; Park, Kun-Young

2017-06-01

The effects of Korean solar salt on an azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colon cancer C57BL/6 mouse model were studied. Korean solar salt samples (SS-S, solar salt from S salt field; SS-Yb, solar salt from Yb salt field), nine-time-baked bamboo salt (BS-9x, made from SS-Yb), purified salt (PS), and SS-G (solar salt from Guérande, France) were orally administered at a concentration of 1% during AOM/DSS colon cancer induction, and compared for their protective effects during colon carcinogenesis in C57BL/6 mice. SS-S and SS-Yb suppressed colon length shortening and tumor counts in mouse colons. Histological evaluation by hematoxylin and eosin staining also revealed suppression of tumorigenesis by SS-S. Conversely, PS and SS-G did not show a similar suppressive efficacy as Korean solar salt. SS-S and SS-Yb promoted colon mRNA expression of an apoptosis-related factor and cell-cycle-related gene and suppressed pro-inflammatory factor. SS-Yb baked into BS-9x further promoted these anti-carcinogenic efficacies. Taken together, the results indicate that Korean solar salt, especially SS-S and SS-Yb, exhibited anti-cancer activity by modulating apoptosis- and inflammation-related gene expression during colon carcinogenesis in mice, and bamboo salt baked from SS-Yb showed enhanced anti-cancer functionality.

A comparison between state-specific and linear-response formalisms for the calculation of vertical electronic transition energy in solution with the CCSD-PCM method.

PubMed

Caricato, Marco

2013-07-28

The calculation of vertical electronic transition energies of molecular systems in solution with accurate quantum mechanical methods requires the use of approximate and yet reliable models to describe the effect of the solvent on the electronic structure of the solute. The polarizable continuum model (PCM) of solvation represents a computationally efficient way to describe this effect, especially when combined with coupled cluster (CC) methods. Two formalisms are available to compute transition energies within the PCM framework: State-Specific (SS) and Linear-Response (LR). The former provides a more complete account of the solute-solvent polarization in the excited states, while the latter is computationally very efficient (i.e., comparable to gas phase) and transition properties are well defined. In this work, I review the theory for the two formalisms within CC theory with a focus on their computational requirements, and present the first implementation of the LR-PCM formalism with the coupled cluster singles and doubles method (CCSD). Transition energies computed with LR- and SS-CCSD-PCM are presented, as well as a comparison between solvation models in the LR approach. The numerical results show that the two formalisms provide different absolute values of transition energy, but similar relative solvatochromic shifts (from nonpolar to polar solvents). The LR formalism may then be used to explore the solvent effect on multiple states and evaluate transition probabilities, while the SS formalism may be used to refine the description of specific states and for the exploration of excited state potential energy surfaces of solvated systems.

Salivary alterations in type 2 (non-insulin-dependent) diabetes mellitus and hypertension.

PubMed

Dodds, M W; Yeh, C K; Johnson, D A

2000-10-01

The aim of this study was to determine whether saliva output and composition are altered in type 2 diabetes mellitus by comparison with a healthy, non-medicated control group, and also a group of hypertensives. From a community-dwelling cohort of Mexican American and European American subjects enrolled in the OH:SALSA oral aging study, we identified 233 subjects with type 2 diabetes mellitus, 227 with hypertension, and 240 healthy control subjects. We collected unstimulated whole (UW) and submandibular/ sublingual (US) saliva, as well as stimulated parotid (SP) and submandibular/ sublingual (SS) saliva. Flow rates were determined, yeast carriage was assayed in UW saliva, and SP and SS saliva samples were analyzed for protein composition. ELISA was used to determine concentrations of an array of specific protein components, with both antimicrobial and other activities. Both diabetic and hypertensive subjects had reduced output of both stimulated and unstimulated submandibular/sublingual saliva. 30% of the diabetic subjects had high oral yeast counts (> or =1000 cfu/mL) compared with 17% of the healthy subjects and 20% of the hypertensives. Significant increases in the concentrations of a number of the protein components were found in the diabetic subjects, specifically, SP lactoferrin, myeloperoxidase (MPO), and salivary peroxidase (SPO), as well as SS total protein, albumin, lactoferrin and secretory IgA. The pattern of decreased flow rates and increased protein concentrations were similar, but consistently greater in diabetics than hypertensives, suggesting that disease-specific mechanisms may be responsible. Diabetics may be more prone to oral dryness and infections than non-diabetics.

