On Not Being Able to Enter Noah's Ark

ERIC Educational Resources Information Center

Adamo, Simonetta M. G.

2010-01-01

The paper describes the psychoanalytic psychotherapy of a patient who had originally been referred at the age of 15 because of his social isolation. In fact, he suffered from high-functioning Asperger's syndrome and lived in an almost delusional world populated by a number of imaginary companions, which he used to counteract a deep void and sense…

Hatchery Spray Cabinet Administration Does Not Damage Avian Coronavirus Infectious Bronchitis Virus Vaccine Based on Analysis by Electron Microscopy and Virus Titration.

PubMed

Roh, Ha-Jung; Jordan, Brian J; Hilt, Deborah A; Ard, Mary B; Jackwood, Mark W

2015-03-01

studies in our laboratory showed that the Arkansas-Delmarva Poultry Industry (Ark-DPI) vaccine given to 1-day-old chickens by hatchery spray cabinet replicated poorly and failed to adequately protect broilers against homologous virus challenge, whereas the same vaccine given by eye-drop did replicate and the birds were protected following homologous virus challenge. To determine if mechanical damage following spray application plays a role in failure of the Ark-DPI vaccine, we examined the morphology of three Ark-DPI vaccines from different manufacturers using an electron microscope and included a Massachusetts (Mass) vaccine as control. One of the Ark-DPI vaccines (vaccine A) and the Mass vaccine had significantly (P < 0.005) fewer spikes than the other two Ark-DPI vaccines. We also found that the Ark-DPI and Mass vaccines had significantly (P < 0.005) fewer spike proteins per virus particle when compared to their respective challenge viruses. This observation is interesting and may provide some insight into the mechanism behind infectious bronchitis virus attenuation. No obvious differences were observed in virus morphology and no consistent trend in the number of spikes per virion was found in before- and after-spray samples. We also determined the vaccine titer before and after spray in embryonated eggs and found that both Ark-DPI and Mass vaccines had a similar drop in titer, 0.40 logi and 0.310 logi, respec10ively. Based on these data, it appears that mechanical damage to the Ark-DPI vaccine is not occurring when delivered by a hatchery spray cabinet, suggesting that some other factor is contributing to the failure of that vaccine when given by that method.

Turning Teachers into Designers: The Case of the Ark of Inquiry

ERIC Educational Resources Information Center

De Vries, Bregje; Schouwenaars, Ilona; Stokhof, Harry

2017-01-01

The Ark of Inquiry seeks to support inquiry-based science education (IBSE) in different countries and school systems across Europe by teachers that may differ in light of their prior experiences with IBSE. Given the differences, the assumption is that teachers need to make adaptations to the approach and materials of the Ark of Inquiry. This study…

Chromosome mapping of the human arrestin (SAG), {beta}-arrestin 2 (ARRB2), and {beta}-adrenergic receptor kinase 2 (ADRBK2) genes

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

Calabrese, G.; Sallese, M.; Stornaiuolo, A.

1994-09-01

Two types of proteins play a major role in determining homologous desensitization of G-coupled receptors: {beta}-adrenergic receptor kinase ({beta}ARK), which phosphorylates the agonist-occupied receptor and its functional cofactor, {beta}-arrestin. Both {beta}ARK and {beta}-arrestin are members of multigene families. The family of G-protein-coupled receptor kinases includes rhodopsin kinase, {beta}ARK1, {beta}ARK2, IT11-A (GRK4), GRK5, and GRK6. The arrestin/{beta}-arrestin gene family includes arrestin (also known as S-antigen), {beta}-arrestin 1, and {beta}-arrestin 2. Here we report the chromosome mapping of the human genes for arrestin (SAG), {beta}arrestin 2 (ARRB2), and {beta}ARK2 (ADRBK2) by fluorescence in situ hybridization (FISH). FISH results confirmed the assignment ofmore » the gene coding for arrestin (SAG) to chromosome 2 and allowed us to refine its localization to band q37. The gene coding for {beta}-arrestin 2 (ARRB2) was mapped to chromosome 17p13 and that coding for {beta}ARK2 (ADRBK2) to chromosome 22q11. 17 refs., 1 fig.« less

S1 of distinct IBV population expressed from recombinant adenovirus confers protection against challenge.

PubMed

Toro, H; Zhang, J F; Gallardo, R A; van Santen, V L; van Ginkel, F W; Joiner, K S; Breedlove, C

2014-06-01

Protective properties of three distinct infectious bronchitis virus (IBV) Ark Delmarva poultry industry (ArkDPI) S1 proteins encoded from replication-defective recombinant adenovirus vectors were investigated. Using a suboptimal dose of each recombinant virus, we demonstrated that IBV S1 amino acid sequences showing > or = 95.8% amino acid identity to the S1 of the challenge strain differed in their ability at conferring protection. Indeed, the S1 sequence of the IBV population previously designated C4 (AdIBVS1.C4), which protected the most poorly, differs from the S1 sequence of population C2 (AdIBVS1.C2), which provided the highest protection, only at amino acid position 56. The fact that a change in one amino acid in this region significantly altered the induction of a protective immune response against this protein provides evidence that the first portion of S1 displays relevant immunoprotective epitopes. Use of an optimal dose of AdIBVS1.C2 effectively protected chickens from clinical signs and significantly reduced viral load after IBV Ark virulent challenge. Moreover, increased numbers of both IgA and IgG IBV-specific antibody secreting lymphocytes were detected in the spleen after challenge. The increased response detected for both IgA and IgG lymphocytes after challenge might be explained by vaccine-induced B memory cells. The fact that a single vaccination with Ad/IBVS1.C2 provides protection against IBV challenge is promising, because Ad-vectored vaccines can be mass delivered by in ovo inoculation using automated in ovo injectors.

33 CFR 207.249 - Ouachita and Black Rivers, Ark. and La., Mile 0.0 to Mile 338.0 (Camden, Ark.) above the mouth of...

Code of Federal Regulations, 2011 CFR

2011-07-01

..., DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE NAVIGATION REGULATIONS § 207.249 Ouachita and Black Rivers, Ark... draft of at least 2 feet less than the depth over sills, or which have projections liable to damage... concerning depth over sills may be obtained from the lockman on duty. (iii) Vessels having chains, lines, or...

The role of ARK in stress-induced apoptosis in Drosophila cells

PubMed Central

Zimmermann, Katja C.; Ricci, Jean-Ehrland; Droin, Nathalie M.; Green, Douglas R.

2002-01-01

The molecular mechanisms of apoptosis are highly conserved throughout evolution. The homologs of genes essential for apoptosis in Caenorhabditis elegans and Drosophila melanogaster have been shown to be important for apoptosis in mammalian systems. Although a homologue for CED-4/apoptotic protease-activating factor (Apaf)-1 has been described in Drosophila, its exact function and the role of the mitochondrial pathway in its activation remain unclear. Here, we used the technique of RNA interference to dissect apoptotic signaling pathways in Drosophila cells. Inhibition of the Drosophila CED-4/Apaf-1–related killer (ARK) homologue resulted in pronounced inhibition of stress-induced apoptosis, whereas loss of ARK did not protect the cells from Reaper- or Grim-induced cell death. Reduction of DIAP1 induced rapid apoptosis in these cells, whereas the inhibition of DIAP2 expression did not but resulted in increased sensitivity to stress-induced apoptosis; apoptosis in both cases was prevented by inhibition of ARK expression. Cells in which cytochrome c expression was decreased underwent apoptosis induced by stress stimuli, Reaper or Grim. These results demonstrate the central role of ARK in stress-induced apoptosis, which appears to act independently of cytochrome c. Apoptosis induced by Reaper or Grim can proceed via a distinct pathway, independent of ARK. PMID:11901172

Studies on Freezing of Shell-Fish-I

NASA Astrophysics Data System (ADS)

Song, Dae Jin; Konagaya, Shiro; Tanaka, Takeo

Ark shell, Anadara broughtonii(Shrenk), are commonly eaten raw or under-done in Korea, Japan, and East Asian countries. Along with a recent remarkable development of culture fisheries, Ark shell has become one of the commercially important shell-fish species. Transportation and storage of large quantities of shell-fish is becoming increasingly important. This work was begun with this background to make clear the effects of temperature and length of storage time on the quality of frozen stored ark shell. Results are as follows : (1) There was little chang in amounts of free and expressible drip from ark shell flesh frozen stored at -40°CdegC for 6 months. Water holding capacity of the same meat was almost constant over 6 months storage. However, a mounts of both drip increased markedly after 2 months storage at -10°C. (2) Protein extractibility of ark shell flesh tended to decrease gradually from the begining when stored at -10°C, while at -20°C, the protein extractibility was stable for 3 months before decreasing gradually. However at -40°C, the protein extractibility was stable for 6 months. It was found that paramyosin was very stable even when the ark shell was frozen stored at -10°C. (3) It was observed that ark shell flesh became tough when frozen. The toughness of ark shell flesh as measured by an instrument increased with frozen storage time and increased temperature. (4) In the smooth muscle, it was histologically observed that initial small ice crystals formed between muscle bundles grew larger during frozen storage. It was found that the higher the storage temperature, the bigger the ice crystals formed. Aggregation of some muscle fiber and empty spaces between muscle bundles were observd after thawed muscles frozen stored at relatively high temperature such as -10°C.

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

PubMed

Coombe, Lauren; Zhang, Jessica; Vandervalk, Benjamin P; Chu, Justin; Jackman, Shaun D; Birol, Inanc; Warren, René L

2018-06-20

The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce ARKS, an alignment-free linked read genome scaffolding methodology that uses linked reads to organize genome assemblies further into contiguous drafts. Our approach departs from other read alignment-dependent linked read scaffolders, including our own (ARCS), and uses a kmer-based mapping approach. The kmer mapping strategy has several advantages over read alignment methods, including better usability and faster processing, as it precludes the need for input sequence formatting and draft sequence assembly indexing. The reliance on kmers instead of read alignments for pairing sequences relaxes the workflow requirements, and drastically reduces the run time. Here, we show how linked reads, when used in conjunction with Hi-C data for scaffolding, improve a draft human genome assembly of PacBio long-read data five-fold (baseline vs. ARKS NG50 = 4.6 vs. 23.1 Mbp, respectively). We also demonstrate how the method provides further improvements of a megabase-scale Supernova human genome assembly (NG50 = 14.74 Mbp vs. 25.94 Mbp before and after ARKS), which itself exclusively uses linked read data for assembly, with an execution speed six to nine times faster than competitive linked read scaffolders (~ 10.5 h compared to 75.7 h, on average). Following ARKS scaffolding of a human genome 10xG Supernova assembly (of cell line NA12878), fewer than 9 scaffolds cover each chromosome, except the largest (chromosome 1, n = 13). ARKS uses a kmer mapping strategy instead of linked read alignments to record and associate the barcode information needed to order and orient draft assembly sequences. The simplified workflow, when compared to that of our initial implementation, ARCS, markedly improves run time performances on experimental human genome datasets. Furthermore, the novel distance estimator in ARKS utilizes barcoding information from linked reads to estimate gap sizes. It accomplishes this by modeling the relationship between known distances of a region within contigs and calculating associated Jaccard indices. ARKS has the potential to provide correct, chromosome-scale genome assemblies, promptly. We expect ARKS to have broad utility in helping refine draft genomes.

Elemental profiling of Noah's Ark shell (Arca noae, Linnaeus, 1758) by plasma optical spectrometry and chemometric tools.

PubMed

Kobelja, Kristina; Nemet, Ivan; Župan, Ivan; Čulin, Jelena; Rončević, Sanda

2016-12-01

Determination of metal content in biominerals provides essential information with respect to relations between biomineralization processes and environmental status. Mussels are species that have a great potential as bio-marker species and therefore, they are in the focus of numerous biomineralization and ecological studies. In this study, elemental profile of mussel shell of Noah's Ark (Arca noe, Linnaeus, 1758), which inhabit eastern Adriatic Sea was obtained by determination of seventeen elements content using inductively coupled plasma optical emission spectrometry (ICP-OES). Shell samples were collected from marine protected area and from marine shipping route in eastern Adriatic Sea. The accuracy of applied analytical procedure based on microwave decomposition of shell samples was tested by use of reference materials of limestone and by matrix-matched standards. By aid of chemometric methods, the elemental profile along with variability of elements content of shell was obtained. The impact of different environment on elements content was established by use of multivariate statistical PCA method. Discernment between two groups of samples was manifested. Among results of main, minor and trace elements content, the last one which denoted to Cd, Co, Cu, Pb, and Mn was expressed as principal distinctive feature of shell samples collected from different sampling sites. Elemental profiling of mussel shell Noah's Ark provides novel insight in species status as well as in environmental status on the observed locations. Copyright © 2016 Elsevier GmbH. All rights reserved.

Astronomical calibration of 40Ar/39Ar reference minerals using high-precision, multi-collector (ARGUSVI) mass spectrometry

NASA Astrophysics Data System (ADS)

Phillips, D.; Matchan, E. L.; Honda, M.; Kuiper, K. F.

2017-01-01

The new generation of multi-collector mass spectrometers (e.g. ARGUSVI) permit ultra-high precision (<0.1%) 40Ar/39Ar geochronology of rocks and minerals. At the same time, the 40Ar/39Ar method is limited by relatively large uncertainties (>1%) in 40K decay constants and the ages of natural reference minerals that form the basis of the technique. For example, reported ages for widely used 40Ar/39Ar reference materials, such as the ca. 28 Ma Fish Canyon Tuff sanidine (FCTs) and the ca. 1.2 Ma Alder Creek Rhyolite sanidine (ACRs), vary by >1%. Recent attempts to independently calibrate these reference minerals have focused on K-Ar analyses of the same minerals and inter-comparisons with astronomically tuned tephras in sedimentary sequences and U-Pb zircon ages from volcanic rocks. Most of these studies used older generation (effectively single-collector) mass spectrometers that employed peak-jumping analytical methods to acquire 40Ar/39Ar data. In this study, we reassess the inter-calibration and ages of commonly used 40Ar/39Ar reference minerals Fish Canyon Tuff sanidine (FCTs), Alder Creek Rhyolite sanidine (ACRs) and Mount Dromedary biotite (MD2b; equivalent to GA-1550 biotite), relative to the astronomically tuned age of A1 Tephra sanidine (A1Ts), Faneromeni section, Crete (Rivera et al., 2011), using a multi-collector ARGUSVI mass spectrometer. These analyses confirm the exceptional precision capability (<0.1%) of this system, compared to most previous studies. All sanidine samples (FCTs, ACRs and A1Ts) exhibit discordant 40Ar/39Ar step-heating spectra, with generally monotonically increasing ages (∼1% gradients). The similarity in these patterns, mass-dependent fractionation modeling, and results from step-crushing experiments on FCTs, which yield younger apparent ages, suggest that the discordance may be due to a combination of recoil loss and redistribution of 39ArK and isotope mass fractionation. In contrast to our previous inferences, these results imply that the sanidine samples are suitable 40Ar/39Ar reference materials, provided appropriate corrections are included for differential recoil loss of 39ArK and contributions from xenocrysts/antecrysts can be resolved. Relative to an age of 6.943 ± 0.005 Ma for A1Ts, we calculate astronomically tuned ages for FCTs, ACRs and MD2b of 28.126 ± 0.019 (0.066%) Ma, 1.18144 ± 0.00068 (0.058%) Ma and 99.125 ± 0.076 (0.077%) Ma, respectively (95% internal errors). These results are consistent with recent 238U/206Pb age data from these localities, but are marginally younger (∼0.2%) than previous 40Ar/39Ar ages inter-calibrated with astronomically tuned tephra from the Mediterranean, and distinctly younger (0.6%) than results optimized against a broad array of 238U/206Pb zircon ages. Consideration of published and assumed recoil loss 39ArK proportions (0.18-0.40%), yields recoil-corrected age estimates of 28.187 ± 0.019 Ma, 1.18404 ± 0.00068 Ma and 99.204 ± 0.076 Ma, respectively. This comparison indicates inherent uncertainties of >0.1% in the 40Ar/39Ar ages of reference minerals without consideration of recoil artefacts, thus limiting the benefits of high precision multi-collector analyses. Significant improvement to the accuracy of the 40Ar/39Ar method (<0.1%) will require further inter-laboratory 40Ar/39Ar studies utilizing multi-collector mass spectrometry, additional constraints on recoil 39ArK loss from reference minerals, further resolution of discrepancies between astronomically tuned sedimentary successions and refinement of the 238U/206Pb zircon age cross-calibration approach.

Understanding Barriers and Facilitators to the use of Clinical Information Systems for Intensive Care Units and Anesthesia Record Keeping: A Rapid Ethnography

PubMed Central

Saleem, Jason J.; Plew, William R.; Speir, Ross C.; Herout, Jennifer; Wilck, Nancy R.; Ryan, Dale Marie; Cullen, Theresa A.; Scott, Jean M.; Beene, Murielle S.; Phillips, Toni

2017-01-01

Objective This study evaluated the current use of commercial-off-the-shelf Clinical Information Systems (CIS) for intensive care units (ICU) and Anesthesia Record Keeping (ARK) for operating rooms and post-anesthesia care recovery settings at three Veterans Affairs Medical Centers (VAMCs). Clinicians and administrative staff use these applications at bedside workstations, in operating rooms, at nursing stations, in physician’s rooms, and in other various settings. The intention of a CIS or an ARK system is to facilitate creation of electronic records of data, assessments, and procedures from multiple medical devices. The US Department of Veterans Affairs (VA) Office of the Chief of Nursing Informatics sought to understand usage barriers and facilitators to optimize these systems in the future. Therefore, a human factors study was carried out to observe the CIS and ARK systems in use at three VAMCs in order to identify best practices and suggested improvements to currently implemented CIS and ARK systems. Methods We conducted a rapid ethnographic study of clinical end-users interacting with the CIS and ARK systems in the critical care and anesthesia care areas in each of three geographically distributed VAMCs. Two observers recorded interactions and/or interview responses from 88 CIS and ARK end-users. We coded and sorted into logical categories field notes from 69 shadowed participants. The team transcribed and combined data from key informant interviews with 19 additional participants with the observation data. We then integrated findings across observations into meaningful patterns and abstracted the data into themes, which translated directly to barriers to effective adoption and optimization of the CIS and ARK systems. Results Effective optimization of the CIS and ARK systems was impeded by: (1) integration issues with other software systems; (2) poor usability; (3) software challenges; (4) hardware challenges; (5) training concerns; (6) unclear roles and lack of coordination among stakeholders; and (7) insufficient technical support. Many of these barriers are multi-faceted and have associated sub-barriers, which are described in detail along with relevant quotes from participants. In addition, regionalized purchases of different CIS and ARK systems, as opposed to enterprise level purchases, contributed to some of the identified barriers. Facilitators to system use included (1) automation and (2) a dedicated facility-level CIS-ARK coordinator. Conclusions We identified barriers that explain some of the challenges with the optimization of the CIS and ARK commercial systems across the Veterans Health Administration (VHA). To help address these barriers, and evolve them into facilitators, we categorized report findings as (1) interface and system-level changes that vendors or VA healthcare systems can implement; (2) implementation factors under VA control and not under VA control; and (3) factors that may be used to inform future application purchases. We outline several recommendations for improved adoption of CIS and ARK systems and further recommend that human factors engineering and usability requirements become an integral part of VA health information technology (HIT) application procurement, customization, and implementation in order to help eliminate or mitigate some of the barriers of use identified in this study. Human factors engineering methods can be utilized to apply a user-centered approach to application requirements specification, application evaluation, system integration, and application implementation. PMID:25843931

Understanding barriers and facilitators to the use of Clinical Information Systems for intensive care units and Anesthesia Record Keeping: A rapid ethnography.

PubMed

Saleem, Jason J; Plew, William R; Speir, Ross C; Herout, Jennifer; Wilck, Nancy R; Ryan, Dale Marie; Cullen, Theresa A; Scott, Jean M; Beene, Murielle S; Phillips, Toni

2015-07-01

This study evaluated the current use of commercial-off-the-shelf Clinical Information Systems (CIS) for intensive care units (ICUs) and Anesthesia Record Keeping (ARK) for operating rooms and post-anesthesia care recovery settings at three Veterans Affairs Medical Centers (VAMCs). Clinicians and administrative staff use these applications at bedside workstations, in operating rooms, at nursing stations, in physician's rooms, and in other various settings. The intention of a CIS or an ARK system is to facilitate creation of electronic records of data, assessments, and procedures from multiple medical devices. The US Department of Veterans Affairs (VA) Office of the Chief of Nursing Informatics sought to understand usage barriers and facilitators to optimize these systems in the future. Therefore, a human factors study was carried out to observe the CIS and ARK systems in use at three VAMCs in order to identify best practices and suggested improvements to currently implemented CIS and ARK systems. We conducted a rapid ethnographic study of clinical end-users interacting with the CIS and ARK systems in the critical care and anesthesia care areas in each of three geographically distributed VAMCs. Two observers recorded interactions and/or interview responses from 88 CIS and ARK end-users. We coded and sorted into logical categories field notes from 69 shadowed participants. The team transcribed and combined data from key informant interviews with 19 additional participants with the observation data. We then integrated findings across observations into meaningful patterns and abstracted the data into themes, which translated directly to barriers to effective adoption and optimization of the CIS and ARK systems. Effective optimization of the CIS and ARK systems was impeded by: (1) integration issues with other software systems; (2) poor usability; (3) software challenges; (4) hardware challenges; (5) training concerns; (6) unclear roles and lack of coordination among stakeholders; and (7) insufficient technical support. Many of these barriers are multi-faceted and have associated sub-barriers, which are described in detail along with relevant quotes from participants. In addition, regionalized purchases of different CIS and ARK systems, as opposed to enterprise level purchases, contributed to some of the identified barriers. Facilitators to system use included (1) automation and (2) a dedicated facility-level CIS-ARK Coordinator. We identified barriers that explain some of the challenges with the optimization of the CIS and ARK commercial systems across the Veterans Health Administration (VHA). To help address these barriers, and evolve them into facilitators, we categorized report findings as (1) interface and system-level changes that vendors or VA healthcare systems can implement; (2) implementation factors under VA control and not under VA control; and (3) factors that may be used to inform future application purchases. We outline several recommendations for improved adoption of CIS and ARK systems and further recommend that human factors engineering and usability requirements become an integral part of VA health information technology (HIT) application procurement, customization, and implementation in order to help eliminate or mitigate some of the barriers of use identified in this study. Human factors engineering methods can be utilized to apply a user-centered approach to application requirements specification, application evaluation, system integration, and application implementation. Published by Elsevier Ireland Ltd.

Natural Hazards Risk Reduction and the ARkStorm Scenario

NASA Astrophysics Data System (ADS)

Cox, D. A.; Dettinger, M. D.; Ralph, F. M.

2016-12-01

The ARkStorm Scenario project began in 2008, led by the USGS Multi-Hazards Demonstration Project (now Science Application for Risk Reduction) in an effort to innovate the application of science to reduce natural-hazard risk associated with large atmospheric-river (AR) storms on the West Coast of the US. The effort involved contributions from many federal, state and academic organizations including NOAA's Environmental Systems Laboratory. The ARkStorm project used new understanding of atmospheric river physics, combined with downscaled meteorological data from two recent ARs (in 1969 and 1986), to describe and model a prolonged sequence of back-to-back storms similar to those that bankrupted California in 1862. With this scientifically plausible (but not worst-case) scenario, the ARkStorm team engaged flood and levee experts to identify plausible flooding extents and durations, created a coastal-storm inundation model (CoSMoS), and California's first landslide susceptibility map, to better understand secondary meteorological and geophysical hazards (flood, wind, landslide, coastal erosion and inundation) across California. Physical damages to homes, infrastructure, agriculture, and the environment were then estimated to calculate the likely social and economic impact to California and the nation. Across California, property damage from the ARkStorm scenario was estimated to exceed 300 billion, mostly from flooding. Including damage and losses, lifeline damages and business interruptions, the total cost of an ARkStorm-sized series of storms came to nearly 725 billion, nearly three times the losses estimated from another SAFRR scenario describing a M7.8 earthquake in southern California. Thus, atmospheric rivers have the potential to be California's other "Big One." Since its creation, the ARkStorm scenario has been used in preparedness exercises by NASA, the US Navy, the State of California, the County of Ventura, and cities and counties in the Tahoe Basin and downstream into Nevada. These efforts have examined how large AR events could plausibly impact many aspects of society and environment, and how to avoid the worst of the disaster outcomes. The ARkStorm scenario will next be used in a climate extremes scenario for the U.S. Southwest.

4950TH Test Group (N) Final Report. Operation PLUMBBOB

DTIC Science & Technology

1980-12-01

READ INSTRUCTIONS BEFORE COMPLETING FORM 1. nlCiniNT’t CAT »LOC MUMBtR 1. TVPC Or RCPONT * PCRIOO COVCRCD ft. PCRrOMUINC ORC. RtPORT...r^ny letterr end gave rapid answers end decisions on individual questions and problen ercas as thej’ arose. The daily shuttle was giro utilised...encr^cmcy power tod con- Irnucd operations. CaT ^nications: All conminications normal except as noted under rrncrks. I.r-^arks: Reference Item

Earth Observations taken by the Expedition 27 Crew

NASA Image and Video Library

2011-05-12

ISS027-E-027019 (12 May 2011) --- Parts of two states highly impacted by recent flooding of the Mississippi River, are pictured in this International Space Station image featuring an area east of Blytheville, Ark., off the right side of the image. Center point coordinates are located at 35.8 degrees north latitude and 89.7 degrees west longitude The areas of Ruckers Place, Tenn. and Tomato, Ark. are surrounded by water, while Barfield, Ark. is still dry behind the levee on the right side of the image. North is toward the bottom of the photo.

Occurrence and distribution of dissolved solids, selenium, and uranium in groundwater and surface water in the Arkansas River Basin from the headwaters to Coolidge, Kansas, 1970-2009

USGS Publications Warehouse

Miller, Lisa D.; Watts, Kenneth R.; Ortiz, Roderick F.; ,

2010-01-01

In 2007, the U.S. Geological Survey (USGS), in cooperation with City of Aurora, Colorado Springs Utilities, Colorado Water Conservation Board, Lower Arkansas Valley Water Conservancy District, Pueblo Board of Water Works, Southeastern Colorado Water Activity Enterprise, Southeastern Colorado Water Conservancy District, and Upper Arkansas Water Conservancy District began a retrospective evaluation to characterize the occurrence and distribution of dissolved-solids (DS), selenium, and uranium concentrations in groundwater and surface water in the Arkansas River Basin based on available water-quality data collected by several agencies. This report summarizes and characterizes available DS, dissolved-selenium, and dissolved-uranium concentrations in groundwater and surface water for 1970-2009 and describes DS, dissolved-selenium, and dissolved-uranium loads in surface water along the main-stem Arkansas River and selected tributary and diversion sites from the headwaters near Leadville, Colorado, to the USGS 07137500 Arkansas River near Coolidge, Kansas (Ark Coolidge), streamgage, a drainage area of 25,410 square miles. Dissolved-solids concentrations varied spatially in groundwater and surface water in the Arkansas River Basin. Dissolved-solids concentrations in groundwater from Quaternary alluvial, glacial drift, and wind-laid deposits (HSU 1) increased downgradient with median values of about 220 mg/L in the Upper Arkansas subbasin (Arkansas River Basin from the headwaters to Pueblo Reservoir) to about 3,400 mg/L in the Lower Arkansas subbasin (Arkansas River Basin from John Martin Reservoir to Ark Coolidge). Dissolved-solids concentrations in the Arkansas River also increased substantially in the downstream direction between the USGS 07086000 Arkansas River at Granite, Colorado (Ark Granite), and Ark Coolidge streamgages. Based on periodic data collected from 1976-2007, median DS concentrations in the Arkansas River ranged from about 64 mg/L at Ark Granite to about 4,060 mg/L at Ark Coolidge representing over a 6,000 percent increase in median DS concentrations. Temporal variations in specific conductance values (which are directly related to DS concentrations) and seasonal variations in DS concentrations and loads were investigated at selected sites in the Arkansas River from Ark Granite to Ark Coolidge. Analyses indicated that, for the most part, specific conductance values (surrogate for DS concentrations) have remained relatively constant or have decreased in the Arkansas River since about 1970. Dissolved-solids concentrations in the Arkansas River were higher during the nonirrigation season (November-February) than during the irrigation season (March-October). Average annual DS loads, however, were higher during the irrigation season than during the nonirrigation season. Average annual DS loads during the irrigation season were at least two times and as much as 23 times higher than average annual DS loads during the nonirrigation season with the largest differences occurring at sites located downstream from the two main-stem reservoirs at USGS 07099400 Arkansas River above Pueblo, Colorado (Ark Pueblo), (which is below Pueblo Reservoir) and USGS 07130500 Arkansas River below John Martin Reservoir, Colorado (Ark below JMR). View report for unabridged abstract.

Estimates of gains and losses from unmeasured sources and sinks for streamflow and dissolved-solids load in selected reaches of the Arkansas River, southeastern Colorado, 2009-2010

USGS Publications Warehouse

Ortiz, Roderick F.

2013-01-01

The Arkansas River is an important municipal water supply and is the primary supply for about 400,000 acres of irrigated land in southeastern Colorado. The suitability of this water for domestic, agricultural, and industrial use is affected by high salinity in parts of the Arkansas River. There is a need to quantify mass loading of dissolved solids (DS) in the Arkansas River. In 2009, the U.S. Geological Survey, in cooperation with the Arkansas River Basin Regional Resource Planning Group and the Colorado Water Conservation Board, began a study to estimate gains and losses from unmeasured sources and sinks for streamflow and DS load in selected reaches of the Arkansas River in southeastern Colorado. Two study reaches were selected for investigation—Canon City to just upstream from Pueblo Reservoir (UARB) and Avondale to Las Animas (LARB). The results from the water-budget analyses indicated that potential areas of unmeasured sources and sinks of streamflow were identifiable in the two study reaches. In the UARB, a substantial volume of water in the subreach from Ark at Canon City to the seasonal gaging station 5 miles downstream (Ark nr Canon City) was unaccounted for by the methodology used in this analysis. The daily gain from unmeasured sources in this subreach was estimated to be about 100 cubic feet per second (ft3/s) or about 20 ft3/s per river mile. Water-budget estimates for the remaining 18 miles of the UARB study reach indicated that gains or losses from unmeasured sources or sinks were within the measurement error as defined for this report. In the LARB, gains and losses from unmeasured sources and sinks were identified in some of the subreaches but the magnitude of the flux generally was small. Unmeasured sources ranging from less than 2 to 3 ft3/s per mile were identified in the river subreaches from Ark at Catlin Dam downstream to Ark at Swink. A streamflow loss was indicated along the subreach from Ark at Nepesta to Ark at Catlin Dam, particularly in 2010. The mechanism and spatial extent of this sink was not identified, and further investigation would be required to better quantify the loss. The results from the analyses of unmeasured sources of DS load indicated that potential source areas were identifiable in the study areas. It might be expected that unmeasured DS load flux would be identified along the same reaches where unmeasured streamflow flux was identified. To that extent, some of the observed results from the analysis of daily DS loading did mirror the streamflow results. In some subreaches of the Arkansas River, however, unmeasured sources and sinks of DS load did not appear to be directly associated with unmeasured sources and sinks of streamflow. In the UARB from Ark at Canon City to Ark nr Canon City, unmeasured gains in DS load were estimated to range from 11 to 22 tons per day per mile in 2009 and from about 8 to 13 tons per day per mile in 2010; streamflow from unmeasured sources was estimated to be about 20 ft3/s per mile along this same reach. Downstream from this short reach, DS load to the river from unmeasured sources was estimated to range from 5.4 to 7.6 tons per day per mile in 2010 for Ark nr Canon City to Ark at Portland and from 11 to 16 tons per day per mile in 2009 for Ark at Portland to Ark nr Portland. Unmeasured gains in streamflow were not identified in either of these subreaches. Several small tributaries with DS concentrations ranging from 3,000 mg/L to as high as 6,000 mg/L enter the river along these subreaches. These inputs may indicate a potential source of groundwater that could affect DS loading in the river. Further investigation would be needed to identify the unmeasured source or sources of DS load to determine the nature and extent of unmeasured inputs. In the LARB, gains in DS load from unmeasured sources were identified for the subreach from Ark nr Avondale to Ark at Nepesta, although no substantial amounts of streamflow from unmeasured sources were identified for this subreach. In 2009, the estimated gain in DS load from unmeasured sources for this subreach was 4.7 tons per day per mile. An increase in DS load from unmeasured sources also was identified along the subreach of the river from Ark at Catlin to Swink; the DS load from unmeasured sources was estimated to range from 10 to 28 tons per day per mile. The only loss of DS load was identified for the subreach from Nepesta to Catlin Dam in 2010. The mechanism and spatial extent of the losses were not identified, and further investigation would be required to better understand the results.

Alveolar ridge keratosis--a retrospective clinicopathological study.

PubMed

Bellato, Lorenzo; Martinelli-Kläy, Carla P; Martinelli, Celso R; Lombardi, Tommaso

2013-04-16

Alveolar ridge keratosis (ARK) is a distinct, benign clinicopathological entity, characterized by a hyperkeratotic plaque or patch that occurs on the alveolar edentulous ridge or on the retromolar trigone, considered to be caused by chronic frictional trauma. The aim of this retrospective study is to present the clinicopathological features of 23 consecutive cases of ARK. The 23 biopsy samples of ARK were selected and pathological features were revised (keratosis, acanthosis, surface architecture, and inflammation). Factors such as the patient's gender, age, anatomical location, tobacco and alcohol use were analyzed. Sixteen out of the 23 cases studied were men and 7 women with a mean age of 55.05 (age ranged from 17 to 88 years). Thirteen cases had a history of tobacco habit, amongst whom, 4 also presented alcohol consumption. All the cases presented only unilateral lesions. Nineteen cases involved the retromolar trigone while 4 cases involved edentulous alveolar ridges. When observed microscopically, the lesions were mainly characterized by moderate to important hyperorthokeratosis. Inflammation was scanty or absent. In four of the cases, the presence of melanin pigment in the superficial corium or in the cytoplasm of macrophages was detected. None of the cases showed any features of dysplasia. Our results reveal that ARK is a benign lesion. However, the high prevalence of smokers amongst the patients might suggest that some potentially malignant disorders such as tobacco associated leukoplakia may clinically mimic ARK.