Cornhusker Army Ammunition Plant Remedial Investigation/Feasibility Study; UST and AST Site Investigation.

DTIC Science & Technology

1997-10-01

50000 1000 500000 Chromium CR JS16/SS18 4.05 5000 6.96 50000 Cobalt CO JS16/SS18 1.42 1000 25 50000 Copper CU JS16/SS18 0.965 2500 5 25000 Cyanide...5000 2 10000 Cadmium CD JS13/SS14 0.515 2000 5 5000 Calcium CA JS13/SS14 72 5000 50 5000 Chromium CR JS13/SS14 0.669 5000 22.4 7500 Cobalt CO JS13...ED SS14 21 ! Barium 130 UGL WELL G0053 24-Mar-92 ED SS14 21 Chromium LT 22.4 UGL WELL G0053 ! 24-Mar-92 ED SS14 21 : Cobalt LT ; 10.8 UGL WELL

Usefulness of Cytokeratin-18M65 in Diagnosing Non-Alcoholic Steatohepatitis in Japanese Population.

PubMed

Hasegawa, Yutaka; Kim, Soo Ryang; Hatae, Takashi; Ohta, Mitsuhiro; Fujinami, Aya; Sugimoto, Kayo; Kim, Ke Ih; Imoto, Susumu; Tohyama, Madoka; Kim, Soo Ki; Ikura, Yoshihiro; Kudo, Masatoshi

2015-10-01

The aim of this study was to evaluate cytokeratin-18M65 (CK-18M65) for distinguishing between simple steatosis (SS) and non-alcoholic steatohepatitis (NASH) against healthy individuals (HIs) in Japanese population. The serum from 24 HIs, 21 patients with SS and 20 patients with NASH were examined. Serum CK-18M65 was measured by enzyme-linked immunosorbent assay. Aspartate aminotransferase was significantly different between NASH patients and HIs with p < 0.0001 (SS patients and HIs: p < 0.0001), as was alanine aminotransferase between NASH patients and HIs with p < 0.0001 (SS patients and HIs: p < 0.0001). Serum CK-18M65 increased in a stepwise fashion in HIs and also in SS and NASH patients. Multivariate logistic regression analysis revealed that NASH could be diagnosed with the use of CK-18M65 alone (p = 0.0285, OR 1.0038, 95% CI 1.0004-1.0073). At the optimal cut-off level of 548 U/l, CK-18M65 had an AUC value of 0.7369, 60.00% sensitivity and 85.70% specificity. In patients with NASH, no significant difference was observed between low fibrosis (Stage 0-1, 794.30 ± 454.41, n = 10) and high fibrosis (Stage 2-3, 809.70 ± 641.43, n = 10; p = 0.5967) and between slight steatosis (<33%, 512.89 ± 229.65, n = 9) and moderate steatosis (≥33%, 655.13 ± 480.78, n = 32) in patients with non-alcoholic fatty liver disease (NAFLD; p = 0.7647) with the use of CK-18M65. Serum CK-18M65 distinguished NASH from SS, but could not assess the severity of steatosis in NAFLD patients or the grade of fibrosis in NASH patients in Japanese population. © 2015 S. Karger AG, Basel.

Clinical Severity Classification using Automated Conjunctival Hyperemia Analysis Software in Patients with Superior Limbic Keratoconjunctivitis.