A proposed role for selective autophagy in regulating auxin-dependent lateral root development under phosphate starvation in Arabidopsis.

PubMed

Sankaranarayanan, Subramanian; Samuel, Marcus A

2015-01-01

Plants respond to limited soil nutrient availability by inducing more lateral roots (LR) to increase the root surface area. At the cellular level, nutrient starvation triggers the process of autophagy through which bulk degradation of cellular materials is achieved to facilitate nutrient mobilization. Whether there is any link between the cellular autophagy and induction of LR had remained unknown. We recently showed that the S-Domain receptor Kinase (ARK2) and U Box/Armadillo Repeat-Containing E3 ligase (PUB9) module is required for lateral root formation under phosphate starvation in Arabidopsis thaliana.(1) We also showed that PUB9 localized to autophagic bodies following either activation by ARK2 or under phosphate starvation and ark2-1/pub9-1 plants displayed lateral root defects with inability to accumulate auxin in the root tips under phosphate starvation.(1) Supplementing exogenous auxin was sufficient to rescue the LR defects in ark2-1/pub9-1 mutant. Blocking of autophagic responses in wild-type Arabidopsis also resulted in inhibition of both lateral roots and auxin accumulation in the root tips indicating the importance of autophagy in mediating auxin accumulation under phosphate starved conditions.(1) Here, we propose a model for ARK2/AtPUB9 module in regulation of lateral root development via selective autophagy.

Analysis and inundation mapping of the April-May 2011 flood at selected locations in northern and eastern Arkansas and southern Missouri

USGS Publications Warehouse

Westerman, Drew A.; Merriman, Katherine R.; De Lanois, Jeanne L.; Berenbrock, Charles

2013-01-01

Precipitation that fell from April 19 through May 3, 2011, resulted in widespread flooding across northern and eastern Arkansas and southern Missouri. The first storm produced a total of approximately 16 inches of precipitation over an 8-day period, and the following storms produced as much as 12 inches of precipitation over a 2-day period. Moderate to major flooding occurred quickly along many streams within Arkansas and Missouri (including the Black, Cache, Illinois, St. Francis, and White Rivers) at levels that had not been seen since the historic 1927 floods. The 2011 flood claimed an estimated 21 lives in Arkansas and Missouri, and damage caused by the flooding resulted in a Federal Disaster Declaration for 59 Arkansas counties that received Federal or State assistance. To further the goal of documenting and understanding floods, the U.S. Geological Survey, in cooperation with the Federal Emergency Management Agency, the U.S. Army Corps of Engineers–Little Rock and Memphis Districts, and Arkansas Natural Resources Commission, conducted a study to summarize meteorological and hydrological conditions before the flood; computed flood-peak magnitudes for 39 streamgages; estimated annual exceedance probabilities for 37 of those streamgages; determined the joint probabilities for 11 streamgages paired to the Mississippi River at Helena, Arkansas, which refers to the probability that locations on two paired streams simultaneously experience floods of a magnitude greater than or equal to a given annual exceedance probability; collected high-water marks; constructed flood-peak inundation maps showing maximum flood extent and water depths; and summarized flood damages and effects. For the period of record used in this report, peak-of-record stage occurred at 24 of the 39 streamgages, and peak-of-record streamflow occurred at 13 of the 30 streamgages where streamflow was determined. Annual exceedance probabilities were estimated to be less than 0.5 percent at three streamgages. The joint probability values for streamgages paired with the Mississippi River at Helena, Ark., streamgage indicate a low probability of concurrent flooding with the paired streamgages. The inundation maps show the flood-peak extent and water depth of flooding for two stream reaches on the White River and two on the Black River; the vicinities of the communities of Holly Grove and Cotton Plant, Ark.; a reach of the White River that includes the crossing of Interstate 40 north of De Valls Bluff, Ark.; and the Tailwaters of Beaver Dam near Eureka Springs, Ark., Table Rock Dam near Branson, Mo., and Bull Shoals Dam near Flippin, Ark. The data and inundation maps can be used for flood response, recovery, and planning efforts by Federal, State, and local agencies.

33 CFR 207.249 - Ouachita and Black Rivers, Ark. and La., Mile 0.0 to Mile 338.0 (Camden, Ark.) above the mouth of...

Code of Federal Regulations, 2010 CFR

2010-07-01

... signals, as follows: (i) One green light to indicate that the lock is open to approaching navigation. (ii... the banks, lock entrances, locks, cribs, dams, piers, fences, trees, buildings, or any other property...

Conservation priorities when species interact: the Noah's Ark metaphor revisited.

PubMed

Courtois, Pierre; Figuieres, Charles; Mulier, Chloé

2014-01-01

This note incorporates ecological interactions into the Noah's Ark problem. In doing so, we arrive at a general model for ranking in situ conservation projects accounting for species interrelations and provide an operational cost-effectiveness method for the selection of best preserving diversity projects under a limited budget constraint.

Conservation Priorities when Species Interact: The Noah's Ark Metaphor Revisited

PubMed Central

Courtois, Pierre; Figuieres, Charles; Mulier, Chloé

2014-01-01

This note incorporates ecological interactions into the Noah's Ark problem. In doing so, we arrive at a general model for ranking in situ conservation projects accounting for species interrelations and provide an operational cost-effectiveness method for the selection of best preserving diversity projects under a limited budget constraint. PMID:25181514

Alternative method of primocane management for primocane-fruiting blackberry and raspberry

USDA-ARS?s Scientific Manuscript database

A study was conducted on ‘Prime-Ark 45’ and ‘Prime-Ark Traveler’ to determine the effects of primocane bending and defoliation on subsequent flowering and fruit development. Our findings indicated that leaf removal stimulated more of the buds pushed. The shoots that developed on bent primocanes we...

Here's Looking at You: Visual Similarity Exacerbates the Moses Illusion for Semantically Similar Celebrities

ERIC Educational Resources Information Center

Davis, Danielle K.; Abrams, Lise

2016-01-01

When people read questions like "How many animals of each kind did Moses take on the ark?", many mistakenly answer "2" despite knowing that Noah sailed the ark. This "Moses illusion" occurs when names share semantic features. Two experiments examined whether shared "visual" concepts (facial features)…

Assignment of the {beta}-arrestin 1 gene (ARRB1) to human chromosome 11q13

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

Calabrese, G.; Morizio, E.; Palka, G.

1994-11-01

Two types of proteins play a major role in determining homologous desensitization of G-coupled receptors: {beta}-adrenergic receptor kinase ({beta}ARK), which phosphorylates the agonist-occupied receptor, and its functional cofactor, {beta}-arrestin. {beta}ARK is a member of a multigene family, consisting of six known subtypes, which have also been named G-protein-coupled receptor kinases (GRK 1 to 6) due to the apparently unique functional association of such kinases with this receptor family. The gene for {beta}ARK1 has been localized to human chromosome 11q13. The four members of the arrestin/{beta}-arrestin gene family identified so far are arrestin, X-arrestin, {beta}-arrestin 1, and {beta}-arrestin 2. Here themore » authors report the chromosome mapping of the human gene for {beta}-arrestin 1 (ARRB1) to chromosome 11q13 by fluorescence in situ hybridization (FISH). Two-color FISH confirmed that the two genes coding for the functionally related proteins {beta}ARK1 and {beta}arrestin 1 both map to 11q13. 16 refs., 1 fig., 1 tab.« less

Anticipating environmental and environmental-health implications of extreme storms: ARkStorm scenario

USGS Publications Warehouse

Plumlee, Geoffrey S.; Alpers, Charles N.; Morman, Suzette A.; San Juan, Carma A.

2016-01-01

The ARkStorm Scenario predicts that a prolonged winter storm event across California would cause extreme precipitation, flooding, winds, physical damages, and economic impacts. This study uses a literature review and geographic information system-based analysis of national and state databases to infer how and where ARkStorm could cause environmental damages, release contamination from diverse natural and anthropogenic sources, affect ecosystem and human health, and cause economic impacts from environmental-remediation, liability, and health-care costs. Examples of plausible ARkStorm environmental and health concerns include complex mixtures of contaminants such as petroleum, mercury, asbestos, persistent organic pollutants, molds, and pathogens; adverse physical and contamination impacts on riverine and coastal marine ecosystems; and increased incidences of mold-related health concerns, some vector-borne diseases, and valley fever. Coastal cities, the San Francisco Bay area, the Sacramento-San Joaquin River Delta, parts of the Central Valley, and some mountainous areas would likely be most affected. This type of screening analysis, coupled with follow-up local assessments, can help stakeholders in California and disaster-prone areas elsewhere better plan for, mitigate, and respond to future environmental disasters.

Implicit–explicit (IMEX) Runge–Kutta methods for non-hydrostatic atmospheric models

DOE PAGES

Gardner, David J.; Guerra, Jorge E.; Hamon, François P.; ...

2018-04-17

The efficient simulation of non-hydrostatic atmospheric dynamics requires time integration methods capable of overcoming the explicit stability constraints on time step size arising from acoustic waves. In this work, we investigate various implicit–explicit (IMEX) additive Runge–Kutta (ARK) methods for evolving acoustic waves implicitly to enable larger time step sizes in a global non-hydrostatic atmospheric model. The IMEX formulations considered include horizontally explicit – vertically implicit (HEVI) approaches as well as splittings that treat some horizontal dynamics implicitly. In each case, the impact of solving nonlinear systems in each implicit ARK stage in a linearly implicit fashion is also explored.The accuracymore » and efficiency of the IMEX splittings, ARK methods, and solver options are evaluated on a gravity wave and baroclinic wave test case. HEVI splittings that treat some vertical dynamics explicitly do not show a benefit in solution quality or run time over the most implicit HEVI formulation. While splittings that implicitly evolve some horizontal dynamics increase the maximum stable step size of a method, the gains are insufficient to overcome the additional cost of solving a globally coupled system. Solving implicit stage systems in a linearly implicit manner limits the solver cost but this is offset by a reduction in step size to achieve the desired accuracy for some methods. Overall, the third-order ARS343 and ARK324 methods performed the best, followed by the second-order ARS232 and ARK232 methods.« less

Implicit-explicit (IMEX) Runge-Kutta methods for non-hydrostatic atmospheric models

NASA Astrophysics Data System (ADS)

Gardner, David J.; Guerra, Jorge E.; Hamon, François P.; Reynolds, Daniel R.; Ullrich, Paul A.; Woodward, Carol S.

2018-04-01

The efficient simulation of non-hydrostatic atmospheric dynamics requires time integration methods capable of overcoming the explicit stability constraints on time step size arising from acoustic waves. In this work, we investigate various implicit-explicit (IMEX) additive Runge-Kutta (ARK) methods for evolving acoustic waves implicitly to enable larger time step sizes in a global non-hydrostatic atmospheric model. The IMEX formulations considered include horizontally explicit - vertically implicit (HEVI) approaches as well as splittings that treat some horizontal dynamics implicitly. In each case, the impact of solving nonlinear systems in each implicit ARK stage in a linearly implicit fashion is also explored. The accuracy and efficiency of the IMEX splittings, ARK methods, and solver options are evaluated on a gravity wave and baroclinic wave test case. HEVI splittings that treat some vertical dynamics explicitly do not show a benefit in solution quality or run time over the most implicit HEVI formulation. While splittings that implicitly evolve some horizontal dynamics increase the maximum stable step size of a method, the gains are insufficient to overcome the additional cost of solving a globally coupled system. Solving implicit stage systems in a linearly implicit manner limits the solver cost but this is offset by a reduction in step size to achieve the desired accuracy for some methods. Overall, the third-order ARS343 and ARK324 methods performed the best, followed by the second-order ARS232 and ARK232 methods.

Implicit–explicit (IMEX) Runge–Kutta methods for non-hydrostatic atmospheric models

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

Gardner, David J.; Guerra, Jorge E.; Hamon, François P.

The efficient simulation of non-hydrostatic atmospheric dynamics requires time integration methods capable of overcoming the explicit stability constraints on time step size arising from acoustic waves. In this work, we investigate various implicit–explicit (IMEX) additive Runge–Kutta (ARK) methods for evolving acoustic waves implicitly to enable larger time step sizes in a global non-hydrostatic atmospheric model. The IMEX formulations considered include horizontally explicit – vertically implicit (HEVI) approaches as well as splittings that treat some horizontal dynamics implicitly. In each case, the impact of solving nonlinear systems in each implicit ARK stage in a linearly implicit fashion is also explored.The accuracymore » and efficiency of the IMEX splittings, ARK methods, and solver options are evaluated on a gravity wave and baroclinic wave test case. HEVI splittings that treat some vertical dynamics explicitly do not show a benefit in solution quality or run time over the most implicit HEVI formulation. While splittings that implicitly evolve some horizontal dynamics increase the maximum stable step size of a method, the gains are insufficient to overcome the additional cost of solving a globally coupled system. Solving implicit stage systems in a linearly implicit manner limits the solver cost but this is offset by a reduction in step size to achieve the desired accuracy for some methods. Overall, the third-order ARS343 and ARK324 methods performed the best, followed by the second-order ARS232 and ARK232 methods.« less

Alveolar ridge keratosis - a retrospective clinicopathological study

PubMed Central

2013-01-01

Background Alveolar ridge keratosis (ARK) is a distinct, benign clinicopathological entity, characterized by a hyperkeratotic plaque or patch that occurs on the alveolar edentulous ridge or on the retromolar trigone, considered to be caused by chronic frictional trauma. The aim of this retrospective study is to present the clinicopathological features of 23 consecutive cases of ARK. Material and methods The 23 biopsy samples of ARK were selected and pathological features were revised (keratosis, acanthosis, surface architecture, and inflammation). Factors such as the patient’s gender, age, anatomical location, tobacco and alcohol use were analyzed. Results Sixteen out of the 23 cases studied were men and 7 women with a mean age of 55.05 (age ranged from 17 to 88 years). Thirteen cases had a history of tobacco habit, amongst whom, 4 also presented alcohol consumption. All the cases presented only unilateral lesions. Nineteen cases involved the retromolar trigone while 4 cases involved edentulous alveolar ridges. When observed microscopically, the lesions were mainly characterized by moderate to important hyperorthokeratosis. Inflammation was scanty or absent. In four of the cases, the presence of melanin pigment in the superficial corium or in the cytoplasm of macrophages was detected. None of the cases showed any features of dysplasia. Conclusion Our results reveal that ARK is a benign lesion. However, the high prevalence of smokers amongst the patients might suggest that some potentially malignant disorders such as tobacco associated leukoplakia may clinically mimic ARK. PMID:23587097

The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function

Treesearch

Lijun Liu; Matthew S. Zinkgraf; H. Earl Petzold; Eric P. Beers; Vladimir Filkov; Andrew Groover

2014-01-01

The class I KNOX homeodomain transcription factor ARBORKNOX1 (ARK1) is a key regulator of vascular cambium maintenance and cell differentiation in Populus. Currently, basic information is lacking concerning the distribution, functional characteristics, and evolution of ARK1 binding in the Populus genome.

1986 Flood Control and Navigation Maps of the Mississippi River

DTIC Science & Technology

1987-01-01

Higgerson Ldg.. Mo. 4 911.3 10 781.5 Grand Lake, Ark. (lake and town) 28 Hodge Ldg.. La. (Diamond Cut-off) 34 IB 667.5 Grand Lake Cul-ofl 28 511.0 Hog...La. Tellier Island. Ark. Tennemo Ldg., Tenn. Tennessee Bar. Miss. Terrapin Neck Cut-oil Terrene Ldg.. Miss. Texas. La. The Jump Theima Ldg

infections bronchitis virus S2 of 4/91 expressed from recombinant virus does not protect against ark-type challenge

USDA-ARS?s Scientific Manuscript database

We previously demonstrated that chickens primed with a recombinant Newcastle disease virus LaSota (rLS) expressing the S2 gene of infectious bronchitis virus (IBV) and boosted with an attenuated IBV Massachusetts (Mass)-type vaccine were protected against IBV Arkansas (Ark)-type virulent challenge. ...

75 FR 44982 - Arkansas Valley Conduit (AVC) and Long-Term Excess Capacity Master Contract, Fryingpan-Arkansas...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-30

... Reservoir due to AVC and Excess Capacity Master Contract operations and potential contributions to flooding... Southeastern for storage of non-Fry-Ark Project water in Pueblo Reservoir, a feature of the Fry-Ark Project... storage in Pueblo Reservoir for entities within its boundaries in the Upper Arkansas basin, Lower Arkansas...

Steering the Ark: A Cultural Center for Children

ERIC Educational Resources Information Center

Drury, Martin

2006-01-01

In this article, the author reflects on his experience developing and running The Ark, a Cultural Center for Children in Dublin, Ireland. The author describes the practice and ten guiding principles behind the center. While acknowledging that arts education and arts practice for and with young people is a rich and varied landscape, within which a…

In vivo morphology of the limbal palisades of vogt correlates with progressive stem cell deficiency in aniridia-related keratopathy.

PubMed

Lagali, Neil; Edén, Ulla; Utheim, Tor Paaske; Chen, Xiangjun; Riise, Ruth; Dellby, Anette; Fagerholm, Per

2013-08-07

To investigate morphologic alterations in the limbal palisades of Vogt in a progressive form of limbal stem cell deficiency. Twenty Norwegian subjects (40 eyes) with congenital aniridia and 9 healthy family members (18 eyes) without aniridia were examined. Clinical grade of aniridia-related keratopathy (ARK) was assessed by slit-lamp biomicroscopy, and tear production and quality, corneal thickness, and sensitivity were additionally measured. The superior and inferior limbal palisades of Vogt and central cornea were examined by laser scanning in vivo confocal microscopy (IVCM). In an aniridia patient with grade 0 ARK, a transparent cornea and normal limbal palisade morphology were found. In grade 1 ARK, 5 of 12 eyes had degraded palisade structures. In the remaining grade 1 eyes and in all 20 eyes with stage 2, 3, and 4 ARK, palisade structures were absent by IVCM. Increasing ARK grade significantly correlated with reduced visual acuity and corneal sensitivity, increased corneal thickness, degree of degradation of superior and inferior palisade structures, reduced peripheral nerves, increased inflammatory cell invasion, and reduced density of basal epithelial cells and central subbasal nerves. Moreover, limbal basal epithelial cell density and central corneal subbasal nerve density were both significantly reduced in aniridia compared to healthy corneas (P = 0.002 and 0.003, respectively). Progression of limbal stem cell deficiency in aniridia correlates with degradation of palisade structures, gradual transformation of epithelial phenotype, onset of inflammation, and a corneal nerve deficit. IVCM can be useful in monitoring early- to late-stage degenerative changes in stem cell-deficient patients.

Additive Runge-Kutta Schemes for Convection-Diffusion-Reaction Equations

NASA Technical Reports Server (NTRS)

Kennedy, Christopher A.; Carpenter, Mark H.

2001-01-01

Additive Runge-Kutta (ARK) methods are investigated for application to the spatially discretized one-dimensional convection-diffusion-reaction (CDR) equations. First, accuracy, stability, conservation, and dense output are considered for the general case when N different Runge-Kutta methods are grouped into a single composite method. Then, implicit-explicit, N = 2, additive Runge-Kutta ARK2 methods from third- to fifth-order are presented that allow for integration of stiff terms by an L-stable, stiffly-accurate explicit, singly diagonally implicit Runge-Kutta (ESDIRK) method while the nonstiff terms are integrated with a traditional explicit Runge-Kutta method (ERK). Coupling error terms are of equal order to those of the elemental methods. Derived ARK2 methods have vanishing stability functions for very large values of the stiff scaled eigenvalue, z(exp [I]) goes to infinity, and retain high stability efficiency in the absence of stiffness, z(exp [I]) goes to zero. Extrapolation-type stage-value predictors are provided based on dense-output formulae. Optimized methods minimize both leading order ARK2 error terms and Butcher coefficient magnitudes as well as maximize conservation properties. Numerical tests of the new schemes on a CDR problem show negligible stiffness leakage and near classical order convergence rates. However, tests on three simple singular-perturbation problems reveal generally predictable order reduction. Error control is best managed with a PID-controller. While results for the fifth-order method are disappointing, both the new third- and fourth-order methods are at least as efficient as existing ARK2 methods while offering error control and stage-value predictors.

Archiving Innovations Preserve Essential Historical Records

NASA Technical Reports Server (NTRS)

2013-01-01

The Apollo 11 mission left on the Moon a silicon disc inscribed with microscopic recreations of messages from 73 countries. NanoArk Corporation of Fairport, New York, built on that NASA technology to develop a fire and water resistant archiving innovation that provides cost savings and security in preserving documents. Since its launch, NanoArk has grown from 2 to 10 employees.

Agricultural damages and losses from ARkStorm scenario flooding in California

USGS Publications Warehouse

Wein, Anne; David Mitchell,; Peters, Jeff; John Rowden,; Johnny Tran,; Alessandra Corsi,; Dinitz, Laura B.

2016-01-01

Scientists designed the ARkStorm scenario to challenge the preparedness of California communities for widespread flooding with a historical precedence and increased likelihood under climate change. California is an important provider of vegetables, fruits, nuts, and other agricultural products to the nation. This study analyzes the agricultural damages and losses pertaining to annual crops, perennial crops, and livestock in California exposed to ARkStorm flooding. Statewide, flood damage is incurred on approximately 23% of annual crop acreage, 5% of perennial crop acreage, and 5% of livestock, e.g., dairy, feedlot, and poultry, acreage. The sum of field repair costs, forgone income, and product replacement costs span $3.7 and $7.1 billion (2009) for a range of inundation durations. Perennial crop loss estimates dominate, and the vulnerability of orchards and vineyards has likely increased with recent expansion. Crop reestablishment delays from levee repair and dewatering more than double annual crop losses in the delta islands, assuming the fragile system does not remain permanently flooded. The exposure of almost 200,000 dairy cows to ARkStorm flooding poses livestock evacuation challenges. Read More: http://ascelibrary.org/doi/abs/10.1061/%28ASCE%29NH.1527-6996.0000174

"It's All Shiny and There's No Pollution": "Barbapapa's Ark," Environmental Influences

ERIC Educational Resources Information Center

Lowe, Virginia

2013-01-01

The environmental picture book "Barbapapa's Ark" was published in 1974. I was keeping a parent-observer record of my two children at the time. The book had a strong influence on them from ages three to six, moving them to query pollution and hunting, in book and environment, and as adults, becoming committed activists for the…

Methylation of CpG island of p14(ARK), p15(INK4b) and p16(INK4a) genes in coke oven workers.

PubMed

Zhang, H; Li, X; Ge, L; Yang, J; Sun, J; Niu, Q

2015-02-01

To detect the blood genomic DNA methylation in coke oven workers and find a possible early screening index for occupational lung cancer, 74 coke oven workers as the exposed group and 47 water pump workers as the controls were surveyed, and urine samples and peripheral blood mononuclear cells (PBMCs) were collected. Airborne benzo[a]pyrene (B[a]P) levels in workplace and urinary 1-hydroxypyrene (1-OH-Py) levels were determined by high-performance liquid chromatography. DNA damage of PBMCs and the p14(ARK), p15(INK4b) and p16(INK4a) gene CpG island methylation in the promoter region were detected by comet assay and methylation-specific polymerase chain reaction techniques, respectively. Results show that compared with the controls, concentration of airborne B[a]Ps was elevated in the coke plant, and urinary 1-OH-Py's level and DNA olive tail moment in comet assay were significantly increased in the coke oven workers, and p14(ARK), p15(INK4b) and p16(INK4a) gene methylation rates were also significantly increased. With the working years and urinary 1-OH-Py's level, the rates of p14(ARK) and p16(INK4a) gene methylation were significantly increased while that of p15(INK4b) gene methylation displayed no statistical change. We conclude that PBMCs' p14(ARK) and p16(INK4a) gene methylation may be used for screening and warning lung cancer in coke oven workers. © The Author(s) 2015.

Dual HER2 targeting impedes growth of HER2 gene-amplified uterine serous carcinoma xenografts.

PubMed

Groeneweg, Jolijn W; Hernandez, Silvia F; Byron, Virginia F; DiGloria, Celeste M; Lopez, Hector; Scialabba, Vanessa; Kim, Minji; Zhang, Ling; Borger, Darrell R; Tambouret, Rosemary; Foster, Rosemary; Rueda, Bo R; Growdon, Whitfield B

2014-12-15

Uterine serous carcinoma (USC) is an aggressive subtype of endometrial cancer that commonly harbors HER2 gene amplification. We investigated the effectiveness of HER2 inhibition using lapatinib and trastuzumab in vitro and in xenografts derived from USC cell lines and USC patient-derived xenografts. Immunohistochemistry and FISH were performed to assess HER2 expression in 42 primary USC specimens. ARK1, ARK2, and SPEC2 cell lines were treated with trastuzumab or lapatinib. Cohorts of mice harboring xenografts derived from ARK2 and SPEC2 cell lines and EnCa1 and EnCa2 primary human USC samples were treated with either vehicle, trastuzumab, lapatinib, or the combination of trastuzumab and lapatinib. Acute and chronic posttreatment tumor samples were assessed for downstream signaling alterations and examined for apoptosis and proliferation. HER2 gene amplification (24%) correlated significantly with HER2 protein overexpression (55%). All models were impervious to single-agent trastuzumab treatment. Lapatinib decreased in vitro proliferation of all cell lines and in vivo growth of HER2-amplified xenografts (ARK2, EnCa1). In addition, dual therapy with trastuzumab and lapatinib resulted in significant antitumor activity only in ARK2 and EnCa1 tumors. Dual HER2 therapy induced on target alteration of downstream MAPK and PI3K pathway mediators only in HER2-amplified models, and was associated with increased apoptosis and decreased proliferation. Although trastuzumab alone did not impact USC growth, dual anti-HER2 therapy with lapatinib led to improved inhibition of tumor growth in HER2-amplified USC and may be a promising avenue for future investigation. ©2014 American Association for Cancer Research.

Lower extremity robotic exoskeleton training: Case studies for complete spinal cord injury walking.

PubMed

Lemaire, Edward D; Smith, Andrew J; Herbert-Copley, Andrew; Sreenivasan, Vidya

2017-01-01

Recent advances in exoskeleton technology has made lower extremity powered exoskeletons (LEPE) a viable treatment tool to restore upright walking mobility to persons with spinal cord injury (SCI). Evaluate ARKE exoskeleton training within a rehabilitation centre environment. Case studies are presented for two male participants, age 41 and 30, motor complete SCI at T6 (N01) and T12 (N02), respectively, as they progress from new LEPE users to independent walking. The ARKE 2.0 LEPE (Bionik Laboratories Inc., Toronto, Canada) was used for all training (hip and knee powered, forearm crutches, control tablet). Data were collected on session times, activity metrics from ARKE system logs, and qualitative questionnaire feedback. N01 required 18, 30-minute training sessions to achieve independent walking. N01 walked independently within the 12 session target. Foot strikes were frequently before the end of the programmed swing phase, which were handled by the ARKE control system. Subjective ratings of LEPE learning, comfort, pain, fatigue, and overall experience were high for sitting-standing and moderate to high for walking. This reflected the complexity of learning to safely walk. Qualitative feedback supported the continuation of LEPE use in rehabilitation settings based on end-user desire for upright mobility.

Noah's Ark-Red Cross Foundation: a Swedish model.

PubMed

Florence, M E

1993-01-01

During the Spring of 1991, the author spent many weeks at the Noah's Ark-Red Cross Foundation, a support service for HIV infected persons, and their families and friends, located in Stockholm, Sweden. The purpose was to study, through interviews, observation and participation, the foundation's interactive model in order to discover what makes it work and share that knowledge with other professionals. The Noah's Ark Model consists of three spheres of activity: service, including reception services and the volunteer programme; information and education, including the Hot Line and the Newsletter; and counselling and support, including the guest house. Staff from each area interact freely with and participate in the activities of other areas. The foundation also utilizes the services of carefully trained volunteers. This use of volunteers makes it unique in Sweden. It is the dedication and flexibility of the staff and volunteers that make this model work. The report of the study follows.

Economic Impact Analyses of Interdisciplinary Multi-hazard Scenarios: ShakeOut and ARkStorm

NASA Astrophysics Data System (ADS)

Wein, A. M.; Rose, A.; Sue Wing, I.; Wei, D.

2011-12-01

U. S. Geological Survey (USGS) scientists are using an interdisciplinary strategy to develop and analyze multi-hazard scenarios to help communities enhance resilience to natural hazard disasters. Two such scenarios are the southern California ShakeOut earthquake and the California ARkStorm winter storm. Both scenarios are multi-hazard: Shakeout ground motions trigger landslides and liquefaction and ARkStorm involves wind, flood, landslide, and coastal hazards. A collaborative scenario-process engages partners and stakeholders throughout the development and use of the scenarios, In doing so, community resilience is enhanced by educating communities about hazards and hazard interdependencies, building networks from scientists to decision makers, exercising emergency management strategies, identifying emergency management issues, and motivating solutions prior to an event. In addition, interdisciplinary scenarios stimulate research on the various steps of analysis (e.g., natural hazard processes, physical damages, societal consequences, and policy connections). In particular, USGS scientists have collaborated with economists to advance methods to estimate the economic impacts (business interruption losses) of disasters. Our economic impact analyses evolved from the economic module in the Federal Emergency Management Agency's loss-estimation tool, HAZUS-MH, to a more encompassing input-output analysis for ShakeOut, to a more sophisticated Computable General Equilibrium model for ARkStorm. The analyses depend on physical damage and restoration time estimates from engineers and geographic analyses of economic assets in hazard zones. Economic resilience strategies are incorporated to represent resourcefulness and ingenuity that avoids potential losses during and after an event. Such strategies operate at three levels of the economy: micro (e.g., ability to catch up on lost production time), meso (e.g., coordination within a sector to share resources), and macro (e.g., price adjustments to redistribute scarce resources). A sensitivity analysis of the ARkStorm economic impact model explores the effects of 1) the magnitude of the shocks (e.g., flood damages to buildings and infrastructure, agricultural productivity, and lifeline service disruptions), 2) the sustainability of the economic resilience strategies, and 3) the amount, timing, and source of reconstruction funds. The inclusion of an economic analysis in ShakeOut and ARkStorm broadens the range of interest in the scenario results. For example, the relative contribution of ShakeOut economic shocks to business interruption losses emphasized the need to reduce the impacts of fire following earthquake and water service disruption. Based on the magnitude and duration of the economic impacts for the ARkStorm scenario, policy experts surmised that business interruption policy time elements would be exceeded and business interruptions would be largely unfunded calling attention to the need for innovative funding solutions. Finally, economic impact analyses inform the question of paying now to mitigate or paying more later to recover.

ARkStorm: A West Coast Storm Scenario

NASA Astrophysics Data System (ADS)

Cox, D. A.; Jones, L. M.; Ralph, F. M.; Dettinger, M. D.; Porter, K.; Perry, S. C.; Barnard, P. L.; Hoover, D.; Wills, C. J.; Stock, J. D.; Croyle, W.; Ferris, J. C.; Plumlee, G. S.; Alpers, C. N.; Miller, M.; Wein, A.; Rose, A.; Done, J.; Topping, K.

2009-12-01

The United Stated Geological Survey (USGS) Multi-Hazards Demonstration Project (MHDP) is preparing a new emergency-preparedness scenario, called ARkStorm, to address massive U.S. West Coast storms analogous to those that devastated California in 1861-62. Storms of this magnitude are projected to become more frequent and intense as a result of climate change. The MHDP has assembled experts from the National Oceanic and Atmospheric Administration (NOAA), USGS, Scripps Institute of Oceanography, the State of California, California Geological Survey, the University of Colorado, the National Center for Atmospheric Research, and other organizations to design the large, but scientifically plausible, hypothetical scenario storm that would provide emergency responders, resource managers, and the public a realistic assessment of what is historically possible. The ARkStorm patterns the 1861 - 1862 historical events but uses modern modeling methods and data from large storms in 1969 and 1986. The ARkStorm draws heat and moisture from the tropical Pacific, forming Atmospheric Rivers (ARs) that grow in size, gain speed, and with a ferocity equal to hurricanes, slam into the U.S. West Coast for several weeks. Using sophisticated weather models and expert analysis, precipitation, snowlines, wind, and pressure data the modelers will characterize the resulting floods, landslides, and coastal erosion and inundation. These hazards will then be translated into the infrastructural, environmental, agricultural, social, and economic impacts. Consideration will be given to catastrophic disruptions to water supplies resulting from impacts on groundwater pumping, seawater intrusion, water supply degradation, and land subsidence. Possible climate-change forces that could exacerbate the problems will also be evaluated. In contrast to the recent U.S. East and Gulf Coast hurricanes, only recently have scientific and technological advances documented the ferocity and strength of possible future West Coast storms. A task of ARkStorm is to elevate the visibility of the very real threats to human life, property, and ecosystems posed by extreme storms on the U.S. West Coast. This enhanced visibility will help increase the preparedness of the emergency management community and the public to such storms. ARkStorm is scheduled to be completed by September 2010 and will be the basis of a state-wide emergency response drill, Golden Guardian, led by the California Emergency Management Agency in 2011.

A TWO-PHASE LOW-VELOCITY OUTFLOW IN THE SEYFERT 1 GALAXY Ark 564

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

Gupta, A.; Mathur, S.; Krongold, Y.

2013-05-10

The Seyfert 1 galaxy Ark 564 was observed with Chandra high-energy transmission gratings for 250 ks. We present the high-resolution X-ray spectrum that shows several associated absorption lines. The photoionization model requires two warm absorbers (WAs) with two different ionization states (log U = 0.39 {+-} 0.03 and log U = -0.99 {+-} 0.13), both with moderate outflow velocities ({approx}100 km s{sup -1}) and relatively low line of sight column densities (log N{sub H} = 20.94 and 20.11 cm{sup -2}). The high-ionization phase produces absorption lines of O VII, O VIII, Ne IX, Ne X, Mg XI, Fe XVII, andmore » Fe XVIII, while the low-ionization phase produces lines at lower energies (O VIand O VII). The pressure-temperature equilibrium curve for the Ark 564 absorber does not have the typical ''S'' shape, even if the metallicity is super-solar; as a result, the two WA phases do not appear to be in pressure balance. This suggests that the continuum incident on the absorbing gas is perhaps different from the observed continuum. We also estimated the mass outflow rate and the associated kinetic energy and find it to be at most 0.009% of the bolometric luminosity of Ark 564. Thus, it is highly unlikely that these outflows provide significant feedback required by the galaxy formation models.« less

Overview of the ARkStorm scenario

USGS Publications Warehouse

Porter, Keith; Wein, Anne; Alpers, Charles N.; Baez, Allan; Barnard, Patrick L.; Carter, James; Corsi, Alessandra; Costner, James; Cox, Dale; Das, Tapash; Dettinger, Mike; Done, James; Eadie, Charles; Eymann, Marcia; Ferris, Justin; Gunturi, Prasad; Hughes, Mimi; Jarrett, Robert; Johnson, Laurie; Le-Griffin, Hanh Dam; Mitchell, David; Morman, Suzette; Neiman, Paul; Olsen, Anna; Perry, Suzanne; Plumlee, Geoffrey; Ralph, Martin; Reynolds, David; Rose, Adam; Schaefer, Kathleen; Serakos, Julie; Siembieda, William; Stock, Jonathan; Strong, David; Wing, Ian Sue; Tang, Alex; Thomas, Pete; Topping, Ken; Wills, Chris; Jones, Lucile

2011-01-01

The U.S. Geological Survey, Multi Hazards Demonstration Project (MHDP) uses hazards science to improve resiliency of communities to natural disasters including earthquakes, tsunamis, wildfires, landslides, floods and coastal erosion. The project engages emergency planners, businesses, universities, government agencies, and others in preparing for major natural disasters. The project also helps to set research goals and provides decision-making information for loss reduction and improved resiliency. The first public product of the MHDP was the ShakeOut Earthquake Scenario published in May 2008. This detailed depiction of a hypothetical magnitude 7.8 earthquake on the San Andreas Fault in southern California served as the centerpiece of the largest earthquake drill in United States history, involving over 5,000 emergency responders and the participation of over 5.5 million citizens. This document summarizes the next major public project for MHDP, a winter storm scenario called ARkStorm (for Atmospheric River 1,000). Experts have designed a large, scientifically realistic meteorological event followed by an examination of the secondary hazards (for example, landslides and flooding), physical damages to the built environment, and social and economic consequences. The hypothetical storm depicted here would strike the U.S. West Coast and be similar to the intense California winter storms of 1861 and 1862 that left the central valley of California impassible. The storm is estimated to produce precipitation that in many places exceeds levels only experienced on average once every 500 to 1,000 years. Extensive flooding results. In many cases flooding overwhelms the state's flood-protection system, which is typically designed to resist 100- to 200-year runoffs. The Central Valley experiences hypothetical flooding 300 miles long and 20 or more miles wide. Serious flooding also occurs in Orange County, Los Angeles County, San Diego, the San Francisco Bay area, and other coastal communities. Windspeeds in some places reach 125 miles per hour, hurricane-force winds. Across wider areas of the state, winds reach 60 miles per hour. Hundreds of landslides damage roads, highways, and homes. Property damage exceeds $300 billion, most from flooding. Demand surge (an increase in labor rates and other repair costs after major natural disasters) could increase property losses by 20 percent. Agricultural losses and other costs to repair lifelines, dewater (drain) flooded islands, and repair damage from landslides, brings the total direct property loss to nearly $400 billion, of which $20 to $30 billion would be recoverable through public and commercial insurance. Power, water, sewer, and other lifelines experience damage that takes weeks or months to restore. Flooding evacuation could involve 1.5 million residents in the inland region and delta counties. Business interruption costs reach $325 billion in addition to the $400 property repair costs, meaning that an ARkStorm could cost on the order of $725 billion, which is nearly 3 times the loss deemed to be realistic by the ShakeOut authors for a severe southern California earthquake, an event with roughly the same annual occurrence probability. The ARkStorm has several public policy implications: (1) An ARkStorm raises serious questions about the ability of existing federal, state, and local disaster planning to handle a disaster of this magnitude. (2) A core policy issue raised is whether to pay now to mitigate, or pay a lot more later for recovery. (3) Innovative financing solutions are likely to be needed to avoid fiscal crisis and adequately fund response and recovery costs from a similar, real, disaster. (4) Responders and government managers at all levels could be encouraged to conduct risk assessments, and devise the full spectrum of exercises, to exercise ability of their plans to address a similar event. (5) ARkStorm can be a reference point for application of Federal Emergency Ma

A DEEP X-RAY VIEW OF THE BARE AGN ARK 120. I. REVEALING THE SOFT X-RAY LINE EMISSION

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

Reeves, J. N.; Braito, V.; Porquet, D.

2016-09-10

The Seyfert 1 galaxy Ark 120 is a prototype example of the so-called class of bare nucleus active galactic nuclei (AGNs), whereby there is no known evidence for the presence of ionized gas along the direct line of sight. Here deep (>400 ks exposure), high-resolution X-ray spectroscopy of Ark 120 is presented from XMM-Newton observations that were carried out in 2014 March, together with simultaneous Chandra /High Energy Transmission Grating exposures. The high-resolution spectra confirmed the lack of intrinsic absorbing gas associated with Ark 120, with the only X-ray absorption present originating from the interstellar medium (ISM) of our ownmore » Galaxy, with a possible slight enhancement of the oxygen abundance required with respect to the expected ISM values in the solar neighborhood. However, the presence of several soft X-ray emission lines are revealed for the first time in the XMM-Newton RGS spectrum, associated with the AGN and arising from the He- and H-like ions of N, O, Ne, and Mg. The He-like line profiles of N, O, and Ne appear velocity broadened, with typical FWHMs of ∼5000 km s{sup −1}, whereas the H-like profiles are unresolved. From the clean measurement of the He-like triplets, we deduce that the broad lines arise from a gas of density n {sub e} ∼ 10{sup 11} cm{sup −3}, while the photoionization calculations infer that the emitting gas covers at least 10% of 4 π steradian. Thus the broad soft X-ray profiles appear coincident with an X-ray component of the optical–UV broad-line region on sub-parsec scales, whereas the narrow profiles originate on larger parsec scales, perhaps coincident with the AGN narrow-line region. The observations show that Ark 120 is not intrinsically bare and substantial X-ray-emitting gas exists out of our direct line of sight toward this AGN.« less

Excimer lasers

NASA Technical Reports Server (NTRS)

Palmer, A. J.; Hess, L. D.; Stephens, R. R.; Pepper, D. M.

1977-01-01

The results of a two-year investigation into the possibility of developing continuous wave excimer lasers are reported. The program included the evaluation and selection of candidate molecular systems and discharge pumping techniques. The K Ar/K2 excimer dimer molecules and the xenon fluoride excimer molecule were selected for study; each used a transverse and capillary discharges pumping technique. Experimental and theoretical studies of each of the two discharge techniques applied to each of the two molecular systems are reported. Discharge stability and fluorine consumption were found to be the principle impediments to extending the XeF excimer laser into the continuous wave regime. Potassium vapor handling problems were the principal difficulty in achieving laser action on the K Ar/K2 system. Of the four molecular systems and pumping techniques explored, the capillary discharge pumped K Ar/K2 system appears to be the most likely candidate for demonstrating continuous wave excimer laser action primarily because of its predicted lower pumping threshold and a demonstrated discharge stability advantage.

ROSAT PSPC observations of NGC 7469 and Ark 120

NASA Technical Reports Server (NTRS)

Brandt, W. N.; Fabian, A. C.; Nandra, K.; Tsuruta, S.

1993-01-01

We present spatial, temporal and spectral analyses of ROSAT Position Sensitive Proportional Counter (PSPC) observations of the Seyfert 1 galaxies NGC 7469 and Ark 120. Both of these sources show evidence for excess emission and more complex 0.1- 2.5 keV spectra than are predicted by simple extrapolations of higher energy power laws. We find that the spectrum of NGC 7469 can be explained by models that have secondary power-law, secondary bremsstrahlung, secondary blackbody or emission-line components. We find evidence for 0.1-2.5 keV intensity variability of NGC 7469. The spectrum of Ark 120 is better described by models with secondary continuum components than by models with sharper spectral features. We discuss the agreement between X-ray and ultraviolet observations of these sources and examine the observations in the context of accretion disc reflection models. The inner parts of discs are likely to be reflective below approximately 0.24 keV, and this reflectivity complicates simple models of the soft excess.

Regional analysis of social characteristics for evacuation resource planning: ARkStorm scenario

USGS Publications Warehouse

Wein, Anne; Ratliff, Jamie L.; Allan Baez,; Sleeter, Rachel

2016-01-01

Local planning is insufficient for regional catastrophes; regional exercises are needed to test emergency plans and decision-making structures. The ARkStorm scenario would trigger a mass evacuation that would be complicated by the social characteristics of populations [e.g., vehicle ownership, age, poverty, English language limitation (ELL), and shelter needs]. Land cover data and dasymetric mapping improves the allocation of residential populations and their social characteristics to the ARkStorm flood zone in 21 counties in California. Numbers and concentrations of county, urban, and rural residents exposed to flooding as well as populations in and out of the scenario flood zone are profiled. The results inform mass evacuation planning by providing a means to (1) examine the sufficiency of mutual aid agreements, (2) underscore planning for carless populations, and (3) tailor multilingual communication strategies. The various geographical distinctions emphasize different challenges throughout the region. It will be important to investigate behavioral responses to warnings, identify evacuation constraints (e.g., shelter capacity versus need), and obtain comparable data on transient populations.

Plate motions, Gondwana dinosaurs, Noah's arks, beached Viking funeral ships, ghost ships, and landspans.

PubMed

Jacobs, Louis L; Strganac, Christopher; Scotese, Christopher

2011-03-01

Gondwana landmasses have served as large-scale biogeographic Noah's Arks and Beached Viking Funeral Ships, as defined by McKenna. The latitudinal trajectories of selected Gondwana dinosaur localities were traced through time in order to evaluate their movement through climate zones relative to those in which they originally formed. The dispersal of fauna during the breakup of Gondwana may have been facilitated by the presence of offshelf islands forming landspans (sensu Iturralde-Vinent and MacPhee) in the Equatorial Atlantic Gateway and elsewhere.

ARkStorm@Tahoe: Stakeholder perspectives on vulnerabilities and preparedness for an extreme storm event in the greater Lake Tahoe, Reno, and Carson City region

USGS Publications Warehouse

Albano, Christine M.; Cox, Dale A.; Dettinger, Michael; Shaller, Kevin; Welborn, Toby L.; McCarthy, Maureen

2014-01-01

Atmospheric rivers (ARs) are strongly linked to extreme winter precipitation events in the Western U.S., accounting for 80 percent of extreme floods in the Sierra Nevada and surrounding lowlands. In 2010, the U.S. Geological Survey developed the ARkStorm extreme storm scenario for California to quantify risks from extreme winter storms and to allow stakeholders to better explore and mitigate potential impacts. To explore impacts on natural resources and communities in montane and adjacent environments, we downscaled the scenario to the greater Lake Tahoe, Reno and Carson City region of northern Nevada and California. This ArkStorm@Tahoe scenario was presented at six stakeholder meetings, each with a different geographic and subject matter focus. Discussions were facilitated by the ARkStorm@Tahoe team to identify social and ecological vulnerabilities to extreme winter storms, science and information needs, and proactive measures that might minimize impacts from this type of event. Information collected in these meetings was used to develop a tabletop emergency response exercise and set of recommendations for increasing resilience to extreme winter storm events in both Tahoe and the downstream communities of Northern Nevada.Over 300 individuals participated in ARkStorm@Tahoe stakeholder meetings and the emergency response exercise, including representatives from emergency response, natural resource and ecosystem management, health and human services, public utilities, and businesses. Interruption of transportation, communications, and lack of power and backup fuel supplies were identified as the most likely and primary points of failure across multiple sectors and geographies, as these interruptions have cascading effects on natural and human systems by impeding emergency response efforts. Other key issues that arose in discussions included contamination risks to water supplies and aquatic ecosystems, especially in the Tahoe Basin and Pyramid Lake, interagency coordination, credentialing, flood management, and coordination of health and human services during such an event. Mitigation options were identified for each of the key issues. Several science needs were identified, particularly the need for improved flood inundation maps. Finally, key lessons learned were identified and may help to increase preparedness, response and recovery from extreme storms in the future.

Good performance of an immunoassay based method for nevirapine measurements in human breast milk.

PubMed

Salado-Rasmussen, Kirsten; Theilgaard, Zahra Persson; Chiduo, Mercy; Pedersen, Court; Gerstoft, Jan; Katzenstein, Terese Lea

2011-07-01

Understanding the distribution of antiretro-virals in breastfeeding HIV-positive mothers is essential, both for prevention of mother-to-child HIV transmission and for research on the development of drug resistance. The ARK nevirapine (NVP)-test is an immunoassay method for nevirapine measurements, developed and validated for plasma use. In this study, the ARK NVP-test was evaluated for measurement of nevirapine concentrations in breast milk. High performance liquid chromatography (HPLC) is the method currently used to determine nevirapine in breast milk. This method, however, requires complicated extraction techniques. The ARK method employs an immunoassay technology and requires a small sample volume (40 μL) and no pre-treatment of the samples. Commercial enzyme and antibody were used and calibration standards and quality controls were prepared from pooled breast milk from HIV-uninfected women. Clinical samples from HIV-infected women receiving a single-dose of nevirapine were analyzed. Precision and accuracy were evaluated with two concentrations of quality control materials analyzed in three replicates on four different days and was <4%, and between 96.5% and 104.6%, respectively. Clinical samples were analyzed and CVs ranged from 0.0% to 11.1%. The median nevirapine concentration in breast milk 1 week post-partum was 0.29 μg/mL (range 0.11-0.90 μg/mL) in women treated with a single-dose of nevirapine. The ease of use and small sample volume makes the ARK assay an attractive alternative to HPLC analyses for determinations of nevirapine concentrations in breast milk.

Expression and Functional Significance of HtrA1 Loss in Endometrial Cancer

PubMed Central

Mullany, Sally A.; Moslemi-Kebria, Mehdi; Rattan, Ramandeep; Khurana, Ashwani; Clayton, Amy; Ota, Takayo; Mariani, Andrea; Podratz, Karl C.; Chien, Jeremy; Shridhar, Viji

2010-01-01

Purpose The purpose of this study was to determine if loss of serine protease HtrA1 in endometrial cancer will promote the invasive potential of EC cell lines. Experimental design Western blot analysis and immunohistochemistry methods were used to determine HtrA1 expression in EC cell lines and primary tumors, respectively. Migration, invasion assays and in vivo xenograft experiment were performed to compare the extent of metastasis between HtrA1 expressing and HtrA-1 knocked down clones. Results Western blot analysis of HtrA1 in 13 EC cell lines revealed complete loss of HtrA1 expression in all 7 papillary serous EC cell lines. Downregulation of HtrA1 in Hec1A and Hec1B cell lines resulted in a 3-4 fold increase in the invasive potential. Exogenous expression of HtrA1 in Ark 1 and Ark 2 cells resulted in 3-4 fold decrease in both invasive and migration potential of these cells. There was an increased rate of metastasis to the lungs associated with HtrA1 downregulation in Hec1B cells compared to control cells with endogenous HtrA1 expression. Enhanced expression of HtrA1 in Ark 2 cells resulted in significantly less tumor nodules metastasizing to the lungs compared to parental or protease deficient (SA mutant) Ark 2 cells. Immunohistochemical (IHC) analysis showed 57% (105/184) of primary EC tumors had low HtrA1 expression. The association of low HtrA1 expression with high-grade endometrioid tumors was statistically significant (p=0.016). Conclusions Collectively, these data indicate loss of HtrA1 may contribute to the aggressiveness and metastatic ability of endometrial tumors. PMID:21098697

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

PubMed

Koslicki, David; Chatterjee, Saikat; Shahrivar, Damon; Walker, Alan W; Francis, Suzanna C; Fraser, Louise J; Vehkaperä, Mikko; Lan, Yueheng; Corander, Jukka

2015-01-01

Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.

On the role of endogenous G-protein βγ subunits in N-type Ca2+ current inhibition by neurotransmitters in rat sympathetic neurones

PubMed Central

Delmas, Patrick; Brown, David A; Dayrell, Mariza; Abogadie, Fe C; Caulfield, Malcolm P; Buckley, Noel J

1998-01-01

Using whole-cell and perforated-patch recordings, we have examined the part played by endogenous G-protein βγ subunits in neurotransmitter-mediated inhibition of N-type Ca2+ channel current ICa) in dissociated rat superior cervical sympathetic neurones. Expression of the C-terminus domain of β-adrenergic receptor kinase 1 (βARK1), which contains the consensus motif (QXXER) for binding Gβγ, reduced the fast (pertussis toxin (PTX)-sensitive) and voltage-dependent inhibition of ICa by noradrenaline and somatostatin, but not the slow (PTX-insensitive) and voltage-independent inhibition induced by angiotensin II. βARK1 peptide reduced GTP-γ-S-induced voltage-dependent and PTX-sensitive inhibition of ICa but not GTP-γ-S-mediated voltage-independent inhibition. Overexpression of Gβ1γ2, which mimicked the voltage-dependent inhibition by reducing ICa density and enhancing basal facilitation, occluded the voltage-dependent noradrenaline- and somatostatin-mediated inhibitions but not the inhibition mediated by angiotensin II. Co-expression of the C-terminus of βARK1 with β1 and γ2 subunits prevented the effects of Gβγ dimers on basal Ca2+ channel behaviour in a manner consistent with the sequestering of Gβγ. The expression of the C-terminus of βARK1 slowed down reinhibition kinetics of ICa following conditioning depolarizations and induced long-lasting facilitation by cumulatively sequestering βγ subunits. Our findings identify endogenous Gβγ as the mediator of the voltage-dependent, PTX-sensitive inhibition of ICa induced by both noradrenaline and somatostatin but not the voltage-independent, PTX-insensitive inhibition by angiotensin II. They also support the view that voltage-dependent inhibition results from a direct Gβγ-Ca2+ channel interaction. PMID:9490860

A class I ADP-ribosylation factor GTPase-activating protein is critical for maintaining directional root hair growth in Arabidopsis.

PubMed

Yoo, Cheol-Min; Wen, Jiangqi; Motes, Christy M; Sparks, J Alan; Blancaflor, Elison B

2008-08-01

Membrane trafficking and cytoskeletal dynamics are important cellular processes that drive tip growth in root hairs. These processes interact with a multitude of signaling pathways that allow for the efficient transfer of information to specify the direction in which tip growth occurs. Here, we show that AGD1, a class I ADP ribosylation factor GTPase-activating protein, is important for maintaining straight growth in Arabidopsis (Arabidopsis thaliana) root hairs, since mutations in the AGD1 gene resulted in wavy root hair growth. Live cell imaging of growing agd1 root hairs revealed bundles of endoplasmic microtubules and actin filaments extending into the extreme tip. The wavy phenotype and pattern of cytoskeletal distribution in root hairs of agd1 partially resembled that of mutants in an armadillo repeat-containing kinesin (ARK1). Root hairs of double agd1 ark1 mutants were more severely deformed compared with single mutants. Organelle trafficking as revealed by a fluorescent Golgi marker was slightly inhibited, and Golgi stacks frequently protruded into the extreme root hair apex of agd1 mutants. Transient expression of green fluorescent protein-AGD1 in tobacco (Nicotiana tabacum) epidermal cells labeled punctate bodies that partially colocalized with the endocytic marker FM4-64, while ARK1-yellow fluorescent protein associated with microtubules. Brefeldin A rescued the phenotype of agd1, indicating that the altered activity of an AGD1-dependent ADP ribosylation factor contributes to the defective growth, organelle trafficking, and cytoskeletal organization of agd1 root hairs. We propose that AGD1, a regulator of membrane trafficking, and ARK1, a microtubule motor, are components of converging signaling pathways that affect cytoskeletal organization to specify growth orientation in Arabidopsis root hairs.

A Class I ADP-Ribosylation Factor GTPase-Activating Protein Is Critical for Maintaining Directional Root Hair Growth in Arabidopsis1[W][OA

PubMed Central

Yoo, Cheol-Min; Wen, Jiangqi; Motes, Christy M.; Sparks, J. Alan; Blancaflor, Elison B.

2008-01-01

Membrane trafficking and cytoskeletal dynamics are important cellular processes that drive tip growth in root hairs. These processes interact with a multitude of signaling pathways that allow for the efficient transfer of information to specify the direction in which tip growth occurs. Here, we show that AGD1, a class I ADP ribosylation factor GTPase-activating protein, is important for maintaining straight growth in Arabidopsis (Arabidopsis thaliana) root hairs, since mutations in the AGD1 gene resulted in wavy root hair growth. Live cell imaging of growing agd1 root hairs revealed bundles of endoplasmic microtubules and actin filaments extending into the extreme tip. The wavy phenotype and pattern of cytoskeletal distribution in root hairs of agd1 partially resembled that of mutants in an armadillo repeat-containing kinesin (ARK1). Root hairs of double agd1 ark1 mutants were more severely deformed compared with single mutants. Organelle trafficking as revealed by a fluorescent Golgi marker was slightly inhibited, and Golgi stacks frequently protruded into the extreme root hair apex of agd1 mutants. Transient expression of green fluorescent protein-AGD1 in tobacco (Nicotiana tabacum) epidermal cells labeled punctate bodies that partially colocalized with the endocytic marker FM4-64, while ARK1-yellow fluorescent protein associated with microtubules. Brefeldin A rescued the phenotype of agd1, indicating that the altered activity of an AGD1-dependent ADP ribosylation factor contributes to the defective growth, organelle trafficking, and cytoskeletal organization of agd1 root hairs. We propose that AGD1, a regulator of membrane trafficking, and ARK1, a microtubule motor, are components of converging signaling pathways that affect cytoskeletal organization to specify growth orientation in Arabidopsis root hairs. PMID:18539780

Implicit-Explicit Time Integration Methods for Non-hydrostatic Atmospheric Models

NASA Astrophysics Data System (ADS)

Gardner, D. J.; Guerra, J. E.; Hamon, F. P.; Reynolds, D. R.; Ullrich, P. A.; Woodward, C. S.

2016-12-01

The Accelerated Climate Modeling for Energy (ACME) project is developing a non-hydrostatic atmospheric dynamical core for high-resolution coupled climate simulations on Department of Energy leadership class supercomputers. An important factor in computational efficiency is avoiding the overly restrictive time step size limitations of fully explicit time integration methods due to the stiffest modes present in the model (acoustic waves). In this work we compare the accuracy and performance of different Implicit-Explicit (IMEX) splittings of the non-hydrostatic equations and various Additive Runge-Kutta (ARK) time integration methods. Results utilizing the Tempest non-hydrostatic atmospheric model and the ARKode package show that the choice of IMEX splitting and ARK scheme has a significant impact on the maximum stable time step size as well as solution quality. Horizontally Explicit Vertically Implicit (HEVI) approaches paired with certain ARK methods lead to greatly improved runtimes. With effective preconditioning IMEX splittings that incorporate some implicit horizontal dynamics can be competitive with HEVI results. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-699187

Changes in hemolymph characteristics of ark shell Scapharaca broughtonii dealt with Vibrio anguillarum challenge in vivo and various of anticoagulants in vitro.

PubMed

Zhou, Liqing; Yang, Aiguo; Liu, Zhihong; Wu, Biao; Sun, Xiujun; Lv, Zhenming; Tian, Ji-Teng; Du, Meirong

2017-02-01

The ark shell Scapharca broughtonii is a commercially important shellfish in China. Alserver's solution (AS), modified Alserver's solution (MAS) and Heparin sodium solution (HSS) are common anticoagulants used for shellfish blood. To observe the immune response mediated by its hemocytes, we challenged in vivo S. broughtonii hemolymph with Vibrio anguillarum and dealt with the following three anticoagulants in vitro: Alserver's solution (AS), modified Alserver's solution (MAS) and Heparin sodium solution (HSS). The methodologies we used were immunostimulation with V. anguillarum, Wright-Giemsa staining, micro-examination, and flow cytometric and hydrolyzing enzyme activity analysis. The results showed that all three types of anticoagulants effectively prevented blood clotting in ark shellfish. The morphology of hemocytes did not significantly change 30 h after anticoagulant treatment, except for the shrinking of hemocytes after administering HSS. The size and permeability of hemocytes changed when treated with the anticoagulants and when stimulated with V. anguillarum. Both alkaline phosphatase (AKP) and acid phosphatase (ACP) in hemocytes and Plasma were measured at different times after they were stimulated with V. anguillarum in HSS and MAS. The AKP enzymatic activity in HSS was somewhat higher than in the MAS anticoagulant, but changes in response to V. anguillarum challenge of enzymatic activity were almost the same in HSS and MAS groups. In conclusion, all three types of anticoagulants may be used for ark shell blood preservation. They all changed the cell-surface characteristics of hemocytes to inhibit clot formation. The AS anticoagulant was appropriate for maintaining white and red cell shapes, while MAS was ideal for retaining throbus cell function. Lastly, HSS was appropriate for maintaining enzymatic activity in hemolymph and function of hemocytes. Following this investigation, we gained insight into the changes in hemolymph characteristic during immune response. Copyright © 2016. Published by Elsevier Ltd.

EZID: Long term identifiers made easy (Invited)

NASA Astrophysics Data System (ADS)

Starr, J.

2013-12-01

Scholarly research is producing ever increasing amounts of digital research data, and this data should be managed throughout the research life cycle both as part of good scientific practice, but also to comply with funder mandates, such as the 2013 OSTP Public Access Memo (http://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf). By assigning unique and persistent identifiers to data objects, data managers can gain control and flexibility over what can be a daunting task. This is due to the fact that the objects can be moved to new locations without disruption to links, as long as the identifier target is maintained. EZID is a tool that makes assigning and maintaining unique, persistent identifiers easy. It was designed and built by California Digital Library (CDL) and has both a user interface and a RESTful API. EZID currently offers services for two globally unique, persistent identifier schemes: Digital Object Identifiers (DOIs) and Archival Resource Keys (ARKs). DOIs are identifiers originating from the publishing world and are in widespread use for journal articles. CDL is able to offer DOIs because of being a founding member of DataCite (http://www.datacite.org/), an international consortium established to provide easier access to scientific research data on the Internet. ARKs are identifiers originating from the library, archive and museum community. Like DOIs, they become persistent when the objects and identifier forwarding information is maintained. DOIs and ARKs have a key role in data management and, therefore, in data management plans. DOIs are the recommended identifier for use in data citation, and ARKs provide the maximum flexibility needed for data documentation and management throughout the early phases of a project. The two identifier schemes are able to be used together, and EZID is made to work with both. EZID clients, coming from education, research, government, and the private sector, are utilizing the tool for these use cases and more.

A deep X-ray view of the bare AGN Ark 120. IV. XMM-Newton and NuSTAR spectra dominated by two temperature (warm, hot) Comptonization processes

NASA Astrophysics Data System (ADS)

Porquet, D.; Reeves, J. N.; Matt, G.; Marinucci, A.; Nardini, E.; Braito, V.; Lobban, A.; Ballantyne, D. R.; Boggs, S. E.; Christensen, F. E.; Dauser, T.; Farrah, D.; Garcia, J.; Hailey, C. J.; Harrison, F.; Stern, D.; Tortosa, A.; Ursini, F.; Zhang, W. W.

2018-01-01

Context. The physical characteristics of the material closest to supermassive black holes (SMBHs) are primarily studied through X-ray observations. However, the origins of the main X-ray components such as the soft X-ray excess, the Fe Kα line complex, and the hard X-ray excess are still hotly debated. This is particularly problematic for active galactic nuclei (AGN) showing a significant intrinsic absorption, either warm or neutral, which can severely distort the observed continuum. Therefore, AGN with no (or very weak) intrinsic absorption along the line of sight, so-called "bare AGN", are the best targets to directly probe matter very close to the SMBH. Aims: We perform an X-ray spectral analysis of the brightest and cleanest bare AGN known so far, Ark 120, in order to determine the process(es) at work in the vicinity of the SMBH. Methods: We present spectral analyses of data from an extensive campaign observing Ark 120 in X-rays with XMM-Newton (4 × 120 ks, 2014 March 18-24), and NuSTAR (65.5 ks, 2014 March 22). Results: During this very deep X-ray campaign, the source was caught in a high-flux state similar to the earlier 2003 XMM-Newton observation, and about twice as bright as the lower-flux observation in 2013. The spectral analysis confirms the "softer when brighter" behavior of Ark 120. The four XMM-Newton/pn spectra are characterized by the presence of a prominent soft X-ray excess and a significant Fe Kα complex. The continuum is very similar above about 3 keV, while significant variability is present for the soft X-ray excess. We find that relativistic reflection from a constant-density, flat accretion disk cannot simultaneously produce the soft excess, broad Fe Kα complex, and hard X-ray excess. Instead, Comptonization reproduces the broadband (0.3-79 keV) continuum well, together with a contribution from a mildly relativistic disk reflection spectrum. Conclusions: During this 2014 observational campaign, the soft X-ray spectrum of Ark 120 below 0.5 keV was found to be dominated by Comptonization of seed photons from the disk by a warm (kTe 0.5 keV), optically-thick corona (τ 9). Above this energy, the X-ray spectrum becomes dominated by Comptonization from electrons in a hot optically thin corona, while the broad Fe Kα line and the mild Compton hump result from reflection off the disk at several tens of gravitational radii.

Transcriptional and Hormonal Regulation of Gravitropism of Woody Stems in Populus[OPEN

PubMed Central

Gerttula, Suzanne; Zinkgraf, Matthew; Lewis, Daniel R.; Brumer, Harry; Hart, Foster; Filkov, Vladimir

2015-01-01

Angiosperm trees reorient their woody stems by asymmetrically producing a specialized xylem tissue, tension wood, which exerts a strong contractile force resulting in negative gravitropism of the stem. Here, we show, in Populus trees, that initial gravity perception and response occurs in specialized cells through sedimentation of starch-filled amyloplasts and relocalization of the auxin transport protein, PIN3. Gibberellic acid treatment stimulates the rate of tension wood formation and gravibending and enhances tissue-specific expression of an auxin-responsive reporter. Gravibending, maturation of contractile fibers, and gibberellic acid (GA) stimulation of tension wood formation are all sensitive to transcript levels of the Class I KNOX homeodomain transcription factor-encoding gene ARBORKNOX2 (ARK2). We generated genome-wide transcriptomes for trees in which gene expression was perturbed by gravistimulation, GA treatment, and modulation of ARK2 expression. These data were employed in computational analyses to model the transcriptional networks underlying wood formation, including identification and dissection of gene coexpression modules associated with wood phenotypes, GA response, and ARK2 binding to genes within modules. We propose a model for gravitropism in the woody stem in which the peripheral location of PIN3-expressing cells relative to the cambium results in auxin transport toward the cambium in the top of the stem, triggering tension wood formation, while transport away from the cambium in the bottom of the stem triggers opposite wood formation. PMID:26410302

Genomics and the Ark: an ecocentric perspective on human history.

PubMed

Zwart, Hub; Penders, Bart

2011-01-01

Views of ourselves in relationship to the rest of the biosphere are changing. Theocentric and anthropocentric perspectives are giving way to more ecocentric views on the history, present, and future of humankind. Novel sciences, such as genomics, have deepened and broadened our understanding of the process of anthropogenesis, the coming into being of humans. Genomics suggests that early human history must be regarded as a complex narrative of evolving ecosystems, in which human evolution both influenced and was influenced by the evolution of companion species. During the agricultural revolution, human beings designed small-scale artificial ecosystems or evolutionary "Arks," in which networks of plants, animals, and microorganisms coevolved. Currently, our attitude towards this process seems subject to a paradoxical reversal. The boundaries of the Ark have dramatically broadened, and genomics is not only being used to increase our understanding of our ecological past, but may also help us to conserve, reconstruct, or even revivify species and ecosystems to whose degradation or (near) extinction we have contributed. This article explores the role of genomics in the elaboration of a more ecocentric view of ourselves with the help of two examples, namely the renaissance of Paleolithic diets and of Pleistocene parks. It argues that an understanding of the world in ecocentric terms requires new partnerships and mutually beneficial forms of collaboration and convergence between life sciences, social sciences, and the humanities.

ARK: Autonomous mobile robot in an industrial environment

NASA Technical Reports Server (NTRS)

Nickerson, S. B.; Jasiobedzki, P.; Jenkin, M.; Jepson, A.; Milios, E.; Down, B.; Service, J. R. R.; Terzopoulos, D.; Tsotsos, J.; Wilkes, D.