PubMed

Kurita, Junki; Shoji, Jun; Inada, Noriko; Yoneda, Tsuyoshi; Sumi, Tamaki; Kobayashi, Masahiko; Hoshikawa, Yasuhiro; Fukushima, Atsuki; Yamagami, Satoru

2018-06-01

Digitization of clinical observation is necessary for assessing the severity of superior limbic keratoconjunctivitis (SLK). This study aimed to use a novel quantitative marker to examine hyperemia in patients with SLK. We included six eyes of six patients with both dry eye disease and SLK (SLK group) and eight eyes of eight patients with Sjögren syndrome (SS group). We simultaneously obtained the objective finding scores by using slit-lamp examination and calculated the superior hyperemia index (SHI) with an automated conjunctival hyperemia analysis software by using photographs of the anterior segment. Three objective finding scores, including papillary formation of the superior palpebral conjunctiva, superior limbal hyperemia and swelling, and superior corneal epitheliopathy, were determined. The SHI was calculated as the superior/temporal ratio of bulbar conjunctival hyperemia by using the software. Fisher's exact test was used to compare a high SHI (≥1.07) ratio between the SLK and SS groups. P-Values < 0.05 were considered statistically significant. The SHI (mean ± standard deviation) in the SLK and SS groups was 1.19 ± 0.50 and 0.69 ± 0.24, respectively. The number of patients with a high SHI (≥1.07) was significantly higher in the SLK group than in the SS group (p < 0.05). The sensitivity and specificity of the SHI in the differential diagnosis between SS and SLK were 66.7% and 87.5%, respectively. An analysis of the association between the objective finding scores and SHI showed that the SHI had a tendency to indicate the severity of superior limbal hyperemia and swelling score in the SLK group. The SHI calculated using the automated conjunctival hyperemia analysis software could successfully quantify superior bulbar conjunctival hyperemia and may be a useful tool for the differential diagnosis between SS and SLK and for the quantitative follow-up of patients with SLK.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Juan; Beltran, Chris J., E-mail: beltran.chris@mayo.edu; Herman, Michael G.

Purpose: To quantitatively and systematically assess dosimetric effects induced by spot positioning error as a function of spot spacing (SS) on intensity-modulated proton therapy (IMPT) plan quality and to facilitate evaluation of safety tolerance limits on spot position. Methods: Spot position errors (PE) ranging from 1 to 2 mm were simulated. Simple plans were created on a water phantom, and IMPT plans were calculated on two pediatric patients with a brain tumor of 28 and 3 cc, respectively, using a commercial planning system. For the phantom, a uniform dose was delivered to targets located at different depths from 10 tomore » 20 cm with various field sizes from 2{sup 2} to 15{sup 2} cm{sup 2}. Two nominal spot sizes, 4.0 and 6.6 mm of 1 σ in water at isocenter, were used for treatment planning. The SS ranged from 0.5 σ to 1.5 σ, which is 2–6 mm for the small spot size and 3.3–9.9 mm for the large spot size. Various perturbation scenarios of a single spot error and systematic and random multiple spot errors were studied. To quantify the dosimetric effects, percent dose error (PDE) depth profiles and the value of percent dose error at the maximum dose difference (PDE [ΔDmax]) were used for evaluation. Results: A pair of hot and cold spots was created per spot shift. PDE[ΔDmax] is found to be a complex function of PE, SS, spot size, depth, and global spot distribution that can be well defined in simple models. For volumetric targets, the PDE [ΔDmax] is not noticeably affected by the change of field size or target volume within the studied ranges. In general, reducing SS decreased the dose error. For the facility studied, given a single spot error with a PE of 1.2 mm and for both spot sizes, a SS of 1σ resulted in a 2% maximum dose error; a SS larger than 1.25 σ substantially increased the dose error and its sensitivity to PE. A similar trend was observed in multiple spot errors (both systematic and random errors). Systematic PE can lead to noticeable hot spots along the field edges, which may be near critical structures. However, random PE showed minimal dose error. Conclusions: Dose error dependence for PE was quantitatively and systematically characterized and an analytic tool was built to simulate systematic and random errors for patient-specific IMPT. This information facilitates the determination of facility specific spot position error thresholds.« less

Anti-cyclic citrullinated peptide antibodies and rheumatoid factor in Sjögren's syndrome.