1994-01-01

This paper describes research on the ARK (Autonomous Mobile Robot in a Known Environment) project. The technical objective of the project is to build a robot that can navigate in a complex industrial environment using maps with permanent structures. The environment is not altered in any way by adding easily identifiable beacons and the robot relies on naturally occurring objects to use as visual landmarks for navigation. The robot is equipped with various sensors that can detect unmapped obstacles, landmarks and objects. In this paper we describe the robot's industrial environment, it's architecture, a novel combined range and vision sensor and our recent results in controlling the robot in the real-time detection of objects using their color and in the processing of the robot's range and vision sensor data for navigation.

viRome: an R package for the visualization and analysis of viral small RNA sequence datasets.

PubMed

Watson, Mick; Schnettler, Esther; Kohl, Alain

2013-08-01

RNA interference (RNAi) is known to play an important part in defence against viruses in a range of species. Second-generation sequencing technologies allow us to assay these systems and the small RNAs that play a key role with unprecedented depth. However, scientists need access to tools that can condense, analyse and display the resulting data. Here, we present viRome, a package for R that takes aligned sequence data and produces a range of essential plots and reports. viRome is released under the BSD license as a package for R available for both Windows and Linux http://virome.sf.net. Additional information and a tutorial is available on the ARK-Genomics website: http://www.ark-genomics.org/bioinformatics/virome. mick.watson@roslin.ed.ac.uk.

SPECTRAL OPTICAL MONITORING OF THE NARROW-LINE SEYFERT 1 GALAXY Ark 564

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

Shapovalova, A. I.; Burenkov, A. N.; Popovic, L. C.

2012-09-15

We present the results of a long-term (1999-2010) spectral optical monitoring campaign of the active galactic nucleus (AGN) Ark 564, which shows a strong Fe II line emission in the optical. This AGN is a narrow-line Seyfert 1 (NLS1) galaxy, a group of AGNs with specific spectral characteristics. We analyze the light curves of the permitted H{alpha}, H{beta}, optical Fe II line fluxes, and the continuum flux in order to search for a time lag between them. Additionally, in order to estimate the contribution of iron lines from different multiplets, we fit the H{beta} and Fe II lines with amore » sum of Gaussian components. We find that during the monitoring period the spectral variation (F{sub max}/F{sub min}) of Ark 564 is between 1.5 for H{alpha} and 1.8 for the Fe II lines. The correlation between the Fe II and H{beta} flux variations is of higher significance than that of H{alpha} and H{beta} (whose correlation is almost absent). The permitted-line profiles are Lorentzian-like and do not change shape during the monitoring period. We investigate, in detail, the optical Fe II emission and find different degrees of correlation between the Fe II emission arising from different spectral multiplets and the continuum flux. The relatively weak and different degrees of correlations between permitted lines and continuum fluxes indicate a rather complex source of ionization of the broad-line emission region.« less

Transcriptional and Hormonal Regulation of Gravitropism of Woody Stems in Populus.

PubMed

Gerttula, Suzanne; Zinkgraf, Matthew; Muday, Gloria K; Lewis, Daniel R; Ibatullin, Farid M; Brumer, Harry; Hart, Foster; Mansfield, Shawn D; Filkov, Vladimir; Groover, Andrew

2015-10-01

Angiosperm trees reorient their woody stems by asymmetrically producing a specialized xylem tissue, tension wood, which exerts a strong contractile force resulting in negative gravitropism of the stem. Here, we show, in Populus trees, that initial gravity perception and response occurs in specialized cells through sedimentation of starch-filled amyloplasts and relocalization of the auxin transport protein, PIN3. Gibberellic acid treatment stimulates the rate of tension wood formation and gravibending and enhances tissue-specific expression of an auxin-responsive reporter. Gravibending, maturation of contractile fibers, and gibberellic acid (GA) stimulation of tension wood formation are all sensitive to transcript levels of the Class I KNOX homeodomain transcription factor-encoding gene ARBORKNOX2 (ARK2). We generated genome-wide transcriptomes for trees in which gene expression was perturbed by gravistimulation, GA treatment, and modulation of ARK2 expression. These data were employed in computational analyses to model the transcriptional networks underlying wood formation, including identification and dissection of gene coexpression modules associated with wood phenotypes, GA response, and ARK2 binding to genes within modules. We propose a model for gravitropism in the woody stem in which the peripheral location of PIN3-expressing cells relative to the cambium results in auxin transport toward the cambium in the top of the stem, triggering tension wood formation, while transport away from the cambium in the bottom of the stem triggers opposite wood formation. © 2015 American Society of Plant Biologists. All rights reserved.

Enracinement or the earth, the originary ark, does not move: on the phenomenological (historical and ontogenetic) origin of common and scientific sense and the genetic method of teaching (for) understanding

NASA Astrophysics Data System (ADS)

Roth, Wolff-Michael

2015-06-01

For many students, the experience with science tends to be alienating and uprooting. In this study, I take up Simone Weil's concepts of enracinement (rooting) and déracinement (uprooting) to theorize the root of this alienation, the confrontation between children's familiarity with the world and unfamiliar/strange scientific conceptions. I build on the works of the phenomenological philosopher Edmund Husserl and the German physics educator Martin Wagenschein (who directly refers to Weil's concepts) to make a case for the rooting function of original/originary experiences and the genetic method to science teaching. The genetic approach allows students to retain their foundational familiarity with the world and their descriptions thereof all the while evolving other (more scientific) ways of explaining natural phenomena.

The Soft-X-Ray Emission of Ark 120. XMM-Newton, NuSTAR, and the Importance of Taking the Broad View

NASA Technical Reports Server (NTRS)

Matt, G.; Marinucci, A.; Guainazzi, M.; Brenneman, L. W.; Elvis, M.; Lohfink, A.; Arevalo, P.; Boggs, S. E.; Cappi, M.; Stern, D.;

The Moses, mega-Moses, and Armstrong illusions: integrating language comprehension and semantic memory.

PubMed

Shafto, M; MacKay, D G

2000-09-01

This study develops a new theory of the Moses illusion, observed in responses to general knowledge questions such as, "How many animals of each kind did Moses take on the Ark?" People often respond "two" rather than "zero" despite knowing that Noah, not Moses, launched the Ark. Our theory predicted two additional types of conceptual error demonstrated here: the Armstrong and mega-Moses illusions. The Armstrong illusion involved questions resembling, "What was the famous line uttered by Louis Armstrong when he first set foot on the moon?" People usually comprehend such questions as valid, despite knowing that Louis Armstrong was a jazz musician who never visited the moon. This Armstrong illusion was not due to misperceiving the critical words (Louis Armstrong), and occurred as frequently as the Moses illusion (with critical words embedded in identical sentential contexts), but less frequently than the mega-Moses illusion caused when Moses and Armstrong factors were combined.

Anticipating and Communicating Plausible Environmental and Health Concerns Associated with Future Disasters: The ShakeOut and ARkStorm Scenarios as Examples

NASA Astrophysics Data System (ADS)

Plumlee, G. S.; Morman, S. A.; Alpers, C. N.; Hoefen, T. M.; Meeker, G. P.

2010-12-01

Disasters commonly pose immediate threats to human safety, but can also produce hazardous materials (HM) that pose short- and long-term environmental-health threats. The U.S. Geological Survey (USGS) has helped assess potential environmental health characteristics of HM produced by various natural and anthropogenic disasters, such as the 2001 World Trade Center collapse, 2005 hurricanes Katrina and Rita, 2007-2009 southern California wildfires, various volcanic eruptions, and others. Building upon experience gained from these responses, we are now developing methods to anticipate plausible environmental and health implications of the 2008 Great Southern California ShakeOut scenario (which modeled the impacts of a 7.8 magnitude earthquake on the southern San Andreas fault, http://urbanearth.gps.caltech.edu/scenario08/), and the recent ARkStorm scenario (modeling the impacts of a major, weeks-long winter storm hitting nearly all of California, http://urbanearth.gps.caltech.edu/winter-storm/). Environmental-health impacts of various past earthquakes and extreme storms are first used to identify plausible impacts that could be associated with the disaster scenarios. Substantial insights can then be gleaned using a Geographic Information Systems (GIS) approach to link ShakeOut and ARkStorm effects maps with data extracted from diverse database sources containing geologic, hazards, and environmental information. This type of analysis helps constrain where potential geogenic (natural) and anthropogenic sources of HM (and their likely types of contaminants or pathogens) fall within areas of predicted ShakeOut-related shaking, firestorms, and landslides, and predicted ARkStorm-related precipitation, flooding, and winds. Because of uncertainties in the event models and many uncertainties in the databases used (e.g., incorrect location information, lack of detailed information on specific facilities, etc.) this approach should only be considered as the first of multiple steps toward a more quantitative, predictive approach to understanding the potential sources, types, environmental behavior, and health implications of HM predicted to result from these disaster scenarios. Although only a first step, this qualitative approach will help enhance planning for, mitigation of, and resilience to environmental-health consequences of future disasters. This qualitative approach also requires careful communication to stakeholders that does not sensationalize or overstate potential problems, but rather conveys plausible impacts and next steps to improve understanding of potential risks and their mitigation.

Dismantling Noah's Ark.

ERIC Educational Resources Information Center

Lorber, Judith

1986-01-01

Presents a prescription for a restructured postindustrial society without gender as an organizing principle. The potential nongendered social order is described in terms of nongendered reproduction, equally valued wage work and a gender-neutral wage structure, and gender-neutral access to authority and power. (SA)

Different distribution patterns of ten virulence genes in Legionella reference strains and strains isolated from environmental water and patients.

PubMed

Zhan, Xiao-Yong; Hu, Chao-Hui; Zhu, Qing-Yi

2016-04-01

Virulence genes are distinct regions of DNA which are present in the genome of pathogenic bacteria and absent in nonpathogenic strains of the same or related species. Virulence genes are frequently associated with bacterial pathogenicity in genus Legionella. In the present study, an assay was performed to detect ten virulence genes, including iraA, iraB, lvrA, lvrB, lvhD, cpxR, cpxA, dotA, icmC and icmD in different pathogenicity islands of 47 Legionella reference strains, 235 environmental strains isolated from water, and 4 clinical strains isolated from the lung tissue of pneumonia patients. The distribution frequencies of these genes in reference or/and environmental L. pneumophila strains were much higher than those in reference non-L. pneumophila or/and environmental non-L. pneumophila strains, respectively. L. pneumophila clinical strains also maintained higher frequencies of these genes compared to four other types of Legionella strains. Distribution frequencies of these genes in reference L. pneumophila strains were similar to those in environmental L. pneumophila strains. In contrast, environmental non-L. pneumophila maintained higher frequencies of these genes compared to those found in reference non-L. pneumophila strains. This study illustrates the association of virulence genes with Legionella pathogenicity and reveals the possible virulence evolution of non-L. pneumophia strains isolated from environmental water.

TOR Complex 2-Regulated Protein Kinase Fpk1 Stimulates Endocytosis via Inhibition of Ark1/Prk1-Related Protein Kinase Akl1 in Saccharomyces cerevisiae.

PubMed

Roelants, Françoise M; Leskoske, Kristin L; Pedersen, Ross T A; Muir, Alexander; Liu, Jeffrey M-H; Finnigan, Gregory C; Thorner, Jeremy

2017-04-01

Depending on the stress, plasma membrane alterations activate or inhibit yeast target of rapamycin (TOR) complex 2, which, in turn, upregulates or downregulates the activity of its essential downstream effector, protein kinase Ypk1. Through phosphorylation of multiple substrates, Ypk1 controls many processes that restore homeostasis. One such substrate is protein kinase Fpk1, which is negatively regulated by Ypk1. Fpk1 phosphorylates and stimulates flippases that translocate aminoglycerophospholipids from the outer to the inner leaflet of the plasma membrane. Fpk1 has additional roles, but other substrates were uncharacterized. We show that Fpk1 phosphorylates and inhibits protein kinase Akl1, related to protein kinases Ark1 and Prk1, which modulate the dynamics of actin patch-mediated endocytosis. Akl1 has two Fpk1 phosphorylation sites (Ark1 and Prk1 have none) and is hypophosphorylated when Fpk1 is absent. Conversely, under conditions that inactivate TORC2-Ypk1 signaling, which alleviates Fpk1 inhibition, Akl1 is hyperphosphorylated. Monitoring phosphorylation of known Akl1 substrates (Sla1 and Ent2) confirmed that Akl1 is hyperactive when not phosphorylated by Fpk1. Fpk1-mediated negative regulation of Akl1 enhances endocytosis, because an Akl1 mutant immune to Fpk1 phosphorylation causes faster dissociation of Sla1 from actin patches, confers elevated resistance to doxorubicin (a toxic compound whose entry requires endocytosis), and impedes Lucifer yellow uptake (a marker of fluid phase endocytosis). Thus, TORC2-Ypk1, by regulating Fpk1-mediated phosphorylation of Akl1, adjusts the rate of endocytosis. Copyright © 2017 Roelants et al.

Long-term monitoring of Ark 120 with Swift

NASA Astrophysics Data System (ADS)

Gliozzi, M.; Papadakis, I. E.; Grupe, D.; Brinkmann, W. P.; Räth, C.

2017-02-01

We report the results of a six-month Swift monitoring campaign of Ark 120, a prototypical `bare' Seyfert 1 galaxy. The lack of intrinsic absorption combined with the nearly contemporaneous coverage of the ultraviolet (UV) and X-ray bands makes it possible to investigate the link between the accretion disc and the putative Comptonization corona. Our observations confirm the presence of substantial temporal variability, with the X-ray characterized by large-amplitude flux changes on time-scales of few days, while the variations in the UV bands are smoother and occur on time-scales of several weeks. The source also shows spectral variability with the X-ray spectrum steepening when the source is brighter. We do not detect any correlation between the UV flux and the X-ray spectral slope. A cross-correlation analysis suggests positive delays between X-rays and the UV emission, favouring a scenario of disc reprocessing. Although the strength of the correlation is moderate with a delay which is not well constrained (7.5 ± 7 d), it is nevertheless indicative of a very large disc reprocessing region, with a separation between the X-ray and the UV-emitting regions, which could be as large as 1000 rG. The Ark 120 correlation results are in agreement with those obtained in similar multiwavelength monitoring studies of active galactic nuclei (AGN). When combined together, the observations so far can be well described by a linear relation between the X-ray/UV delays and the mass of the central black hole. Within the context of the simplest scenario, where these delays correspond to light-travel times, the implied distance between the X-ray source and the optical/UV disc reprocessing region in these AGN should be of the order of many hundreds of gravitational radii.

Experimental evaluation of fluorescent (alizarin red S and calcein) and clip-tag markers for stock assessment of ark shell, Anadara broughtonii

NASA Astrophysics Data System (ADS)

Zhou, Shanshan; Zhang, Xiumei; Li, Wentao; Li, Long; Cai, Xingyuan

2017-03-01

Release programs to enhance stocks of ark shell ( Anadara broughtonii) have been undertaken in a number of Asian countries, but their effectiveness has rarely been investigated owing to a lack of marking methods. The quality and longevity of fluorescent markers, alizarin red S (ARS) and calcein (CAL) (200 and 300 mg/L), as well as clip tags, were tested on juvenile A. broughtonii. No significant differences in survival or shell growth were observed in juveniles stained with either of the two fluorochromes after a 160-day culture period, but the retention rate was 100% after 1 year. Fluorescent marks (≥grade 3) were observable microscopically in juveniles stained with the two fluorochromes, and some fluorescent marks (≥grade 4) were visible with the naked eye after 1 year. ARS-marked shells were brighter than those marked with CAL, and shells marked with 300 mg/L of the fluorochromes were easier to detect than those marked with 200 mg/L. Clip tags were incorporated into the shell as the bivalve grew, and the retention rate was 64.25% after 160 days. Significant differences in survival (at 30 days), shell length (at 60, 90, 120, and 160 days), and wet weight (at 90, 120, and 160 days) were observed between the clip-tagged and control groups (all P< 0.05), indicating that the tags may have passive effects on the ark shell. The results suggest that both ARS and CAL are suitable to mark A. broughtonii for large-scale restocking programs, and that optimal marking quality was achieved with 300 mg/L ARS. Lighter and smaller clip tags need to be developed to reduce injury and increase survival rate of clams.

Early Adolescence.

ERIC Educational Resources Information Center

Cronin, Linda L.; Padilla, Michael J.

1984-01-01

Describes science activities related to endangered species designed to sensitize students to the process of extinction; learn of the human role in that process; and emphasize the importance of National Wildlife Week. Provides activities and games such as drift traps, webbing, making corrections, What animal am I?, and Noah's Ark. (JM)

Children as Illustrators: A Transcultural Experience.

ERIC Educational Resources Information Center

Hurwitz, Al

1980-01-01

The author discusses his cross cultural study of the painting styles of 9- to 12-year-old children in Australia, New Zealand, and South Korea. He compares their art products--all illustrations of the Noah's Ark story. A sample of the drawings illustrates the text. (SJL)

27 CFR 9.185 - Texoma.

Code of Federal Regulations, 2010 CFR

2010-04-01

...; and (2) Texarkana, Tex.; Ark.; Okla.; La., 1953, revised 1972. (c) Boundary. The Texoma viticultural... the Red River eastward along the Texas-Oklahoma State line, passes onto the Texarkana map, and... Texarkana map crosses the county line; then (4) Continues southwest in a straight line for approximately 13...

27 CFR 9.185 - Texoma.

Code of Federal Regulations, 2012 CFR

2012-04-01

...; and (2) Texarkana, Tex.; Ark.; Okla.; La., 1953, revised 1972. (c) Boundary. The Texoma viticultural... the Red River eastward along the Texas-Oklahoma State line, passes onto the Texarkana map, and... Texarkana map crosses the county line; then (4) Continues southwest in a straight line for approximately 13...

27 CFR 9.185 - Texoma.

Code of Federal Regulations, 2013 CFR

2013-04-01

...; and (2) Texarkana, Tex.; Ark.; Okla.; La., 1953, revised 1972. (c) Boundary. The Texoma viticultural... the Red River eastward along the Texas-Oklahoma State line, passes onto the Texarkana map, and... Texarkana map crosses the county line; then (4) Continues southwest in a straight line for approximately 13...

27 CFR 9.185 - Texoma.

Code of Federal Regulations, 2011 CFR

2011-04-01

...; and (2) Texarkana, Tex.; Ark.; Okla.; La., 1953, revised 1972. (c) Boundary. The Texoma viticultural... the Red River eastward along the Texas-Oklahoma State line, passes onto the Texarkana map, and... Texarkana map crosses the county line; then (4) Continues southwest in a straight line for approximately 13...

27 CFR 9.185 - Texoma.

Code of Federal Regulations, 2014 CFR

2014-04-01

...; and (2) Texarkana, Tex.; Ark.; Okla.; La., 1953, revised 1972. (c) Boundary. The Texoma viticultural... the Red River eastward along the Texas-Oklahoma State line, passes onto the Texarkana map, and... Texarkana map crosses the county line; then (4) Continues southwest in a straight line for approximately 13...

An approximation algorithm for the Noah's Ark problem with random feature loss.

PubMed

Hickey, Glenn; Blanchette, Mathieu; Carmi, Paz; Maheshwari, Anil; Zeh, Norbert

2011-01-01

The phylogenetic diversity (PD) of a set of species is a measure of their evolutionary distinctness based on a phylogenetic tree. PD is increasingly being adopted as an index of biodiversity in ecological conservation projects. The Noah's Ark Problem (NAP) is an NP-Hard optimization problem that abstracts a fundamental conservation challenge in asking to maximize the expected PD of a set of taxa given a fixed budget, where each taxon is associated with a cost of conservation and a probability of extinction. Only simplified instances of the problem, where one or more parameters are fixed as constants, have as of yet been addressed in the literature. Furthermore, it has been argued that PD is not an appropriate metric for models that allow information to be lost along paths in the tree. We therefore generalize the NAP to incorporate a proposed model of feature loss according to an exponential distribution and term this problem NAP with Loss (NAPL). In this paper, we present a pseudopolynomial time approximation scheme for NAPL.

The novel 2016 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations: phenotypic, genetic and reference genome characterization.

PubMed

Unemo, Magnus; Golparian, Daniel; Sánchez-Busó, Leonor; Grad, Yonatan; Jacobsson, Susanne; Ohnishi, Makoto; Lahra, Monica M; Limnios, Athena; Sikora, Aleksandra E; Wi, Teodora; Harris, Simon R

2016-11-01

Gonorrhoea and MDR Neisseria gonorrhoeae remain public health concerns globally. Enhanced, quality-assured, gonococcal antimicrobial resistance (AMR) surveillance is essential worldwide. The WHO global Gonococcal Antimicrobial Surveillance Programme (GASP) was relaunched in 2009. We describe the phenotypic, genetic and reference genome characteristics of the 2016 WHO gonococcal reference strains intended for quality assurance in the WHO global GASP, other GASPs, diagnostics and research worldwide. The 2016 WHO reference strains (n = 14) constitute the eight 2008 WHO reference strains and six novel strains. The novel strains represent low-level to high-level cephalosporin resistance, high-level azithromycin resistance and a porA mutant. All strains were comprehensively characterized for antibiogram (n = 23), serovar, prolyliminopeptidase, plasmid types, molecular AMR determinants, N. gonorrhoeae multiantigen sequence typing STs and MLST STs. Complete reference genomes were produced using single-molecule PacBio sequencing. The reference strains represented all available phenotypes, susceptible and resistant, to antimicrobials previously and currently used or considered for future use in gonorrhoea treatment. All corresponding resistance genotypes and molecular epidemiological types were described. Fully characterized, annotated and finished references genomes (n = 14) were presented. The 2016 WHO gonococcal reference strains are intended for internal and external quality assurance and quality control in laboratory investigations, particularly in the WHO global GASP and other GASPs, but also in phenotypic (e.g. culture, species determination) and molecular diagnostics, molecular AMR detection, molecular epidemiology and as fully characterized, annotated and finished reference genomes in WGS analysis, transcriptomics, proteomics and other molecular technologies and data analysis. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Memory and the Moses illusion: failures to detect contradictions with stored knowledge yield negative memorial consequences.

PubMed

Bottoms, Hayden C; Eslick, Andrea N; Marsh, Elizabeth J

2010-08-01

Although contradictions with stored knowledge are common in daily life, people often fail to notice them. For example, in the Moses illusion, participants fail to notice errors in questions such as "How many animals of each kind did Moses take on the Ark?" despite later showing knowledge that the Biblical reference is to Noah, not Moses. We examined whether error prevalence affected participants' ability to detect distortions in questions, and whether this in turn had memorial consequences. Many of the errors were overlooked, but participants were better able to catch them when they were more common. More generally, the failure to detect errors had negative memorial consequences, increasing the likelihood that the errors were used to answer later general knowledge questions. Methodological implications of this finding are discussed, as it suggests that typical analyses likely underestimate the size of the Moses illusion. Overall, answering distorted questions can yield errors in the knowledge base; most importantly, prior knowledge does not protect against these negative memorial consequences.

Runaways.

ERIC Educational Resources Information Center

Greenberg, Keith Elliot

This essay with photographs describes the experiences of two runaways, examining why they left home and how they found help. Although runaways have a reputation for being irresponsible, they usually have good reasons for leaving home. The nun who ran Noah's Ark, where both the runaways featured found shelter and help, estimated that only about two…

Aperiodicity Correction for Rotor Tip Vortex Measurements

DTIC Science & Technology

2011-05-01

where α = 1.25643. The Iversen and the transitional models are not closed-form solutions but are formulated as solutions to an ordinary differential ...edition, 1932, pp. 592– 593. [7] Oseen, C. W., “ Uber Wirbelbewegung in Einer Reibenden Flussigkeit,” Ark. J. Mat. Astrom. Fys., Vol. 7, (Nonumber), 1912

Smithsonian's NOAHS: Keepers of the Ark. The New Explorers.

ERIC Educational Resources Information Center

Sheldon, Louisa; McCoy, Barbara; Leong, Kirsten; Wallace, Gwendolyn; Barwick, Allen; Reymund, Trudi

The New Opportunities in Animal Health Sciences (NOAHS) Center at the National Zoological Park in Washington, DC. is dedicated to expanding understanding of the biological factors, including the critical role of biodiversity, that influence animal survival. This set of activities includes a description of NOAHS and the NOAHS mission, and letters…

Stuff the Dodos

ERIC Educational Resources Information Center

Stringer, John

2009-01-01

The author picked up a lovely greetings card the other day. The front carried a picture of an overloaded ark. The caption read "And Noah saith "Stuff the dodos"--and behold, it was so". This is an attractive but rather simplistic explanation of extinction. The author is writing in the wake of some extraordinary events, as Professor Michael Reiss,…

Kandinsky's "Composition VI": Heideggerian Poetry in Noah's Ark

ERIC Educational Resources Information Center

Hall, Joshua M.

2012-01-01

The author will begin his investigation of Wassily Kandinsky's painting "Composition VI" with Kandinsky's own commentary on the painting. He will then turn to the analysis of Kandinsky and the "Compositions" in John Sallis's book "Shades." Using this analysis as his point of departure, the author will consider how "Composition VI" resonates with…

Macronutrients in soils and plants, and their impacts on animal and human health

USDA-ARS?s Scientific Manuscript database

Soil supplies an abundance of macronutrients necessary for plants to grow and thrive under a variety of environmental conditions around the world. The capability of soil to store and release these nutrients supports our existence. Scientists from USDA-ARS in Raleigh NC and at the University of Ark...

Psychosocial Prevention Education: A Comparison of Traditional vs. Thematic Prevention Programming for Youth

ERIC Educational Resources Information Center

Newgent, Rebecca A.; Higgins, Kristin K.; Belk, Stephanie E.; Behrend, Bonni A. Nickens; Dunbar, Kelly A.

2011-01-01

Group counseling has been highlighted as one effective intervention for at-risk students, yet debate remains as to the comparable efficacy of traditional interventions versus thematic interventions. This study compared two psychosocial educational programs, the PEGS and ARK Programs, designed to help elementary school students with social skills…

Seed Size, Ginning Rate, and Net Ginning Energy Requirement in Upland Cotton

USDA-ARS?s Scientific Manuscript database

Not much information is available in the literature on the effect of seed size on ginning efficiency in upland cotton. In 2015, nine diverse upland cotton cultivars and germplasm were planted at two locations in Stoneville, MS to test the above relationship. Two of the cultivars (Ark 9317-26 and DP ...

"From England with Love"… ARK, Heterarchies and Global "Philanthropic Governance"

ERIC Educational Resources Information Center

Olmedo, Antonio

2014-01-01

The recent emergence of "new" venture philanthropists, social entrepreneurs and neoliberal policy advocates and the new ways in which they configure and perform their political agendas have brought important changes in the way in which education policy is enacted. This study takes some of the ideas sketched in previous work further and…

The usability of ark clam shell (Anadara granosa) as calcium precursor to produce hydroxyapatite nanoparticle via wet chemical precipitate method in various sintering temperature.

PubMed

Khiri, Mohammad Zulhasif Ahmad; Matori, Khamirul Amin; Zainuddin, Norhazlin; Abdullah, Che Azurahanim Che; Alassan, Zarifah Nadakkavil; Baharuddin, Nur Fadilah; Zaid, Mohd Hafiz Mohd

2016-01-01

This paper reported the uses of ark clam shell calcium precursor in order to form hydroxyapatite (HA) via the wet chemical precipitation method. The main objective of this research is to acquire better understanding regarding the effect of sintering temperature in the fabrication of HA. Throughout experiment, the ratio of Ca:P were constantly controlled, between 1.67 and 2.00. The formation of HA at these ratio was confirmed by means of energy-dispersive X-ray spectroscopy analysis. In addition, the effect of sintering temperature on the formation of HA was observed using X-ray diffraction analysis, while the structural and morphology was determined by means of field emission scanning electron microscopy. The formation of HA nanoparticle was recorded (~35-69 nm) in the form of as-synthesize HA powder. The bonding compound appeared in the formation of HA was carried out using Fourier transform infrared spectroscopy such as biomaterials that are expected to find potential applications in orthopedic and biomedical industries .

Antecedent precipitation index determined from CST estimates of rainfall

NASA Technical Reports Server (NTRS)

Martin, David W.

1992-01-01

This paper deals with an experimental calculation of a satellite-based antecedent precipitation index (API). The index is also derived from daily rain images produced from infrared images using an improved version of GSFC's Convective/Stratiform Technique (CST). API is a measure of soil moisture, and is based on the notion that the amount of moisture in the soil at a given time is related to precipitation at earlier times. Four different CST programs as well as the Geostationary Operational Enviroment Satellite (GOES) Precipitation Index developed by Arkin in 1979 are compared to experimental results, for the Mississippi Valley during the month of July. Rain images are shown for the best CST code and the ARK program. Comparisons are made as to the accuracy and detail of the results for the two codes. This project demonstrates the feasibility of running the CST on a synoptic scale. The Mississippi Valley case is well suited for testing the feasibility of monitoring soil moisture by means of CST. Preliminary comparisons of CST and ARK indicate significant differences in estimates of rain amount and distribution.

The Effect of Ivermectin in Seven Strains of Aedes aegypti (Diptera: Culicidae) Including a Genetically Diverse Laboratory Strain and Three Permethrin Resistant Strains

PubMed Central

Deus, K. M.; Saavedra-rodriguez, K.; Butters, M. P.; Black, W. C.; Foy, B. D.

2014-01-01

Seven different strains of Aedes aegypti (L.), including a genetically diverse laboratory strain, three laboratory-selected permethrin-resistant strains, a standard reference strain, and two recently colonized strains were fed on human blood containing various concentrations of ivermectin. Ivermectin reduced adult survival, fecundity, and hatch rate of eggs laid by ivermectin-treated adults in all seven strains. The LC50 of ivermectin for adults and the concentration that prevented 50% of eggs from hatching was calculated for all strains. Considerable variation in adult survival after an ivermectin-bloodmeal occurred among strains, and all three permethrin-resistant strains were significantly less susceptible to ivermectin than the standard reference strain. The hatch rate after an ivermectin bloodmeal was less variable among strains, and only one of the permethrin-resistant strains differed significantly from the standard reference strain. Our studies suggest that ivermectin induces adult mortality and decreases the hatch rate of eggs through different mechanisms. A correlation analysis of log-transformed LC50 among strains suggests that permethrin and ivermectin cross-resistance may occur. PMID:22493855

Comparison of Haemophilus parasuis reference strains and field isolates by using random amplified polymorphic DNA and protein profiles

PubMed Central

2012-01-01

Background Haemophilus parasuis is the causative agent of Glässer’s disease and is a pathogen of swine in high-health status herds. Reports on serotyping of field strains from outbreaks describe that approximately 30% of them are nontypeable and therefore cannot be traced. Molecular typing methods have been used as alternatives to serotyping. This study was done to compare random amplified polymorphic DNA (RAPD) profiles and whole cell protein (WCP) lysate profiles as methods for distinguishing H. parasuis reference strains and field isolates. Results The DNA and WCP lysate profiles of 15 reference strains and 31 field isolates of H. parasuis were analyzed using the Dice and neighbor joining algorithms. The results revealed unique and reproducible DNA and protein profiles among the reference strains and field isolates studied. Simpson’s index of diversity showed significant discrimination between isolates when three 10mer primers were combined for the RAPD method and also when both the RAPD and WCP lysate typing methods were combined. Conclusions The RAPD profiles seen among the reference strains and field isolates did not appear to change over time which may reflect a lack of DNA mutations in the genes of the samples. The recent field isolates had different WCP lysate profiles than the reference strains, possibly because the number of passages of the type strains may affect their protein expression. PMID:22703293

76 FR 16808 - Notice of Invitation to Participate In Coal Exploration License, Utah

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-25

...] Notice of Invitation to Participate In Coal Exploration License, Utah AGENCY: Bureau of Land Management... Ark Land Company on a pro rata cost sharing basis in its program for the exploration of coal deposits... participate in this coal exploration license was published, once each week for 2 consecutive weeks, in the...

77 FR 25734 - Notice of Invitation To Participate in Coal Exploration License, Utah

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-01

...] Notice of Invitation To Participate in Coal Exploration License, Utah AGENCY: Bureau of Land Management... Ark Land Company on a pro rata cost-sharing basis in its program for the exploration of coal deposits... participate in this coal exploration license was published once each week for 2 consecutive weeks in The...

The Intelligence Revolution: A Historical Perspective

DTIC Science & Technology

1988-10-01

Reconnaissance ......................................................... 233 William E. Burrows The Intelligence Revolution’s Impact on Postw ar D iplom...Session V The Impact of the Intelligence Revolution on Current Military Posture Chair: Ray S. Cline Rem arks by a Select Panel...its influence have been decisive, as is so widely believed? In addressing this question it is important to distinguish between the impact of

Dinosaurs on the Ark: The Creation Museum

ERIC Educational Resources Information Center

Asma, Stephen T.

2007-01-01

In this article, the author describes the Creation Museum, founded by Ken A. Ham and designed as a rebuttal to the evolutionary view taken by other natural history museums. He discusses the socially conservative roots of the museum's exhibits, and presents Ham's answers to questions about the museum. The message of the museum is that the Bible is…

Use of Naval Force in Crises: A Theory of Stratified Crisis Interaction. Volume 1

DTIC Science & Technology

1988-12-01

of other Western navies. On November 9, 1970, a Soviet Kotlin -class destroyer that had been harassing the British aircraft carrier Ark Royal and her...with the destroyer USS Lawe (DD 763) and the America. On March 31, 1972, a Soviet Kotlin -class destroyer harassed USS Sims (DE 1059) and USS Pratt

Being in Relationship: Paradoxical Truths and Opportunities for Change in Foster Care

ERIC Educational Resources Information Center

Mann, Janet C.; Kretchmar, Molly D.; Worsham, Nancy L.