PubMed

Barcelos, Filipe; Abreu, Isabel; Patto, José Vaz; Trindade, Hélder; Teixeira, Ana

2009-01-01

The purpose of this study was to evaluate the prevalence and clinical significance of anti-cyclic citrullinated peptide antibodies (anti-CCP-Abs), IgM and IgA rheumatoid factors (RFs) in primary Sjögren's Syndrome (pSS). We compared clinical and serological characteristics of 31 pSS and 31 Rheumatoid Arthritis (RA) patients. Both, anti-CCP-Abs and RFs (IgM, IgA) directed against Fc determinants of IgG from humans and rabbit were detected by enzyme-linked immunosorbent assay (ELISA). We included 31 blood donors as control group for the evaluation of RFs and anti-CCP-Abs. Nine (29%) pSS patients presented arthritis, and 10 (32,3%) RA patients also had secondary Sjögren's syndrome (sSS) RESULTS: IgM and IgA RFs prevalence was similar in pSS and RA, whichever the antigene (Human or Rabbit IgG) used. However, RA patients with sSS showed a tendency to present more often RF positivity, longer disease duration and higher ESR and CRP when compared with pSS patients with arthritis. Anti-CCP-Abs were detected in 64,5% of RA patients and in only 6,9% of pSS patients (p<0,0005). Anti-CCP-Abs were more often positive in RA patients with sSS (RA/sSS) (8 patients, 80%) than in RA patients without sSS (18 patients, 58,1%), and were absent in pSS patients with arthritis. RF-positive pSS patients presented more often pulmonary involvement and higher inflammatory parameters, and less often neuropathy compared to RF-negative patients. In controls, anti-CCP-Abs were absent and RFs were negligible. Anti-CCP-Abs were detected in only a few pSS patients, none of whom presented arthritis, which contrasts with the high frequency of these antibodies in RA/sSS. These results suggest that anti-CCP-Abs could be useful in the distinction between pSS and RA with sSS. Although not useful for the differential diagnosis between RA and pSS, RFs may have a prognostic role in pSS.

Impaired myogenic response and autoregulation of cerebral blood flow is rescued in CYP4A1 transgenic Dahl salt-sensitive rat

PubMed Central

Fan, Fan; Geurts, Aron M.; Murphy, Sydney R.; Pabbidi, Mallikarjuna R.; Jacob, Howard J.

2014-01-01

We have reported that a reduction in renal production of 20-HETE contributes to development of hypertension in Dahl salt-sensitive (SS) rats. The present study examined whether 20-HETE production is also reduced in the cerebral vasculature of SS rats and whether this impairs the myogenic response and autoregulation of cerebral blood flow (CBF). The production of 20-HETE, the myogenic response of middle cerebral arteries (MCA), and autoregulation of CBF were compared in SS, SS-5BN rats and a newly generated CYP4A1 transgenic rat. 20-HETE production was 6-fold higher in cerebral arteries of CYP4A1 and SS-5BN than in SS rats. The diameter of the MCA decreased to 70 ± 3% to 65 ± 6% in CYP4A1 and SS-5BN rats when pressure was increased from 40 to 140 mmHg. In contrast, the myogenic response of MCA isolated from SS rats did not constrict. Administration of a 20-HETE synthesis inhibitor, HET0016, abolished the myogenic response of MCA in CYP4A1 and SS-5BN rats but had no effect in SS rats. Autoregulation of CBF was impaired in SS rats compared with CYP4A1 and SS-5BN rats. Blood-brain barrier leakage was 5-fold higher in the brain of SS rats than in SS-5BN and SS.CYP4A1 rats. These findings indicate that a genetic deficiency in the formation of 20-HETE contributes to an impaired myogenic response in MCA and autoregulation of CBF in SS rats and this may contribute to vascular remodeling and cerebral injury following the onset of hypertension. PMID:25540098

Genome-Wide Analysis of the Sucrose Synthase Gene Family in Grape (Vitis vinifera): Structure, Evolution, and Expression Profiles

PubMed Central

Zhu, Xudong; Wang, Mengqi; Li, Xiaopeng; Jiu, Songtao; Wang, Chen; Fang, Jinggui

2017-01-01

Sucrose synthase (SS) is widely considered as the key enzyme involved in the plant sugar metabolism that is critical to plant growth and development, especially quality of the fruit. The members of SS gene family have been identified and characterized in multiple plant genomes. However, detailed information about this gene family is lacking in grapevine (Vitis vinifera L.). In this study, we performed a systematic analysis of the grape (V. vinifera) genome and reported that there are five SS genes (VvSS1–5) in the grape genome. Comparison of the structures of grape SS genes showed high structural conservation of grape SS genes, resulting from the selection pressures during the evolutionary process. The segmental duplication of grape SS genes contributed to this gene family expansion. The syntenic analyses between grape and soybean (Glycine max) demonstrated that these genes located in corresponding syntenic blocks arose before the divergence of grape and soybean. Phylogenetic analysis revealed distinct evolutionary paths for the grape SS genes. VvSS1/VvSS5, VvSS2/VvSS3 and VvSS4 originated from three ancient SS genes, which were generated by duplication events before the split of monocots and eudicots. Bioinformatics analysis of publicly available microarray data, which was validated by quantitative real-time reverse transcription PCR (qRT-PCR), revealed distinct temporal and spatial expression patterns of VvSS genes in various tissues, organs and developmental stages, as well as in response to biotic and abiotic stresses. Taken together, our results will be beneficial for further investigations into the functions of SS gene in the processes of grape resistance to environmental stresses. PMID:28350372

Shear stress regulates endothelial microparticle release.

PubMed

Vion, Anne-Clémence; Ramkhelawon, Bhama; Loyer, Xavier; Chironi, Gilles; Devue, Cecile; Loirand, Gervaise; Tedgui, Alain; Lehoux, Stéphanie; Boulanger, Chantal M

2013-05-10

Endothelial activation and apoptosis release membrane-shed microparticles (EMP) that emerge as important biological effectors. Because laminar shear stress (SS) is a major physiological regulator of endothelial survival, we tested the hypothesis that SS regulates EMP release. EMP levels were quantified by flow cytometry in medium of endothelial cells subjected to low or high SS (2 and 20 dyne/cm(2)). EMP levels augmented with time in low SS conditions compared with high SS conditions. This effect was sensitive to extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) and Rho kinases inhibitors but unaffected by caspase inhibitors. Low SS-stimulated EMP release was associated with increased endothelial Rho kinases and ERK1/2 activities and cytoskeletal reorganization. Overexpression of constitutively active RhoA stimulated EMP release under high SS. We also examined the effect of nitric oxide (NO) in mediating SS effects. L-NG-nitroarginine methyl ester (L-NAME), but not D-NG-nitroarginine methyl ester, increased high SS-induced EMP levels by 3-fold, whereas the NO donor S-nitroso-N-acetyl-D,L-penicillamine (SNAP) decreased it. L-NAME and SNAP did not affect Rho kinases and ERK1/2 activities. Then, we investigated NO effect on membrane remodeling because microparticle release is abolished in ABCA1-deficient cells. ABCA1 expression, which was greater under low SS than under high SS, was augmented by L-NAME under high SS and decreased by SNAP under low SS conditions. Altogether, these results demonstrate that sustained atheroprone low SS stimulates EMP release through activation of Rho kinases and ERK1/2 pathways, whereas atheroprotective high SS limits EMP release in a NO-dependent regulation of ABCA1 expression and of cytoskeletal reorganization. These findings, therefore, identify endothelial SS as a physiological regulator of microparticle release.

Lactic acid bacteria increase antiallergic effect of Artemisia princeps pampanini SS-1.