2011-01-01

This article focuses on the experience of "Desirae," a young mother who participated with her children in services at The Children's Ark, an attachment-based intervention for families in foster care. The story of Desirae and her children highlights both the sometimes paradoxical truths about families fractured by addiction, abuse, and neglect and…

Children's Observations about the Art in Picture Books.

ERIC Educational Resources Information Center

Stewig, John Warren

This report establishes a foundation of information about how children in classroom settings develop visual literacy. Data was gathered during five 45-minute sessions with a second and a fourth grade classroom during which children looked at pictures in four versions of the Noah's Ark tale. The intent was to elicit whatever children chose to say…

Talking and Writing about Noah Variants.

ERIC Educational Resources Information Center

Stewig, John Warren

1997-01-01

Examines student responses to four versions of the Noah's Ark tale. Finds that the second- and fourth-grade children were interested in talking about the visuals in picture books. Notes a wide range in the amount of writing children did in response to the art, and that the written products were far less skilled and spirited than the discussion.…

The Value of Risk: Noah's Ark at the Skirball Cultural Center

ERIC Educational Resources Information Center

Bernstein, Sheri; Gittleman, Marni

2010-01-01

In this article Bernstein and Gittleman address the role of risk in creating an exhibition that is of value to the public and is aligned with their cultural institution's core values. Through an examination of the development process, the authors present lessons that can assist others who are interested in undertaking an exhibition with similar…

76 FR 71124 - Caddo Valley Railroad Company-Abandonment Exemption-in Pike and Clark Counties, AR

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-16

... DEPARTMENT OF TRANSPORTATION Surface Transportation Board [Docket No. AB 1076 (Sub-No. 1X)] Caddo Valley Railroad Company--Abandonment Exemption--in Pike and Clark Counties, AR On October 27, 2011, Caddo... 17.55 miles, in Pike and Clark Counties, Ark. (the line).\\1\\ The line traverses United States Postal...

33 CFR 162.90 - White River, Arkansas Post Canal, Arkansas River, and Verdigris River between Mississippi River...

Code of Federal Regulations, 2011 CFR

2011-07-01

... Mississippi River Ark., and Catoosa, Okla. (2) Bridges, wharves and other structures. All bridges, wharves, and other structures in or over the waterways described in paragraph (a)(1) of this section. (3... their not being drawn away from the bank by winds, currents, or the suction of passing vessels. Towlines...

33 CFR 162.90 - White River, Arkansas Post Canal, Arkansas River, and Verdigris River between Mississippi River...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Mississippi River Ark., and Catoosa, Okla. (2) Bridges, wharves and other structures. All bridges, wharves, and other structures in or over the waterways described in paragraph (a)(1) of this section. (3... their not being drawn away from the bank by winds, currents, or the suction of passing vessels. Towlines...

Effect of seed size on ginning Efficiency in Upland Cotton (Gossypium hirsutum L.)

USDA-ARS?s Scientific Manuscript database

Not much information is available in the literature on the effect of seed size on ginning efficiency in upland cotton. In 2015 and 2016 nine diverse upland cotton cultivars and germplasm lines were planted at two locations in Stoneville, MS to test the above relationship. Two of the cultivars (Ark 9...

The reference strain Aeromonas hydrophicla CIP 57.50 should be reclassified as Aeromonas salmonicida CIP 57.50.

PubMed

Miñana-Galbis, David; Farfàn, Maribel; Lorén, J Gaspar; Fusté, M Carmen

2010-03-01

The use of reference strains is a critical element for the quality control of different assays, from the development of molecular methods to the evaluation of antimicrobial activities. Most of the strains used in these assays are not type strains and some of them are cited erroneously because of subsequent reclassifications and descriptions of novel species. In this study, we propose that the reference strain Aeromonas hydrophila CIP 57.50 be reclassified as Aeromonas salmonicida CIP 57.50 based on phenotypic characterization and sequence analyses of the cpn60, dnaJ, gyrB and rpoD genes.

IPv6 Geolocation Using Latency Constraints

DTIC Science & Technology

2014-03-01

CDF area regions for ONE2ONE . . . . . . . . . . . . . . . . . . . . 37 ix THIS PAGE INTENTIONALLY LEFT BLANK x List of Tables Table 2.1 Number of... List of Acronyms and Abbreviations Ark archipelago AS autonomous system ASN autonomous system number BGP Border Gateway Protocol CAIDA Cooperative...request registered information by the organization such as the organization’s phone number , administrator, or physical address [19]. The DNS is a

The Legs Problem--For All Ages

ERIC Educational Resources Information Center

Way, Jenni

2005-01-01

This article presents an example of a versatile multi-solution problem that can be used right across the primary years. The basic problem is: "Noah saw 16 legs go past him into the Ark. How many creatures did he see?" Any even number can be used, although, 2 legs allows only one answer and with 16 legs there are already 14 different…

Discovering the Lost Ark of Possibilities: Bringing Visibility to the Invisible Art Form of Film Music in Your Music Classroom

ERIC Educational Resources Information Center

Keown, Daniel J.

2015-01-01

Conventional music learning in schools could benefit from the study of the music from films, television, and video games. This article offers practical applications for including film music as an outlet for analysis, an interdisciplinary compositional art form, a viable teaching tool, and an authentic performance/production experience. Music…

NOAA Photo Library - NOAA's Ark/Animals Album

Science.gov Websites

options banner CATALOG View ALL images contained in the collection. Click on thumbnails to view larger images. ALBUMS Images are arranged by themes. Click on thumbnails to view larger images. Note that not all images are contained in the albums - select the above option to view ALL current images. NOAA's

Maximizing phylogenetic diversity in biodiversity conservation: Greedy solutions to the Noah's Ark problem.

PubMed

Hartmann, Klaas; Steel, Mike

2006-08-01

The Noah's Ark Problem (NAP) is a comprehensive cost-effectiveness methodology for biodiversity conservation that was introduced by Weitzman (1998) and utilizes the phylogenetic tree containing the taxa of interest to assess biodiversity. Given a set of taxa, each of which has a particular survival probability that can be increased at some cost, the NAP seeks to allocate limited funds to conserving these taxa so that the future expected biodiversity is maximized. Finding optimal solutions using this framework is a computationally difficult problem to which a simple and efficient "greedy" algorithm has been proposed in the literature and applied to conservation problems. We show that, although algorithms of this type cannot produce optimal solutions for the general NAP, there are two restricted scenarios of the NAP for which a greedy algorithm is guaranteed to produce optimal solutions. The first scenario requires the taxa to have equal conservation cost; the second scenario requires an ultrametric tree. The NAP assumes a linear relationship between the funding allocated to conservation of a taxon and the increased survival probability of that taxon. This relationship is briefly investigated and one variation is suggested that can also be solved using a greedy algorithm.

Ark and Archive: Making a Place for Long-Term Research on Barro Colorado Island, Panama.

PubMed

Raby, Megan

2015-12-01

Barro Colorado Island (BCI), Panama, may be the most studied tropical forest in the world. A 1,560-hectare island created by the flooding of the Panama Canal, BCI became a nature reserve and biological research station in 1923. Contemporaries saw the island as an "ark" preserving a sample of primeval tropical nature for scientific study. BCI was not simply "set aside," however. The project of making it a place for science significantly reshaped the island through the twentieth century. This essay demonstrates that BCI was constructed specifically to allow long-term observation of tropical organisms--their complex behaviors, life histories, population dynamics, and changing species composition. An evolving system of monitoring and information technology transformed the island into a living scientific "archive," in which the landscape became both an object and a repository of scientific knowledge. As a research site, BCI enabled a long-term, place-based form of collective empiricism, focused on the study of the ecology of a single tropical island. This essay articulates tropical ecology as a "science of the archive" in order to examine the origins of practices of environmental surveillance that have become central to debates about global change and conservation.

Genotyping of Indian antigenic, vaccine, and field Brucella spp. using multilocus sequence typing.

PubMed

Shome, Rajeswari; Krithiga, Natesan; Shankaranarayana, Padmashree B; Jegadesan, Sankarasubramanian; Udayakumar S, Vishnu; Shome, Bibek Ranjan; Saikia, Girin Kumar; Sharma, Narendra Kumar; Chauhan, Harshad; Chandel, Bharat Singh; Jeyaprakash, Rajendhran; Rahman, Habibur

2016-03-31

Brucellosis is one of the most important zoonotic diseases that affects multiple livestock species and causes great economic losses. The highly conserved genomes of Brucella, with > 90% homology among species, makes it important to study the genetic diversity circulating in the country. A total of 26 Brucella spp. (4 reference strains and 22 field isolates) and 1 B. melitensis draft genome sequence from India (B. melitensis Bm IND1) were included for sequence typing. The field isolates were identified by biochemical tests and confirmed by both conventional and quantitative polymerase chain reaction (qPCR) targeting bcsp 31Brucella genus-specific marker. Brucella speciation and biotyping was done by Bruce ladder, probe qPCR, and AMOS PCRs, respectively, and genotyping was done by multilocus sequence typing (MLST). The MLST typing of 27 Brucella spp. revealed five distinct sequence types (STs); the B. abortus S99 reference strain and 21 B. abortus field isolates belonged to ST1. On the other hand, the vaccine strain B. abortus S19 was genotyped as ST5. Similarly, B. melitensis 16M reference strain and one B. melitensis field isolate were grouped into ST7. Another B. melitensis field isolate belonged to ST8 (draft genome sequence from India), and only B. suis 1330 reference strain was found to be ST14. The sequences revealed genetic similarity of the Indian strains to the global reference and field strains. The study highlights the usefulness of MLST for typing of field isolates and validation of reference strains used for diagnosis and vaccination against brucellosis.

Establishment of a matrix-assisted laser desorption ionization time-of-flight mass spectrometry database for rapid identification of infectious achlorophyllous green micro-algae of the genus Prototheca.

PubMed

Murugaiyan, J; Ahrholdt, J; Kowbel, V; Roesler, U

2012-05-01

The possibility of using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of pathogenic and non-pathogenic species of the genus Prototheca has been recently demonstrated. A unique reference database of MALDI-TOF MS profiles for type and reference strains of the six generally accepted Prototheca species was established. The database quality was reinforced after the acquisition of 27 spectra for selected Prototheca strains, with three biological and technical replicates for each of 18 type and reference strains of Prototheca and four strains of Chlorella. This provides reproducible and unique spectra covering a wide m/z range (2000-20 000 Da) for each of the strains used in the present study. The reproducibility of the spectra was further confirmed by employing composite correlation index calculation and main spectra library (MSP) dendrogram creation, available with MALDI Biotyper software. The MSP dendrograms obtained were comparable with the 18S rDNA sequence-based dendrograms. These reference spectra were successfully added to the Bruker database, and the efficiency of identification was evaluated by cross-reference-based and unknown Prototheca identification. It is proposed that the addition of further strains would reinforce the reference spectra library for rapid identification of Prototheca strains to the genus and species/genotype level. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

Identification and growth characteristics of pink pigmented oxidative bacteria, Methylobacterium mesophilicum and biovars isolated from chlorinated and raw water supplies.

PubMed

O'Brien, J R; Murphy, J M

1993-01-01

Pink pigmented bacteria were isolated from a blood bank water purification unit, a municipal town water supply (tap water), and an island (untreated) ground water source. A total of thirteen strains including two reference strains of pink pigmented bacteria were compared in a numerical phenotypic study using 119 binary characters. Three clusters were derived, one major cluster of eleven strains was subdivided into two sub-clusters on the basis of methanol utilization. Five strains were facultative methylotrophs and were classified as Methylobacterium mesophilicum biovar 1. The other six strains did not utilize methanol, but on the basis of high phenotypic similarity of 83.6% were classified as M. mesophilicum biovar 2. The single reference strain comprising cluster 2 Pseudomonas extorquens NCIB 9399 was assigned to the genus Methylobacterium and classified as M. extorquens. Cluster 3 was the single reference strain Rhizobium CB 376.

AFOSR Technical Report Summaries, April-June 1986,

DTIC Science & Technology

1986-06-01

C1HARGE DENSITY. ELECTRODES. INTERrACIAL TENSION. PRESSURE, SIIRFACE PROPERTIES. CORROSION INHIBITION, MOLECULES, ORGANIC COMPOUNDS . SORPTION . FILMS... Perfluorinated derivatives of hydrocarbon Compounds usually ewhibit different propeties than their hydrocarbon analogues. The perfluoro crown ether-s are m.arkedly...Binary Hydrocarbon Mixtures, AD-A166 130 Materials for Emergency Repair AD-A167 094 of Runways. -BROMINE COMPOUNDS AD-Ai64 225 tCHEMICAL LASERS Analysis of

An Analysis of Economic Retention Models for Excess Stock in a Stochastic Demand Environment

DTIC Science & Technology

1994-03-01

then begin getkar kcadle; -2: It tins! -- 0.25 then got~arkCoide: .0; end; end; pmocodaze inItIasleAxrays Waer oboaen. thQAirY. kOtevel. SSADtW. SSALM...1837 Tularosa Rd. Lompoc, California 12. LCDR Kevin Maher, Code 041 Navy Ships Parts Control Center 5450 Carlisle Pike P.O. Box 2020 Mechanicsburg, Pennsylvania 17055-0788 183

ARkStorm@Tahoe: Science as a foundation for discussing, recognizing and mitigating storm-disaster vulnerabilities in mountain and downstream communities

NASA Astrophysics Data System (ADS)

McCarthy, M.; Dettinger, M. D.; Kauneckis, D. L.; Cox, D. A.; Albano, C.; Welborn, T.

2014-12-01

Atmospheric rivers (ARs) have historically caused ~80% of the most extreme winter storms and largest floods in California and parts of northwestern Nevada. In 2010, the U.S. Geological Survey developed the ARkStorm extreme-storm scenario to quantify risks from extreme winter storms and to allow stakeholders to explore and mitigate potential impacts. The scenario was constructed by concatenating two historical AR sequences and quantified by simulating them using a regional-weather model nested within global weather fields, resulting in a climatologically plausible 23-day storm sequence. The ARkStorm@Tahoe scenario was presented at six meetings with over 300 participants from local agencies, first-responders and local communities, each meeting having a different geographic or sectoral focus. These stakeholder meetings and an 18-question survey identified a wide range of social and ecological vulnerabilities to extreme winter storms, science and information needs to prepare and mitigate consequenses, and proactive measures to minimize impacts. Interruption of transportation, communications, and lack of power and backup fuel supplies were identified as the most likely and primary points of failure across multiple sectors and geographies, as these interruptions have cascading effects on natural and human environments by impeding emergency response efforts. Natural resource impacts of greatest concern include flooding, impacts to water quality, spread and establishment of invasive species, and interactions with other disturbance types (e.g., fire, landslides). Science needs include improved monitoring and models to facilitate better prediction and response, real-time and forecast inundation mapping to understand flood risks, and vulnerability assessments related to geomorphic hazards and water quality impacts. Results from this effort highlight several opportunities for increasing the resilience of communities and the environment to extreme storm events. Information collected in these meetings was used to develop a "tabletop" emergency-response exercise with over 120 participants in March 2014, as well as reports back to the community including specific recommendations for increasing preparedness, response, recovery, and resilience to extreme winter storm events.

Rapid identification of oral Actinomyces species cultivated from subgingival biofilm by MALDI-TOF-MS

PubMed Central

Stingu, Catalina S.; Borgmann, Toralf; Rodloff, Arne C.; Vielkind, Paul; Jentsch, Holger; Schellenberger, Wolfgang; Eschrich, Klaus

2015-01-01

Background Actinomyces are a common part of the residential flora of the human intestinal tract, genitourinary system and skin. Isolation and identification of Actinomyces by conventional methods is often difficult and time consuming. In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has become a rapid and simple method to identify bacteria. Objective The present study evaluated a new in-house algorithm using MALDI-TOF-MS for rapid identification of different species of oral Actinomyces cultivated from subgingival biofilm. Design Eleven reference strains and 674 clinical strains were used in this study. All the strains were preliminarily identified using biochemical methods and then subjected to MALDI-TOF-MS analysis using both similarity-based analysis and classification methods (support vector machine [SVM]). The genotype of the reference strains and of 232 clinical strains was identified by sequence analysis of the 16S ribosomal RNA (rRNA). Results The sequence analysis of the 16S rRNA gene of all references strains confirmed their previous identification. The MALDI-TOF-MS spectra obtained from the reference strains and the other clinical strains undoubtedly identified as Actinomyces by 16S rRNA sequencing were used to create the mass spectra reference database. Already a visual inspection of the mass spectra of different species reveals both similarities and differences. However, the differences between them are not large enough to allow a reliable differentiation by similarity analysis. Therefore, classification methods were applied as an alternative approach for differentiation and identification of Actinomyces at the species level. A cross-validation of the reference database representing 14 Actinomyces species yielded correct results for all species which were represented by more than two strains in the database. Conclusions Our results suggest that a combination of MALDI-TOF-MS with powerful classification algorithms, such as SVMs, provide a useful tool for the differentiation and identification of oral Actinomyces. PMID:25597306

Complete Genome Sequence of Acinetobacter baumannii CIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses.

PubMed

Krahn, Thomas; Wibberg, Daniel; Maus, Irena; Winkler, Anika; Pühler, Alfred; Poirel, Laurent; Schlüter, Andreas

2015-07-30

The complete genome sequence for the reference strain Acinetobacter baumannii CIP 70.10 (ATCC 15151) was established. The strain was isolated in France in 1970, is susceptible to most antimicrobial compounds, and is therefore of importance for comparative genome analyses with clinical multidrug-resistant (MDR) A. baumannii strains to study resistance development and acquisition in this emerging human pathogen. Copyright © 2015 Krahn et al.

Brucella abortus Strain 2308 Wisconsin Genome: Importance of the Definition of Reference Strains

PubMed Central

Suárez-Esquivel, Marcela; Ruiz-Villalobos, Nazareth; Castillo-Zeledón, Amanda; Jiménez-Rojas, César; Roop II, R. Martin; Comerci, Diego J.; Barquero-Calvo, Elías; Chacón-Díaz, Carlos; Caswell, Clayton C.; Baker, Kate S.; Chaves-Olarte, Esteban; Thomson, Nicholas R.; Moreno, Edgardo; Letesson, Jean J.; De Bolle, Xavier; Guzmán-Verri, Caterina

2016-01-01

Brucellosis is a bacterial infectious disease affecting a wide range of mammals and a neglected zoonosis caused by species of the genetically homogenous genus Brucella. As in most studies on bacterial diseases, research in brucellosis is carried out by using reference strains as canonical models to understand the mechanisms underlying host pathogen interactions. We performed whole genome sequencing analysis of the reference strain B. abortus 2308 routinely used in our laboratory, including manual curated annotation accessible as an editable version through a link at https://en.wikipedia.org/wiki/Brucella#Genomics. Comparison of this genome with two publically available 2308 genomes showed significant differences, particularly indels related to insertional elements, suggesting variability related to the transposition of these elements within the same strain. Considering the outcome of high resolution genomic techniques in the bacteriology field, the conventional concept of strain definition needs to be revised. PMID:27746773

An Exposition on the Nonlinear Kinematics of Shells, Including Transverse Shearing Deformations

NASA Technical Reports Server (NTRS)

Nemeth, Michael P.

2013-01-01

An in-depth exposition on the nonlinear deformations of shells with "small" initial geometric imperfections, is presented without the use of tensors. First, the mathematical descriptions of an undeformed-shell reference surface, and its deformed image, are given in general nonorthogonal coordinates. The two-dimensional Green-Lagrange strains of the reference surface derived and simplified for the case of "small" strains. Linearized reference-surface strains, rotations, curvatures, and torsions are then derived and used to obtain the "small" Green-Lagrange strains in terms of linear deformation measures. Next, the geometry of the deformed shell is described mathematically and the "small" three-dimensional Green-Lagrange strains are given. The deformations of the shell and its reference surface are related by introducing a kinematic hypothesis that includes transverse shearing deformations and contains the classical Love-Kirchhoff kinematic hypothesis as a proper, explicit subset. Lastly, summaries of the essential equations are given for general nonorthogonal and orthogonal coordinates, and the basis for further simplification of the equations is discussed.

Genetic characterization of Vibrio vulnificus strains isolated from oyster samples in Mexico.

PubMed

Guerrero, Abraham; Gómez Gil Rodríguez, Bruno; Wong-Chang, Irma; Lizárraga-Partida, Marcial Leonardo

2015-01-01

Vibrio vulnificus strains were isolated from oysters that were collected at the main seafood market in Mexico City. Strains were characterized with regard to vvhA, vcg genotype, PFGE, multilocus sequence typing (MLST), and rtxA1. Analyses included a comparison with rtxA1 reference sequences. Environmental (vcgE) and clinical (vcgC) genotypes were isolated at nearly equal percentages. PFGE had high heterogeneity, but the strains clustered by vcgE or vcgC genotype. Select housekeeping genes for MLST and primers that were designed for rtxA1 domains divided the strains into two clusters according to the E or C genotype. Reference rtxA1 sequences and those from this study were also clustered according to genotype. These results confirm that this genetic dimorphism is not limited to vcg genotyping, as other studies have reported. Some environmental C genotype strains had high similarity to reference strains, which have been reported to be virulent, indicating a potential risk for oyster consumers in Mexico City.

Serotypes in Saccharomyces telluris: Their relation to source of isolation

USGS Publications Warehouse

Hasenclever, H.F.; Kocan, R.M.

1973-01-01

Three serotypes have been characterized with three reference strains of Saccharomyces telluris and designated as A, B, and C. One reference strain of Torpulopsis bovina, the imperfect form of S. telluris, belonged to serotype B. Strains of S. telluris isolated from four columbid species were serotyped. All 98 strains of this yeast isolated from Columba livia belonged to serotype B. Three other columbid species, C. leucocephala, C. fasciata, and Zenaidura macroura harbored strains of serotype C only. Serotype A was not isolated from any of the avian species.

Edge Triggered Apparatus and Method for Measuring Strain in Bragg Gratings

NASA Technical Reports Server (NTRS)

Froggatt, Mark E. (Inventor)

2003-01-01

An apparatus and method for measuring strain of gratings written into an optical fiber. Optical radiation is transmitted over one or more contiguous predetermined wavelength ranges into a reference optical fiber network and an optical fiber network under test to produce a plurality of reference interference fringes and measurement interference fringes, respectively. The reference and measurement fringes are detected, and the reference fringes trigger the sampling of the measurement fringes. This results in the measurement fringes being sampled at 2(pi) increments of the reference fringes. Each sampled measurement fringe of each wavelength sweep is transformed into a spatial domain waveform. The spatial domain waveforms are summed to form a summation spatial domain waveform that is used to determine location of each grating with respect to a reference reflector. A portion of each spatial domain waveform that corresponds to a particular grating is determined and transformed into a corresponding frequency spectrum representation. The strain on the grating at each wavelength of optical radiation is determined by determining the difference between the current wavelength and an earlier, zero-strain wavelength measurement.

Serological diversity demonstrable by a set of monoclonal antibodies to eight serotypes of the mutans streptococci.

PubMed

Ota, F; Ota, M; Mahmud, Z H; Mohammad, A; Yamato, M; Kassu, A; Kato, Y; Tomotake, H; Batoni, G; Campa, M

2006-01-01

A set of monoclonal antibodies were prepared by the conventional cell fusion of myeloma cells (SP2/0-Ag14) with spleen cells from BALB/c mice immunised with whole cells of a strain of mutans streptococci. Their specificities were examined against 35 reference strains of mutans streptococci, 34 reference strains of other oral streptococci and 8 reference strains of other microorganisms often inhabiting the oral cavity. Specificity was examined by enzyme immunoassay using whole cells. A total of 52 strains, consisting of 19 strains isolated in Japan, 19 strains isolated in Italy and 14 strains isolated in England, were characterised by conventional physiological and biochemical tests and then serotyped by the use of 8 monoclonal antibodies with different specificities. They were also confirmed by guanine-plus-cytosine contents of their nucleic acid and DNA-DNA hybridisation test. The results indicated that all monoclonal antibodies are useful for identification of 8 serotypes of the mutans streptococci responsible for dental caries. They also suggest the existence of more serological varieties among mutans species.

"Enracinement" or the Earth, the Originary Ark, Does Not Move: On the Phenomenological (Historical and Ontogenetic) Origin of Common and Scientific Sense and the Genetic Method of Teaching (For) Understanding

ERIC Educational Resources Information Center

Roth, Wolff-Michael

2015-01-01

For many students, the experience with science tends to be alienating and uprooting. In this study, I take up Simone Weil's concepts of "enracinement" (rooting) and "déracinement" (uprooting) to theorize the root of this alienation, the confrontation between children's familiarity with the world and unfamiliar/strange…

Teachers' Readiness to Use Inquiry-Based Learning: An Investigation of Teachers' Sense of Efficacy and Attitudes toward Inquiry-Based Learning

ERIC Educational Resources Information Center

Silm, Gerli; Tiitsaar, Kai; Pedaste, Margus; Zacharia, Zacharias C.; Papaevripidou, Marios

2017-01-01

The use of inquiry-based learning (IBL) is encouraged in schools, as it has been shown to be an effective method for raising students' motivation in STEM subjects and increasing their understanding of scientific concepts. Nevertheless, IBL is not very often used in classrooms by teachers due to different (perceived) obstacles. Within the Ark of…

Determining How to Best Predict Navy Recruiting Using Various Economic Variables

DTIC Science & Technology

2015-03-01

M ., & Ajzen , I . (1975). Belief, attitude, intention and behavior: An introduction to theory and research. Reading, MA: Addison-Wesley. Leonhardt, D... Fishbein & Ajzen , 1975), behavioral intentions are strong predictors of actual behavior. The higher propensity rates are at a given time inherently...J. R., Arkes, J., Fair, C. C., Sharp, J., & Totten, M . (2002). Military recruiting and retention after the fiscal year 2000 military pay (MR-1532-OSD

Engineering chimeras for Noah's ark.

PubMed

Dixon, B

1984-04-01

Chimeras, or animals containing the tissues of two or more distinct genetic types, have been successfully created from goat-sheep combinations by research teams at the ARC Institute of Animal Physiology in Cambridge, England, and the Justus-Liebig-Universitat in Giessen, West Germany. Dixon describes the methods used in this research and goes on to discuss the future potential for creating true hybrids capable of reproducing themselves, perhaps even involving human-animal combinations.

Annual Report on U.S. Army Civil Works Activities, Fiscal Year 1954, Vol. 1

DTIC Science & Technology

1954-12-10

Reservoir, Tex ______ 1948 July 1953 ___________ Reservoir. Pine Bluff, Ark ____________ 1953 April 1954 __________ Local protection. During the year...Perry County Drainage and Levee Districts, Nos. 1, 2, and 3, Mo. Pine Flat Reservoir, Calif_ ______________ _ Red River Levees and Bank...conduits at Pine Flat Dam from the 15 originally considered to 10, with a saving of $500,000 in construction cost. Comparable savings will be made on

Annual Report of the Chief of Engineers, U.S. Army, on Civil Works Activities 1960. Volume 1

DTIC Science & Technology

1960-01-01

M artin, Colo_._....... ........... .... Lookout Point, Oreg . . . . .. .. ... Lucky Peak, Idaho ... . . -- ... Pine Flat, Calif...2 Barren , Ky M-------------- ar 60 1964 Do. Princeton, W. Va---------- ------ Mar 60 1961 Local protection. Proctor, Tex------------------- Jun 60...Arkansas River crested at Pine Bluff, Ark., in October 1959 at a stage of 25 feet, about 1 foot above flood stage. The St. Francis River crested at St

The coming megafloods

USGS Publications Warehouse

Dettinger, Michael D.; Ingram, B. Lynn

2013-01-01

Scientists who created a simulated megastorm, called ARkStorm, that was patterned after the 1861 flood but was less severe, found that such a torrent could force more than a million people to evacuate and cause $400 billion in losses if it happened in California today. Forecasters are getting better at predicting the arrival of atmospheric rivers, which will improve warnings about flooding from the common storms and about the potential for catastrophe from a megastorm.

The sunk cost effect across species: A review of persistence in a course of action due to prior investment.

PubMed

Magalhães, Paula; Geoffrey White, K

2016-05-01

The sunk cost effect is the bias or tendency to persist in a course of action due to prior investments of effort, money or time. At the time of the only review on the sunk cost effect across species (Arkes & Ayton, 1999), research with nonhuman animals had been ecological in its nature, and the findings about the effect of past investments on current choice were inconclusive. However, in the last decade a new line of experimental laboratory-based research has emerged with the promise of revolutionizing the way we approach the study of the sunk cost effect in nonhumans. In the present review we challenge Arkes and Ayton's conclusion that the sunk cost effect is exclusive to humans, and describe evidence for the sunk cost effect in nonhuman animals. By doing so, we also challenge the current explanations for the sunk cost effect in humans, as they are not applicable to nonhumans. We argue that a unified theory is called for, because different independent variables, in particular, investment amount, have the same influence on the sunk cost effect across species. Finally, we suggest possible psychological mechanisms shared across different species, contrast and depreciation, that could explain the sunk cost effect. © 2016 Society for the Experimental Analysis of Behavior.

Medical resource preparation and allocation for humanitarian assistance based on module organization.

PubMed

Zhu, Min; Chen, Ruxue; Zhong, Shaobo; Qian, Yangming; Huang, Quanyi

2017-02-01

This research aims to associate the allocation of medical resources with the function of the modular organization and the possible needs for humanitarian assistance missions. The overseas humanitarian medical assistance mission, which was sent after a disaster on the hospital ship Peace Ark, part of China's People's Liberation Army (PLA) Navy, was considered as study model. The cases used for clustering and matching sample formation were randomly selected from the existing information related to Peace Ark's mission. Categories of the reusable resources clustered by this research met the requirement of the actual consumption almost completely (more than 95%) and the categories of non-reusable resources met the requirement by more than 80%. In the mission's original resource preparing plan, more than 30% of the non-reusable resource categories remained unused during the mission. In the original resource preparing plan, some key non-reusable resources inventories were completely exhausted at the end of the mission, while 5% to 30% of non-reusable resources remained in the resource allocation plan generated by this research at the end of the mission. The medical resource allocation plan generated here can enhance the supporting level for the humanitarian assistance mission. This research could lay the foundation for an assistant decision-making system for humanitarian assistance mission.

Computer-automated ABCD versus dermatologists with different degrees of experience in dermoscopy.

PubMed

Piccolo, Domenico; Crisman, Giuliana; Schoinas, Spyridon; Altamura, Davide; Peris, Ketty

2014-01-01

Dermoscopy is a very useful and non-invasive technique for in vivo observation and preoperative diagnosis of pigmented skin lesions (PSLs) inasmuch as it enables analysis of surface and subsurface structures that are not discernible to the naked eye. The authors used the ABCD rule of dermoscopy to test the accuracy of melanoma diagnosis with respect to a panel of 165 PSLs and the intra- and inter-observer diagnostic agreement obtained between three dermatologists with different degrees of experience, one General Practitioner and a DDA for computer-assisted diagnosis (Nevuscreen(®), Arkè s.a.s., Avezzano, Italy). 165 Pigmented Skin Lesions from 165 patients were selected. Histopathological examination revealed 132 benign melanocytic skin lesions and 33 melanomas. The kappa statistic, sensitivity, specificity and predictive positive and negative values were calculated to measure agreement between all the human observers and in comparison with the automated DDA. Our results revealed poor reproducibility of the semi-quantitative algorithm devised by Stolz et al. independently of observers' experience in dermoscopy. Nevuscreen(®) (Arkè s.a.s., Avezzano, Italy) proved to be 'user friendly' to all observers, thus enabling a more critical evaluation of each lesion and representing a helpful tool for clinicians without significant experience in dermoscopy in improving and achieving more accurate diagnosis of PSLs.

Radiation resistance of lactobacilli isolated from radurized meat relative to growth and environment.

PubMed

Hastings, J W; Holzapfel, W H; Niemand, J G

1986-10-01

Of 113 lactobacilli isolated from radurized (5 kGy) minced meat, 7 Lactobacillus sake strains, 1 L. curvatus strain, and 1 L. farciminis strain were used for radiation resistance studies in a semisynthetic substrate (i.e., modified MRS broth). Five reference Lactobacillus spp., one Staphylococcus aureus strain, and one Salmonella typhimurium strain were used for comparative purposes. All L. sake isolates exhibited the phenomenon of being more resistant to gamma-irradiation in the exponential (log) phase than in the stationary phase of their growth cycles by a factor of 28%. Four references strains also exhibited this phenomenon, with L. sake (DSM 20017) showing a 68% increase in resistance in the log phase over the stationary phase. This phenomenon was not common to all bacteria tested and is not common to all strains with high radiation resistance. Four L. sake isolates and three reference strains were used in radiation sensitivity testing in a natural food system (i.e., meat). The bacteria were irradiated in minced meat and packaged under four different conditions (air, vacuum, CO2, and N2). Organisms exhibited the highest death rate (lowest D10 values [doses required to reduce the logarithm of the bacterial population by 1] ) under CO2 packaging conditions, but resistance to irradiation was increased under N2. The D10 values of the isolates were generally greater than those of the reference strains. The D10 values were also higher (approximately two times) in meat than in semisynthetic growth medium.

Radiation resistance of lactobacilli isolated from radurized meat relative to growth and environment.