PubMed

Lee, Seung-Hoon; Shin, Yong-Wook; Bae, Eun-Ah; Lee, Bomi; Min, Sungwon; Baek, Nam-In; Chung, Hae-Gon; Kim, Nam-Jae; Kim, Dong-Hyun

2006-09-01

Artemisia princeps Pampanini, which is called Ssajuarissuk in Korean (SS-1), was fermented with lactic acid bacteria (LAB) and their passive cutaneous anaphylaxis reaction-inhibitory activity was investigated. Of these fermented agents, SS-1 extract fermented with Bifidobacterium infantis K-525 (F-SS-1) most effectively inhibited the release of P-hexosamindase from RBL-2H3 cells induced IgE. In IgE-induced RBL-2H3 cells, F-SS-1 inhibited proinflammatory cytokines IL-6 and TNF-alpha mRNA expression. Oral administration of SS-1 and F-SS-1 to mice inhibited passive cutaneous anaphylaxis (PCA) reaction induced by IgE and scratching behaviors induced by compound 48/80. The inhibitory activity of F-SS-1 against scratching behaviors was more effective than that of SS-1. These findings suggest that the fermentation of SS-1 with LAB can increase its antiallergic activity.

Teleost Fish-Specific Preferential Retention of Pigmentation Gene-Containing Families After Whole Genome Duplications in Vertebrates

PubMed Central

Lorin, Thibault; Brunet, Frédéric G.; Laudet, Vincent; Volff, Jean-Nicolas

2018-01-01

Vertebrate pigmentation is a highly diverse trait mainly determined by neural crest cell derivatives. It has been suggested that two rounds (1R/2R) of whole-genome duplications (WGDs) at the basis of vertebrates allowed changes in gene regulation associated with neural crest evolution. Subsequently, the teleost fish lineage experienced other WGDs, including the teleost-specific Ts3R before teleost radiation and the more recent Ss4R at the basis of salmonids. As the teleost lineage harbors the highest number of pigment cell types and pigmentation diversity in vertebrates, WGDs might have contributed to the evolution and diversification of the pigmentation gene repertoire in teleosts. We have compared the impact of the basal vertebrate 1R/2R duplications with that of the teleost-specific Ts3R and salmonid-specific Ss4R WGDs on 181 gene families containing genes involved in pigmentation. We show that pigmentation genes (PGs) have been globally more frequently retained as duplicates than other genes after Ts3R and Ss4R but not after the early 1R/2R. This is also true for non-pigmentary paralogs of PGs, suggesting that the function in pigmentation is not the sole key driver of gene retention after WGDs. On the long-term, specific categories of PGs have been repeatedly preferentially retained after ancient 1R/2R and Ts3R WGDs, possibly linked to the molecular nature of their proteins (e.g., DNA binding transcriptional regulators) and their central position in protein-protein interaction networks. Taken together, our results support a major role of WGDs in the diversification of the pigmentation gene repertoire in the teleost lineage, with a possible link with the diversity of pigment cell lineages observed in these animals compared to other vertebrates. PMID:29599177

Evaluation of Genome-Enabled Selection for Bacterial Cold Water Disease Resistance Using Progeny Performance Data in Rainbow Trout: Insights on Genotyping Methods and Genomic Prediction Models.

PubMed

Vallejo, Roger L; Leeds, Timothy D; Fragomeni, Breno O; Gao, Guangtu; Hernandez, Alvaro G; Misztal, Ignacy; Welch, Timothy J; Wiens, Gregory D; Palti, Yniv

2016-01-01

Bacterial cold water disease (BCWD) causes significant economic losses in salmonid aquaculture, and traditional family-based breeding programs aimed at improving BCWD resistance have been limited to exploiting only between-family variation. We used genomic selection (GS) models to predict genomic breeding values (GEBVs) for BCWD resistance in 10 families from the first generation of the NCCCWA BCWD resistance breeding line, compared the predictive ability (PA) of GEBVs to pedigree-based estimated breeding values (EBVs), and compared the impact of two SNP genotyping methods on the accuracy of GEBV predictions. The BCWD phenotypes survival days (DAYS) and survival status (STATUS) had been recorded in training fish (n = 583) subjected to experimental BCWD challenge. Training fish, and their full sibs without phenotypic data that were used as parents of the subsequent generation, were genotyped using two methods: restriction-site associated DNA (RAD) sequencing and the Rainbow Trout Axiom® 57 K SNP array (Chip). Animal-specific GEBVs were estimated using four GS models: BayesB, BayesC, single-step GBLUP (ssGBLUP), and weighted ssGBLUP (wssGBLUP). Family-specific EBVs were estimated using pedigree and phenotype data in the training fish only. The PA of EBVs and GEBVs was assessed by correlating mean progeny phenotype (MPP) with mid-parent EBV (family-specific) or GEBV (animal-specific). The best GEBV predictions were similar to EBV with PA values of 0.49 and 0.46 vs. 0.50 and 0.41 for DAYS and STATUS, respectively. Among the GEBV prediction methods, ssGBLUP consistently had the highest PA. The RAD genotyping platform had GEBVs with similar PA to those of GEBVs from the Chip platform. The PA of ssGBLUP and wssGBLUP methods was higher with the Chip, but for BayesB and BayesC methods it was higher with the RAD platform. The overall GEBV accuracy in this study was low to moderate, likely due to the small training sample used. This study explored the potential of GS for improving resistance to BCWD in rainbow trout using, for the first time, progeny testing data to assess the accuracy of GEBVs, and it provides the basis for further investigation on the implementation of GS in commercial rainbow trout populations.

Evaluation of Genome-Enabled Selection for Bacterial Cold Water Disease Resistance Using Progeny Performance Data in Rainbow Trout: Insights on Genotyping Methods and Genomic Prediction Models

PubMed Central

Vallejo, Roger L.; Leeds, Timothy D.; Fragomeni, Breno O.; Gao, Guangtu; Hernandez, Alvaro G.; Misztal, Ignacy; Welch, Timothy J.; Wiens, Gregory D.; Palti, Yniv

2016-01-01

Bacterial cold water disease (BCWD) causes significant economic losses in salmonid aquaculture, and traditional family-based breeding programs aimed at improving BCWD resistance have been limited to exploiting only between-family variation. We used genomic selection (GS) models to predict genomic breeding values (GEBVs) for BCWD resistance in 10 families from the first generation of the NCCCWA BCWD resistance breeding line, compared the predictive ability (PA) of GEBVs to pedigree-based estimated breeding values (EBVs), and compared the impact of two SNP genotyping methods on the accuracy of GEBV predictions. The BCWD phenotypes survival days (DAYS) and survival status (STATUS) had been recorded in training fish (n = 583) subjected to experimental BCWD challenge. Training fish, and their full sibs without phenotypic data that were used as parents of the subsequent generation, were genotyped using two methods: restriction-site associated DNA (RAD) sequencing and the Rainbow Trout Axiom® 57 K SNP array (Chip). Animal-specific GEBVs were estimated using four GS models: BayesB, BayesC, single-step GBLUP (ssGBLUP), and weighted ssGBLUP (wssGBLUP). Family-specific EBVs were estimated using pedigree and phenotype data in the training fish only. The PA of EBVs and GEBVs was assessed by correlating mean progeny phenotype (MPP) with mid-parent EBV (family-specific) or GEBV (animal-specific). The best GEBV predictions were similar to EBV with PA values of 0.49 and 0.46 vs. 0.50 and 0.41 for DAYS and STATUS, respectively. Among the GEBV prediction methods, ssGBLUP consistently had the highest PA. The RAD genotyping platform had GEBVs with similar PA to those of GEBVs from the Chip platform. The PA of ssGBLUP and wssGBLUP methods was higher with the Chip, but for BayesB and BayesC methods it was higher with the RAD platform. The overall GEBV accuracy in this study was low to moderate, likely due to the small training sample used. This study explored the potential of GS for improving resistance to BCWD in rainbow trout using, for the first time, progeny testing data to assess the accuracy of GEBVs, and it provides the basis for further investigation on the implementation of GS in commercial rainbow trout populations. PMID:27303436

Low-cost stainless-steel wool anodes modified with polyaniline and polypyrrole for high-performance microbial fuel cells

NASA Astrophysics Data System (ADS)

Sonawane, Jayesh M.; Patil, Sunil A.; Ghosh, Prakash C.; Adeloju, Samuel B.