PubMed Central

Hastings, J W; Holzapfel, W H; Niemand, J G

1986-01-01

Of 113 lactobacilli isolated from radurized (5 kGy) minced meat, 7 Lactobacillus sake strains, 1 L. curvatus strain, and 1 L. farciminis strain were used for radiation resistance studies in a semisynthetic substrate (i.e., modified MRS broth). Five reference Lactobacillus spp., one Staphylococcus aureus strain, and one Salmonella typhimurium strain were used for comparative purposes. All L. sake isolates exhibited the phenomenon of being more resistant to gamma-irradiation in the exponential (log) phase than in the stationary phase of their growth cycles by a factor of 28%. Four references strains also exhibited this phenomenon, with L. sake (DSM 20017) showing a 68% increase in resistance in the log phase over the stationary phase. This phenomenon was not common to all bacteria tested and is not common to all strains with high radiation resistance. Four L. sake isolates and three reference strains were used in radiation sensitivity testing in a natural food system (i.e., meat). The bacteria were irradiated in minced meat and packaged under four different conditions (air, vacuum, CO2, and N2). Organisms exhibited the highest death rate (lowest D10 values [doses required to reduce the logarithm of the bacterial population by 1] ) under CO2 packaging conditions, but resistance to irradiation was increased under N2. The D10 values of the isolates were generally greater than those of the reference strains. The D10 values were also higher (approximately two times) in meat than in semisynthetic growth medium. PMID:3096207

Generational Theory and the U.S. Army: Harnessing the True Power of Human Capital

DTIC Science & Technology

2011-04-01

World. McGraw Hill: New Y ark City 2009, Page 11. 5. Ibid, 11. 6. Paul Taylor and Scott Keeter. Millennials : A Portrait of Generation Next. Pew...8 Figure 2. Millennials Outpace Older Americans in Technology Use (Pew Research Center) ....... 9 iv Table of Contents...Generation Y Soldiers (Captain and Staff Sergeant and below) on a regular basis. This is potentially problematic in that unique to today, more so

75 FR 80894 - Delta Southern Railroad, Inc.-Abandonment Exemption-in Desha and Chicot Counties, Ark.

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-23

... 49 CFR 1152.27(b)(2) will be due no later than 10 days after service of a decision granting the petition for exemption. Each OFA must be accompanied by a $1,500 filing fee. See 49 CFR 1002.2(f)(25). All... January 12, 2011. Each trail use request must be accompanied by a $250 filing fee. See 49 CFR 1002.2(f)(27...

Prediction Markets for Defense Acquisition: The Devil is in the Details

DTIC Science & Technology

2010-05-01

1 Bill Gates, Pete Coughlan, Noah Myung, Jeremy Arkes Professors of Economics Naval Postgraduate School Prediction Markets for Defense Acquisition...Acquisition: The Devil is in the Details 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) 5d. PROJECT NUMBER 5e...TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) Naval Postgraduate School,Monterey,CA,93943 8. PERFORMING

CEO summit, Part 3. Loading the ark.

PubMed

Howe, G E; Peddie, E C; Eales, H P; Swedish, J; Chapman, T W; Clay, P; Gaintner, J R

1996-03-20

There's a flood of change coming, and health care executives are quickly building and loading big boats to sail to the future. But what do you take--and what do you leave behind? What will be needed in the new world--and what won't? In the third of an exclusive four-part series planned by McManis Associates and co-sponsored by Hospitals & Health Networks, some top CEOs talk about their travel plans.

Bullet Trap Feasibility Assessment and Implementation Plan. (Technology Identification).

DTIC Science & Technology

1996-03-01

reduce costs, perhaps one of their premier assets is income generation . Projectiles fired into and recovered from TEC System products can be resold...ombat shooting scenarios with up to 15 individual targets as far away as 300 yards. Page 7 \\IEUMATIC TARGET SYSTEMS gt reliable . portable and... SYYSTEM ] 3DULAR BALLISTIC PANELS (MBPs) A~rking with recycled rubber tire products, DUE- RON has created the proprietary MBP System ,or use in the

Implications of the ’Nuclear Winter’ Thesis.

DTIC Science & Technology

1985-06-24

not provide significant relief by warming the planet o ozone depletion would increase exposure to ultraviolet light ( UV -B) Technical Uncertainties in...pgs. 37. - ------------ "When Light is Put Away, Ecological Effects of Nuclear War," The Counterfeit Ark: Crisis Relocation for Nuclear War, 1984, 13...Mary, "Biologists Paint an Icy Picture . . ., Washington Post, November 1, 1983, 1 pg. 56. McWilliams, Rita, "Hill Told Money Won’t Buy Nuclear

Serotyping, Genotyping, and Antimicrobial Susceptibility of Ornithobacterium rhinotracheale Isolates from Mexico.

PubMed

Peña-Vargas, Edgar Rafael; Vega-Sánchez, Vicente; Morales-Erasto, Vladimir; Trujillo-Ruíz, Héctor Hugo; Talavera-Rojas, Martín; Soriano-Vargas, Edgardo

2016-09-01

The bacterium Ornithobacterium rhinotracheale is associated with respiratory disease and septicemia in poultry. In this study, 9 reference strains and a total of 23 isolates of O. rhinotracheale from respiratory diseased poultry from Mexico were serotyped and genotyped. Furthermore, the antimicrobial susceptibility of isolates and reference strains of O. rhinotracheale were determined. All isolates belong to serotype A and showed a clonal relationship. All reference strains and isolates were resistant to colistin, fosfomycin, gentamicin, kanamycin, streptomycin, and trimethoprim-sulfamethoxazole. These results should eventually be helpful in planning strategies for the control of O. rhinotracheale infections in poultry in Mexico.

Assessment of immune response to meningococcal disease: comparison of a whole-blood assay and the serum bactericidal assay.

PubMed

Ison, C A; Anwar, N; Cole, M J; Galassini, R; Heyderman, R S; Klein, N J; West, J; Pollard, A J; Morley, S; Levin and the Meningococcal, R e

1999-10-01

A whole-blood assay (WBA), which assesses the complete bactericidal activity of blood, was compared with the serum bactericidal assay (SBA), which measures antibody and complement mediated cell lysis. Twenty children infected with serogroup B strains and 25 infected with serogroup C strains were studied 8-12 weeks after disease, and 29 healthy children were used as controls. The infecting strain (convalescent children only) and two reference strains, MC58 (B:15:P1.7, 16) and NCTC 8554 (C:NT:P1.5) were used. In children previously infected with a serogroup B strain, bactericidal activity was detected in 95% and 85% to their infecting strain by the WBA (>50% killing) and the SBA (s), respectively. Bactericidal activity to the reference serogroup B and C strain was detected by WBA in 70 and 75% of children, respectively, and the SBA in 45% and 20%. In contrast bactericidal activity was detected to both serogroup C strains in >80% of children previously infected with a serogroup C strain using either assay and in 48% (WBA) and 20% (SBA) to the reference serogroup B strain. Levels of bactericidal activity were detectable in fewer control children. Children convalescing from meningococcal disease develop an immune response to their infecting strain, detectable by both the WBA and SBA, which is independent of age. However, the WBA appears to be a more sensitive measure of bactericidal activity to heterologous strains than the SBA. Copyright 1999 Academic Press.

Taxonomy of Probiotic Microorganisms

NASA Astrophysics Data System (ADS)

Felis, Giovanna E.; Dellaglio, Franco; Torriani, Sandra

When referring to probiotics, one refers to probiotic strains, i.e., the microbial individuals, sub-cultures of billion of almost identical cells ideally derived from the same mother cell. Therefore, beneficial effects attributed to probiotics are ascribed in fact to specific strains. However, these strains have to be, by law, clearly identified at the species level (Pineiro and Stanton, 2007). In fact, probiotics have to be safe for consumption, and the evaluation of QPS - qualified presumption of safety - status by the European Food Safety Authority (EFSA) (Opinion, 2007) is discussed for species, not for single strains.

Detection of a Bacteriophage Gene Encoding a Mu-like Portal Protein in Haemophilus parasuis Reference Strains and Field Isolates by Nested Polymerase Chain Reaction

USDA-ARS?s Scientific Manuscript database

A nested PCR assay was developed to determine the presence of a gene encoding a bacteriophage Mu-like portal protein, gp29, in 15 reference strains and 31 field isolates of Haemophilus parasuis. Specific primers, based on the gene’s sequence, were utilized. A majority of the virulent reference strai...

Specificity of monoclonal antibodies to strains of Dickeya sp. that cause bacterial heart rot of pineapple.

PubMed

Peckham, Gabriel D; Kaneshiro, Wendy S; Luu, Van; Berestecky, John M; Alvarez, Anne M

2010-10-01

During a severe outbreak of bacterial heart rot that occurred in pineapple plantations on Oahu, Hawaii, in 2003 and years following, 43 bacterial strains were isolated from diseased plants or irrigation water and identified as Erwinia chrysanthemi (now Dickeya sp.) by phenotypic, molecular, and pathogenicity assays. Rep-PCR fingerprint patterns grouped strains from pineapple plants and irrigation water into five genotypes (A-E) that differed from representatives of other Dickeya species, Pectobacterium carotovorum and other enteric saprophytes isolated from pineapple. Monoclonal antibodies produced following immunization of mice with virulent type C Dickeya sp. showed only two specificities. MAb Pine-1 (2D11G1, IgG1 with kappa light chain) reacted to all 43 pineapple/water strains and some reference strains (D. dianthicola, D. chrysanthemi, D. paradisiaca, some D. dadantii, and uncharacterized Dickeya sp.) but did not react to reference strains of D. dieffenbachiae, D. zeae, or one of the two Malaysian pineapple strains. MAb Pine-2 (2A7F2, IgG3 with kappa light chain) reacted to all type B, C, and D strains but not to any A or E strains or any reference strains except Dickeya sp. isolated from Malaysian pineapple. Pathogenicity tests showed that type C strains were more aggressive than type A strains when inoculated during cool months. Therefore, MAb Pine-2 distinguishes the more virulent type C strains from less virulent type A pineapple strains and type E water strains. MAbs with these two specificities enable development of rapid diagnostic tests that will distinguish the systemic heart rot pathogen from opportunistic bacteria associated with rotted tissues. Use of the two MAbs in field assays also permits the monitoring of a known subpopulation and provides additional decision tools for disease containment and management practices.

Release of Mercury Mine Tailings from Mine Impacted Watersheds by Extreme Events Resulting from Climate Change

NASA Astrophysics Data System (ADS)

Rytuba, J. J.

2015-12-01

An increase in intensity and frequency of extreme events resulting from climate change is expected to result in extreme precipitation events on both regional and local scales. Extreme precipitation events have the potential to mobilize large volumes of mercury (Hg) mine tailings in watersheds where tailings reside in the floodplain downstream from historic Hg mines. The California Hg mineral belt produced one third of the worlds Hg from over 100 mines from the 1850's to 1972. In the absence of environmental regulations, tailings were disposed of into streams adjacent to the mines in order to have them transported from the mine site during storm events. Thus most of the tailings no longer reside at the mine site. Addition of tailings to the streams resulted in stream aggradation, increased over-bank flow, and deposition of tailings in the floodplain for up to 25 kms downstream from the mines. After cessation of mining, the decrease in tailings entering the streams resulted in degradation, incision of the streams into the floodplain, and inability of the streams to access the floodplain. Thus Hg tailings have remained stored in the floodplain since cessation of mining. Hg phases in these tailings consist of cinnabar, metacinnabar and montroydite based on EXAFS analysis. Size analysis indicates that Hg phases are fine grained, less than 1 um. The last regional scale extreme precipitation events to effect the entire area of the California Hg mineral belt were the ARkStorm events of 1861-1862 that occurred prior to large scale Hg mining. Extreme regional ARkStorm precipitation events as well as local summer storms, such as the July 2006 flood in the Clear Creek Hg mining district, are expected to increase in frequency and have the potential to remobilize the large volume of tailings stored in floodplain deposits. Although Hg mine remediation has decreased Hg release from mine sites in a period of benign climate, no remediation efforts have addressed the large source of Hg residing in floodplain deposits. This Hg source in a period of climate change poses a significant environmental risk to aquatic systems downstream from Hg mine-impacted watersheds. An extreme ARkStorm event is estimated to potentially remobilize an amount of Hg equivalent to that released in the past during the peak period of unregulated Hg mining in California.

Radiation resistance of lactobacilli isolated from radurized meat relative to growth and environment. [Lactobacillus sake; Lactobacillus curvatus; Lactobacillus farciminis; Staphylococcus aureus; Salmonella typimurium

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

Hastings, J.W.; Holzapfel, W.H.; Niemand, J.G.

1986-10-01

Of 113 lactobacilli isolated from radurized (5 kGy) minced meat, 7 Lactobacillus sake strains, 1 L. curvatus strain, and 1 L. farciminis strain were used for radiation resistance studies in a semisynthetic substrate (i.e., modified MRS broth). Five reference Lactobacillus spp. one Staphylococcus aureus strain, and one Salmonella typhimurium strain were used for comparative purposes. All L. sake isolates exhibited the phenomenon of being more resistant to gamma-irradiation in the exponential (log) phase than in the stationary phase of their growth cycles by a factor of 28%. Four reference strains also exhibited this phenomenon, with L. sake (DSM 20017) showingmore » a 68% increase in resistance in the log phase over the stationary phase. This phenomenon was not common to all bacteria tested and is not common to all strains with high radiation resistance. Four L. sake isolates and three reference strains were used in radiation sensitivity testing in a natural food system (i.e., meat). The bacteria were irradiated in minced meat and packaged under four different conditions (air, vacuum, CO/sub 2/, and N/sub 2/). Organisms exhibited the highest death rate (lowest D/sub 10/ values (doses required to reduce the logarithm of the bacterial population by 1) under CO/sub 2/ packaging conditions, but resistance to irradiation was increased under N/sub 2/. The D/sup 10/ values of the isolates were generally greater than those of the reference strains. The D/sup 10/ values were also higher (approximately two times) in meat than in a semisynthetic growth medium.« less

Unique transposon landscapes are pervasive across Drosophila melanogaster genomes

PubMed Central

Rahman, Reazur; Chirn, Gung-wei; Kanodia, Abhay; Sytnikova, Yuliya A.; Brembs, Björn; Bergman, Casey M.; Lau, Nelson C.

2015-01-01

To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of >300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, >500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (<25%) of transposon families comprise the majority (>70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains. PMID:26578579

Identification and characterization of Serpulina hyodysenteriae by restriction enzyme analysis and Southern blot analysis.

PubMed Central

Sotiropoulos, C; Coloe, P J; Smith, S C

1994-01-01

Chromosomal DNA restriction enzyme analysis and Southern blot hybridization were used to characterize Serpulina hyodysenteriae strains. When chromosomal DNAs from selected strains (reference serotypes) of S. hyodysenteriae were digested with the restriction endonuclease Sau3A and hybridized with a 1.1-kb S. hyodysenteriae-specific DNA probe, a common 3-kb band was always detected in S. hyodysenteriae strains but was absent from Serpulina innocens strains. When the chromosomal DNA was digested with the restriction endonuclease Asp 700 and hybridized with two S. hyodysenteriae-specific DNA probes (0.75 and 1.1 kb of DNA), distinct hybridization patterns for each S. hyodysenteriae reference strain and the Australian isolate S. hyodysenteriae 5380 were detected. Neither the 1.1-kb nor the 0.75-kb DNA probe hybridized with Asp 700- or Sau3A-digested S. innocens chromosomal DNA. The presence of the 3-kb Sau3A DNA fragment in S. hyodysenteriae reference strains from diverse geographical locations shows that this fragment is conserved among S. hyodysenteriae strains and can be used as a species-specific marker. Restriction endonuclease analysis and Southern blot hybridization with these well-defined DNA probes are reliable and accurate methods for species-specific and strain-specific identification of S. hyodysenteriae. Images PMID:7914209

Analysis of Flow Behavior Within An Integrated Computer-Communication Network,

DTIC Science & Technology

1979-05-01

Howard. Plan today for tomorrows data/voice nets. Data Communications 7, 9 (Sep. 1978), 51-62. 24. F-ark, Howard, and Gitman , Israel. Inteqrated DoD...computer networks. NTC-74, San Diego, CA., (Dec. 2-4, 1974), 1032-1037. 31. Gitman , I., Frank, H., Occhiogrosso, B., and Hsieh, W. Issues in integrated...switched networks agree on standard interface. Data Communications, (May/June 1978), 25)-39. 36. Hsieh, W., Gitman , I., and Occhiogrosso, B. Design of

Performance Evaluation of NoSQL Databases: A Case Study

DTIC Science & Technology

2015-02-01

a centralized relational database. The customer decided to consider NoSQL technologies for two specific uses, namely:  the primary data store for...17 custom specific 6. FU NoSQL availab data mo arking of data g a specific wo sin benchmark f hmark for tran le workload de o publish meas their...The choice of a particular NoSQL database imposes a specific distributed software architecture and data model, and is a major determinant of the

Behavior of variable V3 region from 16S rDNA of lactic acid bacteria in denaturing gradient gel electrophoresis.

PubMed

Ercolini, D; Moschetti, G; Blaiotta, G; Coppola, S

2001-03-01

Separation of amplified V3 region from 16S rDNA by denaturing gradient gel electrophoresis (DGGE) was tested as a tool for differentiation of lactic acid bacteria commonly isolated from food. Variable V3 regions of 21 reference strains and 34 wild strains referred to species belonging to the genera Pediococcus, Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, Weissella, and Streptococcus were analyzed. DGGE profiles obtained were species-specific for most of the cultures tested. Moreover, it was possible to group the remaining LAB reference strains according to the migration of their 16S V3 region in the denaturing gel. The results are discussed with reference to their potential in the analysis of LAB communities in food, besides shedding light on taxonomic aspects.

Trace Metals in Noah's Ark Shells (Arca noae Linnaeus, 1758): Impact of Tourist Season and Human Health Risk.

PubMed

Ivanković, Dušica; Erk, Marijana; Župan, Ivan; Čulin, Jelena; Dragun, Zrinka; Bačić, Niko; Cindrić, Ana-Marija

2016-10-01

Commercially important bivalve Noah's Ark shell (Arca noae Linnaeus, 1758) represents a high-quality seafood product, but the data on levels of metal contaminants that could pose a human health risk and also on some essential elements that are important for health protection are lacking. This study examined the concentrations of Cd, Pb, Cr, Ni, Cu, Co, and Zn in the soft tissue of A. noae from harvesting area in the central Adriatic Sea, to survey whether heavy metals are within the acceptable limits for public health and whether tourism could have an impact on them. The concentrations of analysed metals varied for Cd: 0.15-0.74, Pb: 0.06-0.26, Cr: 0.11-0.34, Ni: 0.09-0.22, Cu: 0.65-1.95, Co: 0.04-0.09, and Zn: 18.3-74.7 mg/kg wet weight. These levels were lower than the permissible limits for safe consummation of seafood, and only for Cd, some precautions should be taken into account if older shellfish were consumed. Increase of Cd, Cr, and Cu in shell tissue was observed during the tourist season at the site closest to the marine traffic routes, indicating that metal levels in shellfish tissue should be monitored especially carefully during the peak tourist season to prevent eventual toxic effects due to increased intake of metals, specifically of Cd.

A Micro-Ark for Cells: Highly Open Porous Polyhydroxyalkanoate Microspheres as Injectable Scaffolds for Tissue Regeneration.

PubMed

Wei, Dai-Xu; Dao, Jin-Wei; Chen, Guo-Qiang

2018-06-19

To avoid large open surgery using scaffold transplants, small-sized cell carriers are employed to repair complexly shaped tissue defects. However, most cell carriers show poor cell adherences and viability. Therefore, polyhydroxyalkanoate (PHA), a natural biopolymer, is used to prepare highly open porous microspheres (OPMs) of 300-360 µm in diameter, combining the advantages of microspheres and scaffolds to serve as injectable carriers harboring proliferating stem cells. In addition to the convenient injection to a defected tissue, and in contrast to poor performances of OPMs made of polylactides (PLA OPMs) and traditional less porous hollow microspheres (PHA HMs), PHA OPMs present suitable surface pores of 10-60 µm and interconnected passages with an average size of 8.8 µm, leading to a high in vitro cell adhesion of 93.4%, continuous proliferation for 10 d and improved differentiation of human bone marrow mesenchymal stem cells (hMSCs). PHA OPMs also support stronger osteoblast-regeneration compared with traditional PHA HMs, PLA OPMs, commercial hyaluronic acid hydrogels, and carrier-free hMSCs in an ectopic bone-formation mouse model. PHA OPMs protect cells against stresses during injection, allowing more living cells to proliferate and migrate to damaged tissues. They function like a micro-Noah's Ark to safely transport cells to a defect tissue. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DISCOVERY OF RELATIVISTIC OUTFLOW IN THE SEYFERT GALAXY Ark 564

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

Gupta, A.; Mathur, S.; Krongold, Y.

2013-07-20

We present Chandra High Energy Transmission Grating Spectra of the narrow-line Seyfert-1 galaxy Ark 564. The spectrum shows numerous absorption lines which are well modeled with low-velocity outflow components usually observed in Seyfert galaxies. There are, however, some residual absorption lines which are not accounted for by low-velocity outflows. Here, we present identifications of the strongest lines as K{alpha} transitions of O VII (two lines) and O VI at outflow velocities of {approx}0.1c. These lines are detected at 6.9{sigma}, 6.2{sigma}, and 4.7{sigma}, respectively, and cannot be due to chance statistical fluctuations. Photoionization models with ultra-high velocity components improve the spectralmore » fit significantly, providing further support for the presence of relativistic outflow in this source. Without knowing the location of the absorber, its mass and energy outflow rates cannot be well constrained; we find E-dot (outflow)/L{sub bol} lower limit of {>=}0.006% assuming a bi-conical wind geometry. This is the first time that absorption lines with ultra-high velocities are unambiguously detected in the soft X-ray band. The presence of outflows with relativistic velocities in active galactic nuclei (AGNs) with Seyfert-type luminosities is hard to understand and provides valuable constraints to models of AGN outflows. Radiation pressure is unlikely to be the driving mechanism for such outflows and magnetohydrodynamic may be involved.« less

Ar/Ar Dating Independent of Monitor Standard Ages

NASA Astrophysics Data System (ADS)

Boswell, S.; Hemming, S. R.

2015-12-01

Because the reported age of an analyzed sample is dependent on the age of the co-irradiated monitor standard(s), Ar/Ar dating is a relative dating technique. There is disagreement at the 1% scale in the age of commonly used monitor standards, and there is a great need to improve the inter-laboratory calibrations. Additionally, new approaches and insights are needed to meet the challenge of bringing the Ar/Ar chronometer to the highest possible precision and accuracy. In this spirit, we present a conceptual framework for Ar/Ar dating that does not depend on the age of monitor standards, but only on the K content of a solid standard. The concept is demonstrated by introducing a re-expressed irradiation parameter (JK) that depends on the ratio of 39ArK to 40Ar* rather than the 40Ar*/39ArK ratio. JK is equivalent to the traditional irradiation parameter J and is defined as JK = (39Ar/40K) • (λ/λe). The ultimate precision and accuracy of the method will depend on how precisely and accurately the 39Ar and 40K can be estimated, and will require isotope dilution measurements of both from the same aliquot. We are testing the workability of our technique at the 1% level by measuring weighed and irradiated hornblende and biotite monitor standards using GLO-1 glauconite to define a calibration curve for argon signals versus abundance.

Assessment of various parameters to improve MALDI-TOF MS reference spectra libraries constructed for the routine identification of filamentous fungi.

PubMed

Normand, Anne-Cécile; Cassagne, Carole; Ranque, Stéphane; L'ollivier, Coralie; Fourquet, Patrick; Roesems, Sam; Hendrickx, Marijke; Piarroux, Renaud

2013-04-08

The poor reproducibility of matrix-assisted desorption/ionization time-of-flight (MALDI-TOF) spectra limits the effectiveness of the MALDI-TOF MS-based identification of filamentous fungi with highly heterogeneous phenotypes in routine clinical laboratories. This study aimed to enhance the MALDI-TOF MS-based identification of filamentous fungi by assessing several architectures of reference spectrum libraries. We established reference spectrum libraries that included 30 filamentous fungus species with various architectures characterized by distinct combinations of the following: i) technical replicates, i.e., the number of analyzed deposits for each culture used to build a reference meta-spectrum (RMS); ii) biological replicates, i.e., the number of RMS derived from the distinct subculture of each strain; and iii) the number of distinct strains of a given species. We then compared the effectiveness of each library in the identification of 200 prospectively collected clinical isolates, including 38 species in 28 genera.Identification effectiveness was improved by increasing the number of both RMS per strain (p<10-4) and strains for a given species (p<10-4) in a multivariate analysis. Addressing the heterogeneity of MALDI-TOF spectra derived from filamentous fungi by increasing the number of RMS obtained from distinct subcultures of strains included in the reference spectra library markedly improved the effectiveness of the MALDI-TOF MS-based identification of clinical filamentous fungi.

Genomic diversity and phylogenetic relationships among lipid-requiring diphtheroids from humans and characterization of Corynebacterium macginleyi sp. nov.

PubMed

Riegel, P; Ruimy, R; de Briel, D; Prévost, G; Jehl, F; Christen, R; Monteil, H

1995-01-01

DNA relatedness experiments were performed with 38 clinical isolates and 13 reference strains of coryneform taxa exhibiting a lipid requirement for optimal growth. Forty-five of these strains split into five genomic groups at the species level, whereas six other strains remained unclustered. Genomospecies II fits Corynebacterium accolens, but the other genomospecies were not genetically related to any of the defined Corynebacterium species. Phylogenetic analyses of genes coding for small-subunit rRNA sequences revealed that two genomospecies (I and III) and C. accolens form a tight cluster within the robust branch that groups all Corynebacterium species presently sequenced. Reference strains of biotypes C-1, C-2, and C-3 of "Corynebacterium pseudogenitalium" were found to fall into genomospecies I, as well as "Corynebacterium tuberculostearicum," Centers for Disease Control and Prevention (CDC) coryneform group G-1, and CDC coryneform group G-2 reference strains. Biochemical tests allowed differentiation between genomospecies except between genomospecies IV and V and between six unclustered strains and genomospecies I. We propose a new classification for these lipid-requiring diphtheroids within the genus Corynebacterium with the delineation of some CDC coryneform group G-1 strains (genomospecies III) as a new species for which the name Corynebacterium macginleyi is proposed. The type strain is strain JCL-2 (CIP 104099), isolated from a human corneal ulcer.

Ultrasound speckle tracking for radial, longitudinal and circumferential strain estimation of the carotid artery--an in vitro validation via sonomicrometry using clinical and high-frequency ultrasound.

PubMed

Larsson, Matilda; Heyde, Brecht; Kremer, Florence; Brodin, Lars-Åke; D'hooge, Jan

2015-02-01

Ultrasound speckle tracking for carotid strain assessment has in the past decade gained interest in studies of arterial stiffness and cardiovascular diseases. The aim of this study was to validate and directly contrast carotid strain assessment by speckle tracking applied on clinical and high-frequency ultrasound images in vitro. Four polyvinyl alcohol phantoms mimicking the carotid artery were constructed with different mechanical properties and connected to a pump generating carotid flow profiles. Gray-scale ultrasound long- and short-axis images of the phantoms were obtained using a standard clinical ultrasound system, Vivid 7 (GE Healthcare, Horten, Norway) and a high-frequency ultrasound system, Vevo 2100 (FUJIFILM, VisualSonics, Toronto, Canada) with linear-array transducers (12L/MS250). Radial, longitudinal and circumferential strains were estimated using an in-house speckle tracking algorithm and compared with reference strain acquired by sonomicrometry. Overall, the estimated strain corresponded well with the reference strain. The correlation between estimated peak strain in clinical ultrasound images and reference strain was 0.91 (p<0.001) for radial strain, 0.73 (p<0.001) for longitudinal strain and 0.90 (p<0.001) for circumferential strain and for high-frequency ultrasound images 0.95 (p<0.001) for radial strain, 0.93 (p<0.001) for longitudinal strain and 0.90 (p<0.001) for circumferential strain. A significant larger bias and root mean square error was found for circumferential strain estimation on clinical ultrasound images compared to high frequency ultrasound images, but no significant difference in bias and root mean square error was found for radial and longitudinal strain when comparing estimation on clinical and high-frequency ultrasound images. The agreement between sonomicrometry and speckle tracking demonstrates that carotid strain assessment by ultrasound speckle tracking is feasible. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Comparative Genomics of Ricketttsia prowazekii Madrid E and Breinl Strains

DTIC Science & Technology

2004-01-01

natural exposure to antibiotic -resistant strains and the use of laboratory-manipulated strains as bio- logical warfare agents (28). The World Health...tussis, in the Cag system in Helicobacter pylori, and in the icm/dot system in Legionella pneumophila (reference 12 and references therein). However, the...transfer by the virulence system of Legionella pneumophila. Science 279:873– 876. 45. Waghela, S. D., F. R. Rurangirwa, S. M. Mahan, C. E. Yunker, T. B

Calibration test of the temperature and strain sensitivity coefficient in regional reference grating method

NASA Astrophysics Data System (ADS)

Wu, Jing; Huang, Junbing; Wu, Hanping; Gu, Hongcan; Tang, Bo

2014-12-01

In order to verify the validity of the regional reference grating method in solve the strain/temperature cross sensitive problem in the actual ship structural health monitoring system, and to meet the requirements of engineering, for the sensitivity coefficients of regional reference grating method, national standard measurement equipment is used to calibrate the temperature sensitivity coefficient of selected FBG temperature sensor and strain sensitivity coefficient of FBG strain sensor in this modal. And the thermal expansion sensitivity coefficient of the steel for ships is calibrated with water bath method. The calibration results show that the temperature sensitivity coefficient of FBG temperature sensor is 28.16pm/°C within -10~30°C, and its linearity is greater than 0.999, the strain sensitivity coefficient of FBG strain sensor is 1.32pm/μɛ within -2900~2900μɛ whose linearity is almost to 1, the thermal expansion sensitivity coefficient of the steel for ships is 23.438pm/°C within 30~90°C, and its linearity is greater than 0.998. Finally, the calibration parameters are used in the actual ship structure health monitoring system for temperature compensation. The results show that the effect of temperature compensation is good, and the calibration parameters meet the engineering requirements, which provide an important reference for fiber Bragg grating sensor is widely used in engineering.

Molecular characterization of the probiotic strain Bacillus cereus var. toyoi NCIMB 40112 and differentiation from food poisoning strains.

PubMed

Klein, Günter

2011-07-01

Bacillus cereus var. toyoi strain NCIMB 40112 (Toyocerin), a probiotic authorized in the European Union as feed additive for swine, bovines, poultry, and rabbits, was characterized by DNA fingerprinting applying pulsed-field gel electrophoresis and multilocus sequence typing and was compared with reference strains (of clinical and environmental origins). The probiotic strain was clearly characterized by pulsed-field gel electrophoresis using the restriction enzymes Apa I and Sma I resulting in unique DNA patterns. The comparison to the clinical reference strain B. cereus DSM 4312 was done with the same restriction enzymes, and again a clear differentiation of the two strains was possible by the resulting DNA patterns. The use of the restriction enzymes Apa I and Sma I is recommended for further studies. Furthermore, multilocus sequence typing analysis revealed a sequence type (ST 111) that was different from all known STs of B. cereus strains from food poisoning incidents. Thus, a strain characterization and differentiation from food poisoning strains for the probiotic strain was possible. Copyright ©, International Association for Food Protection

[The characteristics of epidemic influenza A and B virus strains circulating in Russia during the 2007-2008 season].

PubMed

Ivanova, V T; Trushakova, S V; Oskerko, T A; Shevchenko, E S; Kolobukhina, L V; Vartanian, R V; Beliakova, N V; Iatsyshina, S B; Feodoritova, E L; Zueva, N D; Burtseva, E I

2009-01-01

In 2007-2008 in Russia, the epidemic upsurge of influenza morbidity was caused by the active circulation of influenza A(H1N1, A(H3N2), and B viruses. The center for Ecology and Epidemiology of Influenza studied 334 epidemic strains. The results of a comparative study of the svirus specificity of commercial test systems (AmpliSens Influenza virus A/B and AmpliSens Influenza virus A/H5N1) for the polymerase chain reaction diagnosis and virological assays, including virus isolation, revealed their high correlation, which confirms that they may be expensively used to monitor the circulation of influenza viruses in the Russian Federation. All the strains were isolated in the MDCK cell culture. Influenza A(H1N1) viruses (n = 127) were antigenic variants of the reference strains A/Solomon Islands/3/06 and A/Brisbane/59107. Influenza A(H3N2) viruses (n = 49) were antigenic variants of the reference strains A/Wisconsin/67/05 and A/Brisbane/10/08. One hundred and fifty seven Influenza B strains were drift variants of the reference strains B/Florida/4/06 and B/Shanghai/361/02 of lineage B/Yamagata/16/88 and one strain, a variant of Malaysia/2506/04 related to lineage B/victoria/2/87. The isolates interacted actively with human 0(I) blood group erythrocytes and much more weakly with chicken ones. All study influenza A(H1N1) viruses (n = 74) preserved their sensitivity to rimantadine while 24 (77%) of the 31 study influenza A(H3N2) virus strains were resistant. A study of the time course of changes in the generation of antibodies in the donor sera obtained in Moscow and the Moscow Region in different periods of the epidemic process revealed an increase in antibodies to the reference influenza A and B virus strains circulating in this period.

Virulence of Serovar C-1 Strains of Avibacterium paragallinarum.