2018-03-01

A conducting polymer coated stainless-steel wool (SS-W) is proposed for use as a low-cost anode for microbial fuel cells (MFCs). When coated with polyaniline (PANi) and polypyrrole (PPy), the pristine SS-W, SS/PANi-W and SS/PPy-W anodes produced maximum current densities of 0.30 ± 0.04, 0.67 ± 0.05, 0.56 ± 0.07 mA cm-2, respectively, in air-cathode MFCs. Also, based on achieved power density, both SS/PANi-W and SS/PPy-W achieved 0.288 ± 0.036 mW cm-2 and 0.187 ± 0.017 mW cm-2, respectively, which were superior to 0.127 ± 0.011 mW cm-2 obtained with pristine SS-W. Further, in comparison with SS-P based anodes, all SS-W based anodes gave improved power densities under similar experimental conditions by at least 70%. Moreover, the charge transfer resistance of the SS-W was much lower (240 ± 25 Ω cm-2) than for the SS-P (3192 ± 239 Ω cm-2). The j0(apparent) values obtained for SS/PANi-W (0.098 ± 0.007 mA cm-2) and SS/PPy-W (0.036 ± 0.004 mA cm-2) anodes were also much higher than that of the pristine SS-W (0.020 ± 0.005 mA cm-2), as well as than those of all SS-P based anodes. The observed enhancement of the bioelectrocatalytic performances were well supported by physicochemical and electrochemical characterisation.

Production of silk sericin/silk fibroin blend nanofibers

PubMed Central

2011-01-01

Silk sericin (SS)/silk fibroin (SF) blend nanofibers have been produced by electrospinning in a binary SS/SF trifluoroacetic acid (TFA) solution system, which was prepared by mixing 20 wt.% SS TFA solution and 10 wt.% SF TFA solution to give different compositions. The diameters of the SS/SF nanofibers ranged from 33 to 837 nm, and they showed a round cross section. The surface of the SS/SF nanofibers was smooth, and the fibers possessed a bead-free structure. The average diameters of the SS/SF (75/25, 50/50, and 25/75) blend nanofibers were much thicker than that of SS and SF nanofibers. The SS/SF (100/0, 75/25, and 50/50) blend nanofibers were easily dissolved in water, while the SS/SF (25/75 and 0/100) blend nanofibers could not be completely dissolved in water. The SS/SF blend nanofibers could not be completely dissolved in methanol. The SS/SF blend nanofibers were characterized by Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry, and differential thermal analysis. FTIR showed that the SS/SF blend nanofibers possessed a random coil conformation and ß-sheet structure. PMID:21867508

What level of estrogenic activity determined by in vitro assays in municipal waste waters can be considered as safe?

PubMed

Jarošová, Barbora; Bláha, Luděk; Giesy, John P; Hilscherová, Klára

2014-03-01

In vitro assays are broadly used tools to evaluate the estrogenic activity in Waste Water Treatment Plant (WWTP) effluents and their receiving rivers. Since potencies of individual estrogens to induce in vitro and in vivo responses can differ it is not possible to directly evaluate risks based on in vitro measures of estrogenic activity. Estrone, 17beta-estradiol, 17alfa-ethinylestradiol and to some extent, estriol have been shown to be responsible for the majority of in vitro estrogenic activity of municipal WWTP effluents. Therefore, in the present study safe concentrations of Estrogenic Equivalents (EEQs-SSE) in municipal WWTP effluents were derived based on simplified assumption that the steroid estrogens are responsible for all estrogenicity determined with particular in vitro assays. EEQs-SSEs were derived using the bioassay and testing protocol-specific in vitro potencies of steroid estrogens, in vivo predicted no effect concentration (PNECs) of these compounds, and their relative contributions to the overall estrogenicity detected in municipal WWTP effluents. EEQs-SSEs for 15 individual bioassays varied from 0.1 to 0.4ng EEQ/L. The EEQs-SSEs are supposed to be increased by use of location-specific dilution factors of WWTP effluents entering receiving rivers. They are applicable to municipal wastewater and rivers close to their discharges, but not to industrial waste waters. Copyright © 2013 Elsevier Ltd. All rights reserved.