PubMed

Trujillo-Ruíz, H H; Shivaprasad, H L; Morales-Erasto, V; Talavera-Rojas, M; Salgado-Miranda, C; Salazar-García, F; Blackall, P J; Soriano-Vargas, E

2016-12-01

The bacterium Avibacterium paragallinarum is the etiologic agent of infectious coryza of chickens. There are nine serovars of A. paragallinarum , and serovar C-1 has emerged in outbreaks of infectious coryza in layer hens in the Americas, with all isolates having been obtained from infectious coryza-vaccinated chickens. In the current study, the clinical and histopathologic outcomes of experimental infections in chickens with A. paragallinarum of serovar C-1 were investigated. The Japanese serovar reference strain, H-18, and a Mexican isolate, ESV-135, were included in the study. No differences in clinical sign scores or morbidity were observed between the two strains. The two bacterial strains caused microscopic lesions of lymphoplasmacytic inflammation in the mucosa of the nasal cavity, infraorbital sinus, and trachea. Similar severe lesions were observed in birds inoculated with both H-18 and ESV-135 strains. The lesions were present 48 hr after inoculation and persisted until day 10 after inoculation. Slight to severe, extensive hemorrhages were observed in the lumen, mucous membranes, and lamina propria of the nasal cavity and infraorbital sinus in most of the chickens inoculated with either the reference strain H-18 or the ESV-135 isolate. Hemorrhages in the upper respiratory tract of chickens experimentally infected with A. paragallinarum are reported here for the first time. The results have confirmed the high virulence of the reference strain H-18 as previously reported and have shown that the Mexican isolate was as virulent as the reference strain. The virulence of A. paragallinarum isolates may play a role in explaining why severe infectious coryza outbreaks are being seen in both vaccinated and nonvaccinated chicken flocks.

Thermophysical Properties of Energetic Ionic Liquids/Nitric Acid Mixtures: Insights from Molecular Dynamics Simulations

DTIC Science & Technology

2013-01-01

W L. Physical properties of concentrated nitric acid . UNT Digital Library. http://digital.library.unt.edu/ark:/67531/metadc56640/.) 23 M. Engelmann... Nitric Acid Mixtures: Insights from Molecular Dynamics Simulations 5a. CONTRACT NUMBER FA9300-11-C-3012 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...Rev. 8-98) Prescribed by ANSI Std. 239.18 1     Thermophysical  Properties  of  Energetic  Ionic  Liquids/ Nitric   Acid

Measuring the Effectiveness of the Apparel Advanced Manufacturing Demonstration Program. Appendices B-E

DTIC Science & Technology

1990-12-30

DAVID were around cleaning up or counting A inventory. One whole floor of CHATHAM modem, automated equipment was __ draped with protective coverings...58 5060 N. Pire Street 11201 Armour Drive hazietor DA i8201 - ;Z Paso 7X 799:5 Mr. Sylvano aonarli Mr. Larry Price -resident Executive Vice...GA880493 Ncrti Ina.ustrl.a ark 440 Armour -:ace. . Rioley TN 38063 - Atlanta GA 30324 r. Riclarc Rin. Mr. Samuel S. Scnowls (y Er, ineerno ana.er

The Natural Law of Strategy: A Contrarian’s Lament

DTIC Science & Technology

2011-08-26

DHS, to produce strategy on ever conceivable necessity or non-necessity. There is a Noah ‟ s Ark of hes and shes, two by two, strategies. The...A Contrarian’s Lament 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK...UNIT NUMBER 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) National Defense University,Near East and South Asia Center for Strategic Studies,2100

Micro-PROUST.

DTIC Science & Technology

1985-06-01

Noah needs to keep track of rainfall in the New Haven area in order to determine when to launch his ark . Write a...UNLSIIDFG92 N 2.. II4II 111220 11111 11J.4 MICROCOPY RESOLUTION TEST CHART S "- )ARDS 1963 A S !!? Ii~ Sii ". . . ," .’ "" o o." .* -. ° . ". * -. * " . -- I...unflagging effort and support in seeing this project through to fruition. V 7 .. ° - . . - , .-. - . - ., S .-’ S 1. ES , " , - u < . i ’ - SiCU,r7

Improved Manufacturing Methods for Navy Peacoats

DTIC Science & Technology

1991-09-30

oaeration requir= S a heavy ;;erd, feed machine II n CC T is can e done either with a r I 2 .’" ark buttonhoie loc-tion with the I Ir fo I...AD-A243 702 F A S H I 0 N I INSTITUTE OF TECHNOLOGYI R E S EARCH DTIC I REPORT SELECTEI.. D D I IMPROVED MANUFACTURING METHODS FOR NAVY PEACOATS I I...A008. I IHenr A/Seesselberg Dir ctor, Advanced Apparel Manufacturing Technology Programs, Fashion Institute of Technology I Noah Bronner Research

Devils in the Dialogue: The Air Force and Congress

DTIC Science & Technology

2011-06-01

the United States, Article I, Section 8. 111th Cong., 1st sess., 2009, S . Doc 111-4. 118 John Haskell, Congress in Context (Philadelphia, PA...Congress. 12 January 2005. http://digital.library.unt.edu/ ark :/67531/metacrs7624/m1/1/high_res_d/98- 558_2005Jan12.pdf 141 HR 91-1570, FY71 DOD...February 2011 260 Shachtman, Noah . ―Pentagon Chief Rips Heart Out of Army‘s ‗Future‘,‖ Wired, 6 April 2009, http://www.wired.com/dangerroom/2009/04

A Literature Review - Problem Definition Studies on Selected Toxic Chemicals. Volume 6. Occupational Health and Safety and Environmental Aspects of Urea-Formaldehyde Resins

DTIC Science & Technology

1978-04-01

to the treated fabrics, the author suggested that -oen might have been sensitized to the feradehyde included in antiperspirant preparations uhich men...used in antiperspirants in this country. A study conducted in Den=-ark shouwed that during 1952-1960 the incidence of formaldehyde eczema due t treated...fabrics had been rising whereas that caused by antiperspirants had disappeared (34). In 1960, formaldehyde in treated fabrics was responsible for 50

Lower Mississippi River Environmental Program. Report 13. Preliminary Environmental Design Considerations Associated with Articulated Concrete Mattress Revetments along the Lower Mississippi River

DTIC Science & Technology

1988-05-01

Engineer Water Resources Support Center, Fort Belvoir, Va. Conner, J. W., Pennington, C. H., and Bosley, T. R. 1983. "Larval Fish of Selected Aquatic ...Mississippi River Environmental Program; Report 13 6a NAME OF PERFORMING ORGANIZATION 6b OFFICE SYMBOL 7a. NAME OF MONITORING ORGANIZATION Aquatic Ecosystem...Jenkins, Aquatic Ecosystem Analysts, PO Box 4188, Fayetteville, Ark. Mr. Stephen P. Cobb, MRC, Vicksburg, Miss., was the project officer and program manager

Whole genome sequence analyses of Xylella fastidiosa PD strains from different geographical regions

USDA-ARS?s Scientific Manuscript database

Genome sequences were determined for two Pierce’s disease (PD) causing Xylella fastidiosa (Xf) strains, one from Florida and one from Taiwan. The Florida strain was ATCC 35879, the type of strain used as a standard reference for related taxonomy research. By contrast, the Taiwan strain used was only...

Phylogenetic relationship of Ornithobacterium rhinotracheale strains.

PubMed

DE Oca-Jimenez, Roberto Montes; Vega-Sanchez, Vicente; Morales-Erasto, Vladimir; Salgado-Miranda, Celene; Blackall, Patrick J; Soriano-Vargas, Edgardo

2018-04-10

The bacterium Ornithobacterium rhinotracheale is associated with respiratory disease in wild birds and poultry. In this study, the phylogenetic analysis of nine reference strains of O. rhinotracheale belonging to serovars A to I, and eight Mexican isolates belonging to serovar A, was performed. The analysis was extended to include available sequences from another 23 strains available in the public domain. The analysis showed that the 40 sequences formed six clusters, I to VI. All eight Mexican field isolates were placed in cluster I. One of the reference strains appears to present genetic diversity not previously recognized and was placed in a new genetic cluster. In conclusion, the phylogenetic analysis of O. rhinotracheale strains, based on the 16S rRNA gene, is a suitable tool for epidemiologic studies.

Validation of the (GTG)(5)-rep-PCR fingerprinting technique for rapid classification and identification of acetic acid bacteria, with a focus on isolates from Ghanaian fermented cocoa beans.

PubMed

De Vuyst, Luc; Camu, Nicholas; De Winter, Tom; Vandemeulebroecke, Katrien; Van de Perre, Vincent; Vancanneyt, Marc; De Vos, Paul; Cleenwerck, Ilse

2008-06-30

Amplification of repetitive bacterial DNA elements through the polymerase chain reaction (rep-PCR fingerprinting) using the (GTG)(5) primer, referred to as (GTG)(5)-PCR fingerprinting, was found a promising genotypic tool for rapid and reliable speciation of acetic acid bacteria (AAB). The method was evaluated with 64 AAB reference strains, including 31 type strains, and 132 isolates from Ghanaian, fermented cocoa beans, and was validated with DNA:DNA hybridization data. Most reference strains, except for example all Acetobacter indonesiensis strains and Gluconacetobacter liquefaciens LMG 1509, grouped according to their species designation, indicating the usefulness of this technique for identification to the species level. Moreover, exclusive patterns were obtained for most strains, suggesting that the technique can also be used for characterization below species level or typing of AAB strains. The (GTG)(5)-PCR fingerprinting allowed us to differentiate four major clusters among the fermented cocoa bean isolates, namely A. pasteurianus (cluster I, 100 isolates), A. syzygii- or A. lovaniensis-like (cluster II, 23 isolates), and A. tropicalis-like (clusters III and IV containing 4 and 5 isolates, respectively). A. syzygii-like and A. tropicalis-like strains from cocoa bean fermentations were reported for the first time. Validation of the method and indications for reclassifications of AAB species and existence of new Acetobacter species were obtained through 16S rRNA sequencing analyses and DNA:DNA hybridizations. Reclassifications refer to A. aceti LMG 1531, Ga. xylinus LMG 1518, and Ga. xylinus subsp. sucrofermentans LMG 18788(T).

Evaluation of the use of various rat strains for immunogenic potency tests of Sabin-derived inactivated polio vaccines.

PubMed

Someya, Yuichi; Ami, Yasushi; Takai-Todaka, Reiko; Fujimoto, Akira; Haga, Kei; Murakami, Kosuke; Fujii, Yoshiki; Shirato, Haruko; Oka, Tomoichiro; Shimoike, Takashi; Katayama, Kazuhiko; Wakita, Takaji

2018-03-01

Slc:Wistar rats have been the only strain used in Japan for purpose of evaluating a national reference vaccine for the Sabin-derived inactivated polio vaccine (sIPV) and the immunogenicity of sIPV-containing products. However, following the discovery that the Slc:Wistar strain was genetically related to the Fischer 344 strain, other "real" Wistar strains, such as Crlj:WI, that are available worldwide were tested in terms of their usefulness in evaluating the immunogenicity of the past and current lots of a national reference vaccine. The response of the Crlj:WI rats against the serotype 1 of sIPV was comparable to that of the Slc:Wistar rats, while the Crlj:WI rats exhibited a higher level of response against the serotypes 2 and 3. The immunogenic potency units of a national reference vaccine determined using the Slc:Wistar rats were reproduced on tests using the Crlj:WI rats. These results indicate that a titer of the neutralizing antibody obtained in response to a given dose of sIPV cannot be directly compared between these two rat strains, but that, more importantly, the potency units are almost equivalent for the two rat strains. Copyright © 2018 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

Investigation of Reference Genes in Vibrio parahaemolyticus for Gene Expression Analysis Using Quantitative RT-PCR.

PubMed

Ma, Yue-Jiao; Sun, Xiao-Hong; Xu, Xiao-Yan; Zhao, Yong; Pan, Ying-Jie; Hwang, Cheng-An; Wu, Vivian C H

2015-01-01

Vibrio parahaemolyticus is a significant human pathogen capable of causing foodborne gastroenteritis associated with the consumption of contaminated raw or undercooked seafood. Quantitative RT-PCR (qRT-PCR) is a useful tool for studying gene expression in V. parahaemolyticus to characterize its virulence factors and understand the effect of environmental conditions on its pathogenicity. However, there is not a stable gene in V. parahaemolyticus that has been identified for use as a reference gene for qRT-PCR. This study evaluated the stability of 6 reference genes (16S rRNA, recA, rpoS, pvsA, pvuA, and gapdh) in 5 V. parahaemolyticus strains (O3:K6-clinical strain-tdh+, ATCC33846-tdh+, ATCC33847-tdh+, ATCC17802-trh+, and F13-environmental strain-tdh+) cultured at 4 different temperatures (15, 25, 37 and 42°C). Stability values were calculated using GeNorm, NormFinder, BestKeeper, and Delta CT algorithms. The results indicated that recA was the most stably expressed gene in the V. parahaemolyticus strains cultured at different temperatures. This study examined multiple V. parahaemolyticus strains and growth temperatures, hence the finding provided stronger evidence that recA can be used as a reference gene for gene expression studies in V. parahaemolyticus.

Assessment of various parameters to improve MALDI-TOF MS reference spectra libraries constructed for the routine identification of filamentous fungi

PubMed Central

2013-01-01

Background The poor reproducibility of matrix-assisted desorption/ionization time-of-flight (MALDI-TOF) spectra limits the effectiveness of the MALDI-TOF MS-based identification of filamentous fungi with highly heterogeneous phenotypes in routine clinical laboratories. This study aimed to enhance the MALDI-TOF MS-based identification of filamentous fungi by assessing several architectures of reference spectrum libraries. Results We established reference spectrum libraries that included 30 filamentous fungus species with various architectures characterized by distinct combinations of the following: i) technical replicates, i.e., the number of analyzed deposits for each culture used to build a reference meta-spectrum (RMS); ii) biological replicates, i.e., the number of RMS derived from the distinct subculture of each strain; and iii) the number of distinct strains of a given species. We then compared the effectiveness of each library in the identification of 200 prospectively collected clinical isolates, including 38 species in 28 genera. Identification effectiveness was improved by increasing the number of both RMS per strain (p<10-4) and strains for a given species (p<10-4) in a multivariate analysis. Conclusion Addressing the heterogeneity of MALDI-TOF spectra derived from filamentous fungi by increasing the number of RMS obtained from distinct subcultures of strains included in the reference spectra library markedly improved the effectiveness of the MALDI-TOF MS-based identification of clinical filamentous fungi. PMID:23565856

Genomic diversity among Corynebacterium jeikeium strains and comparison with biochemical characteristics and antimicrobial susceptibilities.

PubMed Central

Riegel, P; de Briel, D; Prévost, G; Jehl, F; Monteil, H

1994-01-01

Levels of DNA relatedness were determined by performing DNA-DNA hybridization experiments (S1 nuclease procedure) with 13 human isolates exhibiting various antimicrobial susceptibility patterns which had been identified as Corynebacterium jeikeium by classical tests and the API Coryne system and with reference strains of C. jeikeium and related taxa. Twelve of 13 isolates which formed three genomic groups showed between 22 and 75% relatedness with the type strain of C. jeikeium. One of these genomic groups included all the strains resistant to penicillin and gentamicin and is genomically related to the C. jeikeium type strain at the species level. In addition, the reference strain of "Corynebacterium genitalium" biotype II was found to belong to this genospecies and therefore can be considered as a synonym of C. jeikeium. In contrast, one isolate and the reference strains of "Corynebacterium pseudogenitalium" biotypes C-3 and C-4 which were assigned to C. jeikeium by the API Coryne system were less than 10% related to the C. jeikeium type strain. These nongenomically related strains can be differentiated from the jeikeium-related strains on the basis of positive acidification from fructose and growth under anaerobic conditions. Furthermore, these strains exhibited full susceptibility to penicillin whereas the strains related to the C. jeikeium type strain are resistant to or only moderately susceptible to penicillin. No genomic relationship was found between C. jeikeium-related strains and other lipophilic coryneforms, identified as Corynebacterium accolens or Corynebacterium group G or F. Our study demonstrates the necessity to perform the fructose fermentation test or respiratory-type test for the correct identification of lipophilic coryneforms as C. jeikeium. Although these strains show genomic diversity at the species level, in a practical aspect, biochemical properties as well as antimicrobial susceptibility may allow the classification of such isolates in this single taxon. PMID:7989533

Genomic diversity among Corynebacterium jeikeium strains and comparison with biochemical characteristics and antimicrobial susceptibilities.

PubMed

Riegel, P; de Briel, D; Prévost, G; Jehl, F; Monteil, H

1994-08-01

Levels of DNA relatedness were determined by performing DNA-DNA hybridization experiments (S1 nuclease procedure) with 13 human isolates exhibiting various antimicrobial susceptibility patterns which had been identified as Corynebacterium jeikeium by classical tests and the API Coryne system and with reference strains of C. jeikeium and related taxa. Twelve of 13 isolates which formed three genomic groups showed between 22 and 75% relatedness with the type strain of C. jeikeium. One of these genomic groups included all the strains resistant to penicillin and gentamicin and is genomically related to the C. jeikeium type strain at the species level. In addition, the reference strain of "Corynebacterium genitalium" biotype II was found to belong to this genospecies and therefore can be considered as a synonym of C. jeikeium. In contrast, one isolate and the reference strains of "Corynebacterium pseudogenitalium" biotypes C-3 and C-4 which were assigned to C. jeikeium by the API Coryne system were less than 10% related to the C. jeikeium type strain. These nongenomically related strains can be differentiated from the jeikeium-related strains on the basis of positive acidification from fructose and growth under anaerobic conditions. Furthermore, these strains exhibited full susceptibility to penicillin whereas the strains related to the C. jeikeium type strain are resistant to or only moderately susceptible to penicillin. No genomic relationship was found between C. jeikeium-related strains and other lipophilic coryneforms, identified as Corynebacterium accolens or Corynebacterium group G or F. Our study demonstrates the necessity to perform the fructose fermentation test or respiratory-type test for the correct identification of lipophilic coryneforms as C. jeikeium. Although these strains show genomic diversity at the species level, in a practical aspect, biochemical properties as well as antimicrobial susceptibility may allow the classification of such isolates in this single taxon.

[Identification of mycobacteria by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry--using reference strains and clinical isolates of Mycobacterium].

PubMed

Niitsuma, Katsunao; Saito, Miwako; Koshiba, Shizuko; Kaneko, Michiyo

2014-05-01

Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) method is being played an important role for the inspection of clinical microorganism as a rapid and the price reduction. Mass spectra obtained by measuring become points of identification whether the peak pattern match any species mass spectral pattern. We currently use MALDI-TOF MS for rapid and accurate diagnosis of inactivated reference and clinical isolates of Mycobacterium because of the improved pretreatment techniques compared with former inspection methods that pose a higher risk of infection to the operator. The identification matching rate of score value (SV) peak pattern spectra was compared with that of conventional methods such as strain diffusion/amplification. Also, cultures were examined after a fixed number of days. Compared with the initial inspection technique, the pretreatment stage of current MALDI-TOF MS inspection techniques can improve the analysis of inactivated acid-fast bacteria that are often used as inspection criteria strains of clinical isolates. Next, we compared the concordance rate for identification between MALDI-TOF MS and conventional methods such as diffusion/amplification by comparison of peak pattern spectra and evaluated SV spectra to identify differences in the culture media after the retention period. In examination of 158 strains of clinical isolated Mycobacterium tuberculosis complex (MTC), the identification coincidence rate in the genus level in a matching pattern was 99.4%, when the species level was included 94.9%. About 37 strains of nontuberculous mycobacteria (NTM), the identification coincidence rate in the genus level was 94.6%. M. bovis BCG (Tokyo strain) in the reference strain was judged by the matching pattern to be MTC, and it suggested that they are M. tuberculosis and affinity species with high DNA homology. Nontuberculous mycobacterial M. gordonae strain JATA 33-01 shared peak pattern spectra, excluding the isolates, with each clinically isolated strain. However, the mass spectra of six M. gordonae clinical isolates suggested polymorphisms with similar mass-to-charge ratios compared with those of the reference strains. The peak pattern spectra of the clinical isolates and reference strains, excluding the NTM M. gordonae strain JATA33-01, were consistent with the peak pattern characteristics of each isolate. However, a comparison between the peak patterns of the reference strains and those of the six clinically isolated M. gordonae strains revealed a similar mass-to-charge ratio, which may indicate few polymorphisms. The SV spectrum of the improved inspection technique showed no fidelity, but it was acceptable after days of culture as indicated by the decrease in SV (0.3 degree). Also, the reproducibility of this method was good, but no difference was observed from the SV of the improved inspection technique, which decreased by approximately 0.3 because of the number of days of culture storage. In addition, expansion of the database and dissemination of regional specificity by genotype analysis of clinical isolates was relevant to the accumulated data, as expected. In future studies, the relevance and regional specificity of clinical isolates by genotype analysis can be determined by stacking the solid media and database penetration.

Definition of the Beijing/W lineage of Mycobacterium tuberculosis on the basis of genetic markers.

PubMed

Kremer, Kristin; Glynn, Judith R; Lillebaek, Troels; Niemann, Stefan; Kurepina, Natalia E; Kreiswirth, Barry N; Bifani, Pablo J; van Soolingen, Dick

2004-09-01

Mycobacterium tuberculosis Beijing genotype strains are highly prevalent in Asian countries and in the territory of the former Soviet Union. They are increasingly reported in other areas of the world and are frequently associated with tuberculosis outbreaks and drug resistance. Beijing genotype strains, including W strains, have been characterized by their highly similar multicopy IS6110 restriction fragment length polymorphism (RFLP) patterns, deletion of spacers 1 to 34 in the direct repeat region (Beijing spoligotype), and insertion of IS6110 in the genomic dnaA-dnaN locus. In this study the suitability and comparability of these three genetic markers to identify members of the Beijing lineage were evaluated. In a well-characterized collection of 1,020 M. tuberculosis isolates representative of the IS6110 RFLP genotypes found in The Netherlands, strains of two clades had spoligotypes characteristic of the Beijing lineage. A set of 19 Beijing reference RFLP patterns was selected to retrieve all Beijing strains from the Dutch database. These reference patterns gave a sensitivity of 98.1% and a specificity of 99.7% for identifying Beijing strains (defined by spoligotyping) in an international database of 1,084 strains. The usefulness of the reference patterns was also assessed with large DNA fingerprint databases in two other European countries and for identification strains from the W lineage found in the United States. A standardized definition for the identification of M. tuberculosis strains belonging to the Beijing/W lineage, as described in this work, will facilitate further studies on the spread and characterization of this widespread genotype family of M. tuberculosis strains.

Whole eye wavefront aberrations in Mexican male subjects.

PubMed

Cantú, Roberto; Rosales, Marco A; Tepichín, Eduardo; Curioca, Andrée; Montes, Victor; Bonilla, Julio

2004-01-01

To analyze the characteristics, incidence, and appearance of wavefront aberrations in undilated, normal, unoperated eyes. Eighty-eight eyes of 44 healthy male Mexican subjects (mean age 25.32 years, range 18 to 36 yr) were divided into three groups based on uncorrected visual acuity of greater than or equal to 20/20, 20/30, or 20/40. UCVA measurements were obtained using an Acuity Max computer screen chart. Wavefront aberrations were measured with the Nidek OPD-Scan ARK 10000, Ver. 1.11b. All measurements were carried out at the same center by the same technician during a single session, following manufacturer instructions. Background illumination was 3 Lux. Wavefront aberration measurements for each group were statistically analyzed using StatView; an average eye was characterized and the resulting aberrations were simulated using MATLAB. We obtained wavefront aberration maps for the 20/20 undilated normal unoperated eyes for total, low, and high order aberration coefficients. Wavefront maps for right eyes were practically the same as those for left eyes. Higher aberrations did not contribute substantially to total wavefront analysis. Average aberrations of this "normal eye" will be used as criteria to decide the necessity of wavefront-guided ablation in our facilities. We will focus on the nearly zero average of high order aberrations in this normal whole eye as a reference to be matched.

[Accuracy of three common optometry methods in examination of refraction in juveniles].

PubMed

Su, Ting; Min, Xiaoshan; Liu, Shuangzhen; Li, Fengyun; Tan, Xingping; Zhong, Yanni; Deng, Shaoling

2016-02-01

To compare the results of the three methods of Suresight handheld autorefractor, table-mounted autorefractor and retinoscopy in examination of juveniles patients with or without cycloplegia.
 Firstly, 156 eyes of 78 juveniles (5 to 17 years old) were examined by using WelchAllyn Suresight handheld autorefractor and NIDEK ARK-510A table-mounted autorefractor with or without cycloplegia; secondly, retinoscopy was performed with cycloplegia.
 The spherical power measured by methods without cycloplegia were significantly greater than those measured with cycloplegia (P<0.05); without cycloplegia, there was no significant difference in spherical power, cylindrical power and cylindrical axis between Suresight handheld autorefractor and retinoscopy (P>0.05). These results were highly consistent, suggesting a tendency towards a short sight. However, the spherical power and cylindrical power measured by table-mounted autorefractor was significantly different (P<0.05); with cycloplegia, there was significant difference in spherical power between Suresight handheld autorefractor and retinoscopy (P<0.05).
 Cycloplegic retinoscopy is necessary for juvenile refraction examination. Under natural pupil situation, Suresight handheld autorefractor is better than table-mounted autorefractor, though both show a myopia tendency. Nevertheless, table-mounted autorefractor can be taken as a recommendation for the prescription of lens trial. As a strong reference for subjective optometry, retinoscopy should be the gold standard for measuring refractive errors.

Full-length genome sequence analysis of four subgroup J avian leukosis virus strains isolated from chickens with clinical hemangioma.

PubMed

Lin, Lulu; Wang, Peikun; Yang, Yongli; Li, Haijuan; Huang, Teng; Wei, Ping

2017-12-01

Since 2014, cases of hemangioma associated with avian leukosis virus subgroup J (ALV-J) have been emerging in commercial chickens in Guangxi. In this study, four strains of the subgroup J avian leukosis virus (ALV-J), named GX14HG01, GX14HG04, GX14LT07, and GX14ZS14, were isolated from chickens with clinical hemangioma in 2014 by DF-1 cell culture and then identified with ELISA detection of ALV group specific antigen p27, the detection of subtype specific PCR and indirect immunofluorescence assay (IFA) with ALV-J specific monoclonal antibody. The complete genomes of the isolates were sequenced and it was found that the gag and pol were relatively conservative, while env was variable especially the gp85 gene. Homology analysis of the env gene sequences showed that the env gene of all the four isolates had higher similarities with the hemangioma (HE)-type reference strains than that of the myeloid leukosis (ML)-type strains, and moreover, the HE-type strains' specific deletion of 205-bp sequence covering the rTM and DR1 in 3'UTR fragment was also found in the four isolates. Further analysis on the sequences of subunits of env gene revealed an interesting finding: the gp85 of isolates GX14ZS14 and GX14HG04 had a higher similarity with HPRS-103 and much lower similarity with the HE-type reference strains resulting in GX14ZS14, GX14HG04, and HPRS-103 being clustered in the same branch, while gp37 had higher similarities with the HE-type reference strains when compared to that of HPRS-103, resulted in GX14ZS14, GX14HG04, and HE-type reference strains being clustered in the same branch. The results suggested that isolates GX14ZS14 and GX14HG04 may be the recombinant strains of the foreign strain HPRS-103 with the local epidemic HE-type strains of ALV-J.

Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker

PubMed Central

Schneider, Kevin L.; Marrero, Glorimar; Alvarez, Anne M.; Presting, Gernot G.

2011-01-01

A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF). Unlike the rRNA genes, dnaA is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of RIF requires genus-specific primers. In silico analysis revealed that RIF has equal or greater ability to differentiate closely related species of Xanthomonas than the widely used ribosomal intergenic spacer region (ITS). Furthermore, in a set of 263 Xanthomonas, Ralstonia and Clavibacter strains, the RIF marker was directly sequenced in both directions with a success rate approximately 16% higher than that for ITS. RIF frameworks for Xanthomonas, Ralstonia and Clavibacter were constructed using 682 reference strains representing different species, subspecies, pathovars, races, hosts and geographic regions, and contain a total of 109 different RIF sequences. RIF sequences showed subspecific groupings but did not place strains of X. campestris or X. axonopodis into currently named pathovars nor R. solanacearum strains into their respective races, confirming previous conclusions that pathovar and race designations do not necessarily reflect genetic relationships. The RIF marker also was sequenced for 24 reference strains from three genera in the Enterobacteriaceae: Pectobacterium, Pantoea and Dickeya. RIF sequences of 70 previously uncharacterized strains of Ralstonia, Clavibacter, Pectobacterium and Dickeya matched, or were similar to, those of known reference strains, illustrating the utility of the frameworks to classify bacteria below the species level and rapidly match unknown isolates to reference strains. The RIF sequence frameworks are available at the online RIF database, RIFdb, and can be queried for diagnostic purposes with RIF sequences obtained from unknown strains in both chromatogram and FASTA format. PMID:21533033

Growth inhibition of oral mutans streptococci and candida by commercial probiotic lactobacilli - an in vitro study

PubMed Central

2010-01-01

Background Probiotic bacteria are suggested to play a role in the maintenance of oral health. Such health promoting bacteria are added to different commercial probiotic products. The aim of the study was to investigate the ability of a selection of lactobacilli strains, used in commercially available probiotic products, to inhibit growth of oral mutans streptococci and C. albicans in vitro. Methods Eight probiotic lactobacilli strains were tested for growth inhibition on three reference strains and two clinical isolates of mutans streptococci as well as two reference strains and three clinical isolates of Candida albicans with an agar overlay method. Results At concentrations ranging from 109 to 105 CFU/ml, all lactobacilli strains inhibited the growth of the mutans streptococci completely with the exception of L. acidophilus La5 that executed only a slight inhibition of some strains at concentrations corresponding to 107 and 105 CFU/ml. At the lowest cell concentration (103 CFU/ml), only L. plantarum 299v and L. plantarum 931 displayed a total growth inhibition while a slight inhibition was seen for all five mutans streptococci strains by L. rhamnosus LB21, L. paracasei F19, L. reuteri PTA 5289 and L. reuteri ATCC 55730. All the tested lactobacilli strains reduced candida growth but the effect was generally weaker than for mutans streptococci. The two L. plantarum strains and L. reuteri ATCC 55730 displayed the strongest inhibition on Candida albicans. No significant differences were observed between the reference strains and the clinical isolates. Conclusion The selected probiotic strains showed a significant but somewhat varying ability to inhibit growth of oral mutans streptococci and Candida albicans in vitro. PMID:20598145

Growth inhibition of oral mutans streptococci and candida by commercial probiotic lactobacilli--an in vitro study.

PubMed

Hasslöf, Pamela; Hedberg, Maria; Twetman, Svante; Stecksén-Blicks, Christina

2010-07-02

Probiotic bacteria are suggested to play a role in the maintenance of oral health. Such health promoting bacteria are added to different commercial probiotic products. The aim of the study was to investigate the ability of a selection of lactobacilli strains, used in commercially available probiotic products, to inhibit growth of oral mutans streptococci and C. albicans in vitro. Eight probiotic lactobacilli strains were tested for growth inhibition on three reference strains and two clinical isolates of mutans streptococci as well as two reference strains and three clinical isolates of Candida albicans with an agar overlay method. At concentrations ranging from 109 to 105 CFU/ml, all lactobacilli strains inhibited the growth of the mutans streptococci completely with the exception of L. acidophilus La5 that executed only a slight inhibition of some strains at concentrations corresponding to 107 and 105 CFU/ml. At the lowest cell concentration (103 CFU/ml), only L. plantarum 299v and L. plantarum 931 displayed a total growth inhibition while a slight inhibition was seen for all five mutans streptococci strains by L. rhamnosus LB21, L. paracasei F19, L. reuteri PTA 5289 and L. reuteri ATCC 55730. All the tested lactobacilli strains reduced candida growth but the effect was generally weaker than for mutans streptococci. The two L. plantarum strains and L. reuteri ATCC 55730 displayed the strongest inhibition on Candida albicans. No significant differences were observed between the reference strains and the clinical isolates. The selected probiotic strains showed a significant but somewhat varying ability to inhibit growth of oral mutans streptococci and Candida albicans in vitro.

Distributed fiber strain and vibration sensor based on Brillouin optical time-domain reflectometry and polarization optical time-domain reflectometry.

PubMed

Wang, Feng; Zhang, Xuping; Wang, Xiangchuan; Chen, Haisheng

2013-07-15

A distributed fiber strain and vibration sensor which effectively combines Brillouin optical time-domain reflectometry and polarization optical time-domain reflectometry is proposed. Two reference beams with orthogonal polarization states are, respectively, used to perform the measurement. By using the signal obtained from either reference beam, the vibration of fiber can be measured from the polarization effect. After combining the signals obtained by both reference beams, the strain can be measured from the Brillouin effect. In the experiment, 10 m spatial resolution, 0.6 kHz frequency measurement range, 2.5 Hz frequency resolution, and 0.2 MHz uncertainty of Brillouin frequency measurement are realized for a 4 km sensing distance.

Increased Biomass Production by Mesophilic Food-Associated Bacteria through Lowering the Growth Temperature from 30°C to 10°C.

PubMed

Seel, Waldemar; Derichs, Julia; Lipski, André

2016-07-01

Five isolates from chilled food and refrigerator inner surfaces and closely related reference strains of the species Escherichia coli, Listeria monocytogenes, Staphylococcus xylosus, Bacillus cereus, Pedobacter nutrimenti, and Pedobacter panaciterrae were tested for the effect of growth temperature (30°C and 10°C) on biomass formation. Growth was monitored via optical density, and biomass formation was measured at the early stationary phase based on the following parameters in complex and defined media: viable cell count, total cell count, cell dry weight, whole-cell protein content, and cell morphology. According to the lack of growth at 1°C, all strains were assigned to the thermal class of mesophiles. Glucose and ammonium consumption related to cell yield were analyzed in defined media. Except for the protein content, temperature had a significant (t test, P < 0.05) effect on all biomass formation parameters for each strain. The results show a significant difference between the isolates and the related reference strains. Isolates achieved an increase in biomass production between 20% and 110% at the 10°C temperature, which is 15 to 25°C lower than their maximum growth rate temperatures. In contrast, reference strains showed a maximum increase of only about 25%, and some reference strains showed no increase or a decrease of approximately 25%. As expected, growth rates for all strains were higher at 30°C than at 10°C, while biomass production for isolates was higher at 10°C than at 30°C. In contrast, the reference strains showed similar growth yields at the two temperatures. This also demonstrates for mesophilic bacterial strains more efficient nutrient assimilation during growth at low temperatures. Until now, this characteristic was attributed only to psychrophilic microorganisms. For several psychrophilic species, increased biomass formation was described at temperatures lower than optimum growth temperatures, which are defined by the highest growth rate. This work shows increased biomass formation at low growth temperatures for mesophilic isolates. A comparison with closely related reference strains from culture collections showed a significantly smaller increase or no increase in biomass formation. This indicates a loss of specific adaptive mechanisms (e.g., cold adaptation) for mesophiles during long-term cultivation. The increased biomass production for mesophiles under low-temperature conditions opens new avenues for a more efficient biotechnological transformation of nutrients to microbial biomass. These findings may also be important for risk assessment of cooled foods since risk potential is often correlated with the cell numbers present in food samples. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Identification of Francisella tularensis by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry: fast, reliable, robust, and cost-effective differentiation on species and subspecies levels.

PubMed

Seibold, E; Maier, T; Kostrzewa, M; Zeman, E; Splettstoesser, W

2010-04-01

Francisella tularensis, the causative agent of tularemia, is a potential agent of bioterrorism. The phenotypic discrimination of closely related, but differently virulent, Francisella tularensis subspecies with phenotyping methods is difficult and time-consuming, often producing ambiguous results. As a fast and simple alternative, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was applied to 50 different strains of the genus Francisella to assess its ability to identify and discriminate between strains according to their designated species and subspecies. Reference spectra from five representative strains of Francisella philomiragia, Francisella tularensis subsp. tularensis, Francisella tularensis subsp. holarctica, Francisella tularensis subsp. mediasiatica, and Francisella tularensis subsp. novicida were established and evaluated for their capability to correctly identify Francisella species and subspecies by matching a collection of spectra from 45 blind-coded Francisella strains against a database containing the five reference spectra and 3,287 spectra from other microorganisms. As a reference method for identification of strains from the genus Francisella, 23S rRNA gene sequencing was used. All strains were correctly identified, with both methods showing perfect agreement at the species level as well as at the subspecies level. The identification of Francisella strains by MALDI-TOF MS and subsequent database matching was reproducible using biological replicates, different culture media, different cultivation times, different serial in vitro passages of the same strain, different preparation protocols, and different mass spectrometers.

Direct coordinate-free derivation of the compatibility equation for finite strains

NASA Astrophysics Data System (ADS)

Ryzhak, E. I.

2014-07-01

The compatibility equation for the Cauchy-Green tensor field (squared tensor of pure extensionwith respect to the reference configuration) is directly derived from the well-known relation expressing this tensor via the vector field determining the mapping (transformation) of the reference configuration into the actual one. The derivation is based on the use of the apparatus of coordinatefree tensor calculus and does not apply any notions and relations of Riemannian geometry at all. The method is illustrated by deriving the well-known compatibility equation for small strains. It is shown that when the obtained compatibility equation for finite strains is linearized, it becomes the compatibility equation for small strains which indirectly confirms its correctness.

The Influence of the In-Situ Clad Staining on the Corrosion of Zircaloy in PWR Water Environment

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

Kammenzind, B.F., Eklund, K.L. and Bajaj, R.

Zircaloy cladding tubes strain in-situ during service life in the corrosive environment of a Pressurized Water Reactor for a variety of reasons. First, the tube undergoes stress free growth due to the preferential alignment of irradiation induced vacancy loops on basal planes. Positive strains develop in the textured tubes along prism orientations while negative strains develop along basal orientations (Reference (a)). Second, early in life, free standing tubes will often shrink by creep in the diametrical direction under the external pressure of the water environment, but potentially grow later in life in the diametrical direction once the expanding fuel pelletmore » contacts the cladding inner wall (Reference (b)). Finally, the Zircaloy cladding absorbs hydrogen as a by product of the corrosion reaction (Reference (c)). Once above the solubility limit in Zircaloy, the hydride precipitates as zirconium hydride (References (c) through (j)). Both hydrogen in solid solution and precipitated as Zirconium hydride cause a volume expansion of the Zircaloy metal (Reference (k)). Few studies are reported on that have investigated the influence that in-situ clad straining has on corrosion of Zircaloy. If Zircaloy corrosion rates are governed by diffusion of anions through a thin passivating boundary layer at the oxide-to-metal interface (References (l) through (n)), in-situ straining of the cladding could accelerate the corrosion process by prematurely breaking that passivating oxide boundary layer. References (o) through (q) investigated the influence that an applied tensile stress has on the corrosion resistance of Zircaloy. Knights and Perkins, Reference (o), reported that the applied tensile stress increased corrosion rates above a critical stress level in 400 C and 475 C steam, but not at lower temperatures nor in dry oxygen environments. This latter observation suggested that hydrogen either in the oxide or at the oxide-to-metal interface is involved in the observed stress effect. Kim et al. (Reference (p)) and Kim and Kim (Reference (q)) more recently investigated the influence that an applied hoop stress has on the corrosion resistance of Zircaloy tubes in a 400 C steam and in a 350 C concentrated lithia water environment. Both of these studies found the applied tensile hoop stress to have no effect on cladding corrosion rates in the 400 C steam environment but to have accelerated corrosion in the lithiated water environment. In both cases, the corrosion acceleration in the lithiated water environment was attributed to the accumulation of the increased hydrogen picked up in the lithiated environment into the tensile regions of the test specimen. Dense hydride rims have been shown, independent of clad strain, to accelerate the corrosion of Zirconium alloys (References (r) and (s)), suggesting that the primary effect of applied stresses on the corrosion of Zircaloy in the above studies is through the accumulation of hydrogen at the oxide-to-metal interface and not through a direct mechanical breakdown of the passivating boundary layer. To further investigate the potential role of in-situ clad straining (or stress) on Zircaloy corrosion rates, two experimental studies were performed. First, several samples that were irradiated with and without an applied stress were destructively examined for the extent of corrosion occurring in strained and nonstrained regions of the test samples. The extent of corrosion was determined, posttest, by metallographic examination. Second, the corrosion process was monitored in-situ using electrochemical impedance spectroscopy on samples exposed out-of-reactor with and without an applied stress. Post test, these autoclave samples were also metallographically examined.« less

Natural Strain

NASA Technical Reports Server (NTRS)

Freed, Alan D.

1997-01-01

Logarithmic strain is the preferred measure of strain used by materials scientists, who typically refer to it as the "true strain." It was Nadai who gave it the name "natural strain," which seems more appropriate. This strain measure was proposed by Ludwik for the one-dimensional extension of a rod with length l. It was defined via the integral of dl/l to which Ludwik gave the name "effective specific strain." Today, it is after Hencky, who extended Ludwik's measure to three-dimensional analysis by defining logarithmic strains for the three principal directions.

Detection of infectious bronchitis virus with the use of real-time quantitative reverse transcriptase-PCR and correlation with virus detection in embryonated eggs.

PubMed

Roh, Ha-Jung; Hilt, Deborah A; Jackwood, Mark W

2014-09-01

Real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assays have been used to detect the presence of challenge virus when the efficacy of infectious bronchitis virus (IBV) vaccine against field viruses is being experimentally evaluated. However, federal guidelines for licensing IBV vaccines indicate that challenge-virus detection following vaccination is to be conducted in embryonated eggs. In this study, we examined qRT-PCR data with the use of universal and type-specific primers and probe sets for IBV detection and compared those data with challenge-virus detection in embryonated eggs to determine if the two methods of evaluating vaccine efficacy are comparable. In addition, we tested the qRT-PCR assays on thermocyclers from two different manufacturers. We found the universal IBV primers and probe set to be comparable to challenge-virus detection in embryonated eggs. However, for some IBV types (Mass41 and Conn on the SmartCycler II and Ark, Mass41, Conn, and GA98 on the ABI 7500) the qRT-PCR assay was more sensitive than virus detection in embryonated eggs. This may simply be due to the universal IBV qRT-PCR assay being more sensitive than virus detection in eggs or to the assay detecting nucleic acid from nonviable virus. This finding is important and needs to be considered when evaluating challenge-virus detection for vaccination and challenge studies, because qRT-PCR could potentially identify positive birds that would otherwise be negative by virus detection in embryonated eggs; thus it could lead to a more stringent measure of vaccine efficacy. We also found that the IBV type-specific primers and probe sets designed in this study were in general less sensitive than the universal IBV primers and probe set. Only the Ark-DPI-spedcific assay on the SmartCycler II and the Ark-DPI-, Mass41-, and DE072/GA98- (for detection of GA98 virus only) specific assays on the ABI 7500 were comparable in sensitivity to virus detection in eggs. We found that a number of variables, including the virus type examined, primers and probe efficiency and stability, and assay conditions, including thermocycler platform, can affect the data obtained from qRT-PCR assays. These results indicate that qRT-PCR assays can be used to detect IBV challenge virus, but each assay, including the assay conditions and thermocycler, should be individually evaluated if those data are expected to be comparable to virus detection in embryonated eggs.

Completed Genome Sequences of Strains from 36 Serotypes of Salmonella

PubMed Central

Robertson, James; Yoshida, Catherine; Gurnik, Simone; Rankin, Marisa

2018-01-01

ABSTRACT We report here the completed closed genome sequences of strains representing 36 serotypes of Salmonella. These genome sequences will provide useful references for understanding the genetic variation between serotypes, particularly as references for mapping of raw reads or to create assemblies of higher quality, as well as to aid in studies of comparative genomics of Salmonella. PMID:29348347

Genome sequences of three strains of Aspergillus flavus for the biological control of Aflatoxin

USDA-ARS?s Scientific Manuscript database

The genomes of three strains of Aspergillus flavus with demonstrated utility for the biological control of aflatoxin were sequenced. These sequences were assembled with MIRA and annotated with Augustus using A. flavus strain 3357 (NCBI EQ963472) as a reference. Each strain had a genome of 36.3 to ...

Limitations of the Mycobacterium tuberculosis reference genome H37Rv in the detection of virulence-related loci.

PubMed

O'Toole, Ronan F; Gautam, Sanjay S

2017-10-01

The genome sequence of Mycobacterium tuberculosis strain H37Rv is an important and valuable reference point in the study of M. tuberculosis phylogeny, molecular epidemiology, and drug-resistance mutations. However, it is becoming apparent that use of H37Rv as a sole reference genome in analysing clinical isolates presents some limitations to fully investigating M. tuberculosis virulence. Here, we examine the presence of single locus variants and the absence of entire genes in H37Rv with respect to strains that are responsible for cases and outbreaks of tuberculosis. We discuss how these polymorphisms may affect phenotypic properties of H37Rv including pathogenicity. Based on our observations and those of other researchers, we propose that use of a single reference genome, H37Rv, is not sufficient for the detection and characterisation of M. tuberculosis virulence-related loci. We recommend incorporation of genome sequences of other reference strains, in particular, direct clinical isolates, in such analyses in addition to H37Rv. Copyright © 2017 Elsevier Inc. All rights reserved.

PFGE standard operating procedures for Listeria monocytogenes: harmonizing the typing of food and clinical strains in Europe.

PubMed

Michelon, Damien; Félix, Benjamin; Vingadassalon, Noemie; Mariet, Jean-François; Larsson, Jonas T; Møller-Nielsen, Eva; Roussel, Sophie

2015-03-01

Listeria monocytogenes is a foodborne pathogen responsible for a severe disease known as listeriosis. The European Centre for Disease Prevention and Control (ECDC) coordinates a network of national public health laboratories (NPHLs) in charge of typing clinical strains. In food, it is the European Union Reference Laboratory for L. monocytogenes (EURL Lm), which manages a network of National Reference Laboratories (NRLs). A pulsed-field gel electrophoresis (PFGE) standard operating procedure (EURL SOP) has been used routinely at the EURL Lm since 2007. The EURL Lm has recommended that NRLs use the EURL SOP, whereas the Statens Serum Institut (SSI), under contract for ECDC, requested that NPHLs use Halpins' SOP (HSOP) published in 2010 for the PulseNet USA network. An update of Halpins' SOP (uHSOP) was published in 2013. To facilitate the exchange of profiles among human and food European reference laboratories, it is crucial to ensure that the PFGE profiles obtained with these different SOPs are comparable. The aim here was to compare the EURL SOP with HSOP and uHSOP. The panel comprised 114 well-characterized SSI/EURL strains. All were characterized at the EURL using both the EURL SOP and uHSOP. Seventy of the 114 strains were also characterized at the SSI using HSOP. The EURL SOP and uHSOP produced indistinguishable combined (ApaI/AscI) profiles for the 114 strains tested. The EURL SOP and HSOP produced indistinguishable combined profiles for 69 of the 70 strains tested. One strain displayed for the AscI profile an additional low-intensity band at 184 kbp with HSOP. For this strain, SSI and EUR Lm had already observed the same profile from NPHLs and NRLs. However, this deviation is minor as it accounted for about 1% of all the 114 combined profiles. This study should facilitate the exchange of reproducible PFGE profiles among human and food reference laboratories.

Draft genome of a Xanthomonas perforans strain associated with pith necrosis.

PubMed

Torelli, Emanuela; Aiello, Dalia; Polizzi, Giancarlo; Firrao, Giuseppe; Cirvilleri, Gabriella

2015-02-01

Xanthomonas perforans causes bacterial spot of tomato and pepper. A genome draft of an unusual isolate (strain 4P1S2), differing in that it was associated with stem pith necrosis, was assembled from Illumina MiSeq sequencing data using the draft of X. perforans strain 91-118 as a reference. The resulting draft (accession number JRWW00000000) largely overlapped with the reference draft. In addition, the reads not mapping on the reference assembly were selected and used for a further assembly, that revealed a large putative plasmid. The analysis of the predicted proteins showed only few gene features that could be potentially implicated in the switch of a phytopathological behavior. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Adaptation of the Sensititre broth microdilution technique to antimicrobial susceptibility testing of Mycoplasma hyopneumoniae.

PubMed

Tanner, A C; Erickson, B Z; Ross, R F

1993-09-01

A broth microdilution technique is described for determining the antimicrobial susceptibility of Mycoplasma hyopneumoniae, using commercially prepared Sensititre plates. Twenty-five field isolates and two reference strains (J & 232), were tested against seven antimicrobials. Field isolates were tested in duplicate and reference strains, four times to estimate reproducibility. Ninety-seven percent of the duplicate MIC results for the field isolates were in agreement, or within one log2 dilution. Similar results were obtained with the reference strains. The isolates were susceptible to lincomycin-spectinomycin, tylosin and oxytetracycline or resistant to amoxycillin, apramycin and erythromycin. Susceptibility to furaltadone varied. This method retains the accuracy and reproducibility of broth MIC determinations, while avoiding the lengthy preparation of antimicrobial dilutions normally associated with more traditional methods.

[Use of multiple locus variable number tandem repeats analysis for the Brucella systematization].

PubMed

Kulakov, Iu K; Kovalev, D A; Misetova, E N; Golovneva, S I; Liapustina, L V; Zheludkov, M M

2012-01-01

The methods of molecular-genetic differentiation to strain level acquire increasing significance in the current system of struggle with brucellosis. MLVA (multiple locus variable number tandem repeats analysis) was selected for molecular-genetic differentiation to strain level and simultaneous establishment of the genetic relationship of investigated Brucella strains. The goal of this work was MLVA typing of three pathogenic Brucella species strains with the analysis of stability of chosen loci, discrimination power and concordance to conventional phenotypic methods of the Brucella differentiation for use in systematization of brucellosis causing agents. Twenty six Brucella strains representing reference (n = 15), vaccine (n = 2) and field strains of three pathogenic Brucella species were tested: B. melitensis (n = 3), B. abortus (n = 2), B. suis (n = 2), and isolates (n = 2) with unidentified taxonomic position using MLVA with 9 pairs primers on known variable loci of Brucella genome. The analysis of the stability of chosen loci, discrimination power on Hunter-Gaston discrimination index (HGDI) and consistency to phenotypic methods of identification was performed. MLVA was confirmed for the results of phenotypic methods of identification, stability of the chosen loci in majority reference, and vaccine strains with a high index of variability HGDI 0.9969 for all loci. A dendrogram was plotted on the basis of MLVA data on distributed Brucella strains in related clusters according to its taxonomic species and biovar positions and construction of 25 genotypes. B. melitensis strains formed cluster related to the reference strain of B. melitensis 63/9 biovar 2. Australian isolates of Brucella 83-4 and Brucella 83-6 isolated from rodents formed a cluster distant from other strains of Brucella. MLVA is a promising method for differentiation of Brucella strains with known and unresolved taxonomic status for their systematization and creation of MLVA genotype catalogue that will promote qualitative improvement of brucellosis surveillance system in Russia.

Establishing quality control ranges for antimicrobial susceptibility testing of Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus: a cornerstone to develop reference strains for Korean clinical microbiology laboratories.

PubMed

Hong, Sung Kuk; Choi, Seung Jun; Shin, Saeam; Lee, Wonmok; Pinto, Naina; Shin, Nari; Lee, Kwangjun; Hong, Seong Geun; Kim, Young Ah; Lee, Hyukmin; Kim, Heejung; Song, Wonkeun; Lee, Sun Hwa; Yong, Dongeun; Lee, Kyungwon; Chong, Yunsop

2015-11-01

Quality control (QC) processes are being performed in the majority of clinical microbiology laboratories to ensure the performance of microbial identification and antimicrobial susceptibility testing by using ATCC strains. To obtain these ATCC strains, some inconveniences are encountered concerning the purchase cost of the strains and the shipping time required. This study was focused on constructing a database of reference strains for QC processes using domestic bacterial strains, concentrating primarily on antimicrobial susceptibility testing. Three strains (Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus) that showed legible results in preliminary testing were selected. The minimal inhibitory concentrations (MICs) and zone diameters (ZDs) of eight antimicrobials for each strain were determined according to the CLSI M23. All resulting MIC and ZD ranges included at least 95% of the data. The ZD QC ranges obtained by using the CLSI method were less than 12 mm, and the MIC QC ranges extended no more than five dilutions. This study is a preliminary attempt to construct a bank of Korean QC strains. With further studies, a positive outcome toward cost and time reduction can be anticipated.

Molecular and Metallic Hydrogen

DTIC Science & Technology

1977-05-01

ANO ADDRESS IL PR09RAM 91.ME XT. CH ~1 The Rand Corporation 1700 Main Street Santa Monica, Ca. .90406 It. CONTROLLING OFFICE NAME AND ADDRE~SS Defense...VOLUME DATA OF STEWART FOR MOLECULAR HYDROGEN P V/V P V/V (bar) o(_ark . 0 1000 3923 0.632 196.1 0.928 5884 0.583 392.2 0.883 7845 0.549 588.4 0.847...will not a *ieve metailic-like densities despite possib* M tbar pressures because, as the result of shock hew, tng, m.’ ch of the pressure is thermal and

Half-life of Xe120

NASA Astrophysics Data System (ADS)

Phillips, A. A.; Andreoiu, C.; Ball, G. C.; Bandyopadhyay, D.; Behr, J. A.; Chupp, T. E.; Finlay, P.; Garrett, P. E.; Grinyer, G. F.; Hackman, G.; Hayden, M. E.; Hyland, B.; Nuss-Warren, S. R.; Pearson, M. R.; Schumaker, M. A.; Smith, M. B.; Svensson, C. E.; Tardiff, E. R.; Valiente-Dobón, J. J.; Warner, T.

2006-08-01

We have measured the half-life of Xe120 using a high-purity germanium (HPGe) detector to monitor the 176, 178, and 762 keV γ rays from Xe120 β+ decay. The result, 46±0.6 min, differs significantly from the value 40±1 min reported by Andersson [Ark. Fys. 28, 37 (1964)]. We have also measured the half-lives of Cs120 and I120 to be 60±0.7 s and 82.1±0.6 min, respectively, both of which are consistent with previous measurements.

Preliminary report on near-surface lignite occurrences, Cleveland County, Arkansas

USGS Publications Warehouse

Heermann, Stephen E.

1983-01-01

Four cross sections were constructed from lithologic descriptions of 43 drill holes in Cleveland County, Ark., in order to illustrate the occurrence of lignite and to relate the lignite beds to the regional stratigraphic framework. Of 43 holes drilled, 8 contained beds of lignite, but only two had beds greater than 30 in. thick. These beds are apparently lenticular and are restricted to the upper 60 ft. of the Cockfield Formation of the Claiborne Group of Middle Eocene age. The Cockfield Formation is at or near the surface west of the Saline River.

Tarnished Armor Erosion of Military Ethics

DTIC Science & Technology

1988-03-23

UNCLASSIFC-ED ?JSAWC MILITAFY STUD’ FS PROGRA.M PAPER Th4 vlev: expressed La th 028paPer are thane of the"athor antd do Vot Dece~ssacl 7 reflect the...NDTV7DUA1L STUDY PROjECT bitoF byAvIbit Lieutenant Colonel Bruce Allen M4a~ sOn , Eli Colonel Timothy Tatum ?roject Adv;iser DISTRIZUTtff STATU=~ At APPIOVeC...activity began to ener,. a od; de was associated with a personage who ultimately becare a ,a p4ayir in the ’ark intrigue. Soon there was connectivity, and

Evaluation of the Biolog automated microbial identification system

NASA Technical Reports Server (NTRS)

Klingler, J. M.; Stowe, R. P.; Obenhuber, D. C.; Groves, T. O.; Mishra, S. K.; Pierson, D. L.

1992-01-01

Biolog's identification system was used to identify 39 American Type Culture Collection reference taxa and 45 gram-negative isolates from water samples. Of the reference strains, 98% were identified to genus level and 76% to species level within 4 to 24 h. Identification of some authentic strains of Enterobacter, Klebsiella, and Serratia was unreliable. A total of 93% of the water isolates were identified.

Genome Sequencing of Steroid Producing Bacteria Using Ion Torrent Technology and a Reference Genome.

PubMed

Sola-Landa, Alberto; Rodríguez-García, Antonio; Barreiro, Carlos; Pérez-Redondo, Rosario

2017-01-01

The Next-Generation Sequencing technology has enormously eased the bacterial genome sequencing and several tens of thousands of genomes have been sequenced during the last 10 years. Most of the genome projects are published as draft version, however, for certain applications the complete genome sequence is required.In this chapter, we describe the strategy that allowed the complete genome sequencing of Mycobacterium neoaurum NRRL B-3805, an industrial strain exploited for steroid production, using Ion Torrent sequencing reads and the genome of a close strain as the reference. This protocol can be applied to analyze the genetic variations between closely related strains; for example, to elucidate the point mutations between a parental strain and a random mutagenesis-derived mutant.

Evaluation of Pyrrolidonyl Arylamidase Activity in Staphylococcus delphini.

PubMed

Compton, Samantha T; Kania, Stephen A; Robertson, Amy E; Lawhon, Sara D; Jenkins, Stephen G; Westblade, Lars F; Bemis, David A

2017-03-01

Clinical reference textbooks lack data for pyrrolidonyl arylamidase (PYR) activity in Staphylococcus delphini This study evaluated PYR activities of 21 S. delphini strains by reference broth, rapid disc, and rapid slide methods. Species and subgroup identifications were confirmed by nucleic acid-based methods and included nine group A and 12 group B strains. Testing by rapid PYR methods with products from four manufacturers was performed at two testing locations, and, with the exception of one strain tested at one location using reagents from one manufacturer, each S. delphini strain tested positive for PYR activity. Therefore, PYR may be a useful single-test adjunct for distinguishing Staphylococcus aureus from S. delphini and other members of the Staphylococcus intermedius group. Copyright © 2017 American Society for Microbiology.

3D Mechanical Models of Crustal Deformation and the Effect of Erosion on the Strain Pattern in SE Alaska

NASA Astrophysics Data System (ADS)

Barker, A. D.; Koons, P. O.; Upton, P.; Hallet, B.

2008-12-01

Employing 3D mechanical modeling to investigate the susceptibility of strain patterns to distinct erosion conditions we have identified a strong connection between surface erosion and strain localization and vertical motion of crustal material. The specific model geometry and boundary conditions are relevant to the dynamic St. Elias orogen of SE Alaska, but the general results and interpretations are universal. To illustrate the effect of erosion we compare results to a reference model without imposed erosion. We consider the crustal response to boundary conditions representing erosion scenarios: 1) regional erosion (~1 mm a-1 over a region ~600 km on a side) and 2) focused incision (~6 mm a-1 in valleys ~10 km wide and 50-100 km long). Whereas regional erosion mimics broader scale mass wasting and periglacial weathering, focused incision represents efficient erosion confined to valley systems similar to the massive Bering, Malaspina and Bagley glaciers of the St. Elias range. Using these boundary conditions we demonstrate significant localization of strain and crustal uplift beneath the sites of erosion. We also show the strain localization pattern adjusts to spatial shifts in erosion arising from substantial (order of 100km) glacial advance or retreat. The magnitude of the strain is higher in each erosion model compared to the reference model. The difference of the strain magnitude between erosion models and reference model depends on the location of the imposed erosion: crustal strain localize most when the forethrust daylights in the zone being eroded. Sustained focused erosion decreases the overall crustal strength beneath the site of erosion due to thinning of the strong brittle crust. Strain naturally concentrates within the weakened zone. Upward advection of warm crust causes further weakening and thereby leads to a tectonic aneurysm.

Minimum inhibitory (MIC) and minimum microbicidal concentration (MMC) of polihexanide and triclosan against antibiotic sensitive and resistant Staphylococcus aureus and Escherichia coli strains

PubMed Central

Assadian, Ojan; Wehse, Katrin; Hübner, Nils-Olaf; Koburger, Torsten; Bagel, Simone; Jethon, Frank; Kramer, Axel

2011-01-01

Background: An in-vitro study was conducted investigating the antimicrobial efficacy of polihexanide and triclosan against clinical isolates and reference laboratory strains of Staphylococcus aureus and Escherichia coli. Methods: The minimal inhibitory concentration (MIC) and the minimal microbicidal concentration (MMC) were determined following DIN 58940-81 using a micro-dilution assay and a quantitative suspension test following EN 1040. Polihexanide was tested in polyethylene glycol 4000, triclosan in aqueous solutions. Results: Against all tested strains the MIC of polihexanide ranged between 1–2 µg/mL. For triclosan the MICs varied depending on strains ranging between 0.5 µg/mL for the reference strains and 64 µg/mL for two clinical isolates. A logRF >5 without and logRF >3 with 0.2% albumin burden was achieved at 0.6 µg/mL triclosan. One exception was S. aureus strain H-5-24, where a triclosan concentration of 0.6 µg/mL required 1 minute without and 10 minutes with albumin burden to achieve the same logRFs. Polihexanide achieved a logRF >5 without and logRF >3 with albumin burden at a concentration of 0.6 µg/mL within 30 sec. The exception was the North-German epidemic MRSA strain, were an application time of 5 minutes was required. Conclusion: The clinical isolates of E. coli generally showed higher MICs against triclosan, both in the micro-dilution assay as well in the quantitative suspension test than comparable reference laboratory strains. For polihexanide and triclosan strain dependant susceptibility was shown. However, both antimicrobial compounds are effective when used in concentrations common in practice. PMID:22242087

Fusion of Three-Dimensional Echocardiographic Regional Myocardial Strain with Cardiac Computed Tomography for Noninvasive Evaluation of the Hemodynamic Impact of Coronary Stenosis in Patients with Chest Pain.

PubMed

Mor-Avi, Victor; Patel, Mita B; Maffessanti, Francesco; Singh, Amita; Medvedofsky, Diego; Zaidi, S Javed; Mediratta, Anuj; Narang, Akhil; Nazir, Noreen; Kachenoura, Nadjia; Lang, Roberto M; Patel, Amit R

2018-06-01

Combined evaluation of coronary stenosis and the extent of ischemia is essential in patients with chest pain. Intermediate-grade stenosis on computed tomographic coronary angiography (CTCA) frequently triggers downstream nuclear stress testing. Alternative approaches without stress and/or radiation may have important implications. Myocardial strain measured from echocardiographic images can be used to detect subclinical dysfunction. The authors recently tested the feasibility of fusion of three-dimensional (3D) echocardiography-derived regional resting longitudinal strain with coronary arteries from CTCA to determine the hemodynamic significance of stenosis. The aim of the present study was to validate this approach against accepted reference techniques. Seventy-eight patients with chest pain referred for CTCA who also underwent 3D echocardiography and regadenoson stress computed tomography were prospectively studied. Left ventricular longitudinal strain data (TomTec) were used to generate fused 3D displays and detect resting strain abnormalities (RSAs) in each coronary territory. Computed tomographic coronary angiographic images were interpreted for the presence and severity of stenosis. Fused 3D displays of subendocardial x-ray attenuation were created to detect stress perfusion defects (SPDs). In patients with stenosis >25% in at least one artery, fractional flow reserve was quantified (HeartFlow). RSA as a marker of significant stenosis was validated against two different combined references: stenosis >50% on CTCA and SPDs seen in the same territory (reference standard A) and fractional flow reserve < 0.80 and SPDs in the same territory (reference standard B). Of the 99 arteries with no stenosis >50% and no SPDs, considered as normal, 19 (19%) had RSAs. Conversely, with stenosis >50% and SPDs, RSAs were considerably more frequent (17 of 24 [71%]). The sensitivity, specificity, and accuracy of RSA were 0.71, 0.81, and 0.79, respectively, against reference standard A and 0.83, 0.81, and 0.82 against reference standard B. Fusion of CTCA and 3D echocardiography-derived resting myocardial strain provides combined displays, which may be useful in determination of the hemodynamic or functional impact of coronary abnormalities, without additional ionizing radiation or stress testing. Copyright © 2018 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.

Identification of clinical isolates of Aspergillus, including cryptic species, by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

PubMed

Vidal-Acuña, M Reyes; Ruiz-Pérez de Pipaón, Maite; Torres-Sánchez, María José; Aznar, Javier

2017-12-08

An expanded library of matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been constructed using the spectra generated from 42 clinical isolates and 11 reference strains, including 23 different species from 8 sections (16 cryptic plus 7 noncryptic species). Out of a total of 379 strains of Aspergillus isolated from clinical samples, 179 strains were selected to be identified by sequencing of beta-tubulin or calmodulin genes. Protein spectra of 53 strains, cultured in liquid medium, were used to construct an in-house reference database in the MALDI-TOF MS. One hundred ninety strains (179 clinical isolates previously identified by sequencing and the 11 reference strains), cultured on solid medium, were blindy analyzed by the MALDI-TOF MS technology to validate the generated in-house reference database. A 100% correlation was obtained with both identification methods, gene sequencing and MALDI-TOF MS, and no discordant identification was obtained. The HUVR database provided species level (score of ≥2.0) identification in 165 isolates (86.84%) and for the remaining 25 (13.16%) a genus level identification (score between 1.7 and 2.0) was obtained. The routine MALDI-TOF MS analysis with the new database, was then challenged with 200 Aspergillus clinical isolates grown on solid medium in a prospective evaluation. A species identification was obtained in 191 strains (95.5%), and only nine strains (4.5%) could not be identified at the species level. Among the 200 strains, A. tubingensis was the only cryptic species identified. We demonstrated the feasibility and usefulness of the new HUVR database in MALDI-TOF MS by the use of a standardized procedure for the identification of Aspergillus clinical isolates, including cryptic species, grown either on solid or liquid media. © The Author 2017. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Alignment verification procedures

NASA Technical Reports Server (NTRS)

Edwards, P. R.; Phillips, E. P.; Newman, J. C., Jr.

1988-01-01

In alignment verification procedures each laboratory is required to align its test machines and gripping fixtures to produce a nearly uniform tensile stress field on an un-notched sheet specimen. The blank specimens (50 mm w X 305 mm l X 2.3 mm th) supplied by the coordinators were strain gauged. Strain gauge readings were taken at all gauges (n = 1 through 10). The alignment verification procedures are as follows: (1) zero all strain gauges while specimen is in a free-supported condition; (2) put strain-gauged specimen in the test machine so that specimen front face (face 1) is in contact with reference jaw (standard position of specimen), tighten grips, and at zero load measure strains on all gauges. (epsilon sub nS0 is strain at gauge n, standard position, zero load); (3) with specimen in machine and at a tensile load of 10 kN measure strains (specimen in standard position). (Strain = epsilon sub nS10); (4) remove specimen from machine. Put specimen in machine so that specimen back face (face 2) is in contact with reference jaw (reverse position of specimen), tighten grips, and at zero load measure strains on all gauges. (Strain - epsilon sub nR0); and (5) with specimen in machine and at tensile load of 10 kN measure strains (specimen in reverse position). (epsilon sub nR10 is strain at gauge n, reverse position, 10 kN load).

Detection of knockdown resistance mutations in the common bed bug, Cimex lectularius (Hemiptera: Cimicidae), in Australia.

PubMed

Dang, Kai; Toi, Cheryl S; Lilly, David G; Bu, Wenjun; Doggett, Stephen L

2015-07-01

Pyrethroid resistance in the common bed bug, Cimex lectularius L., has been reported worldwide. An important resistance mechanism is via knockdown resistance (kdr) mutations, notably V419L and L925I. Information regarding this kdr-type resistance mechanism is unknown in Australia. This study aims to examine the status of kdr mutations in Australian C. lectularius strains. Several modern field-collected strains and museum-preserved reference collections of Australian C. lectularius were examined. Of the field strains (2007-2013), 96% had the known kdr mutations (L925I or both V419L/L925I). The 'Adelaide' strain (2013) and samples from the preserved reference collections (1994-2002) revealed no known kdr mutations. A novel mutation I936F was apparent in the insecticide-resistant 'Adelaide' strain, one strain from Perth (with L925I) and the majority of the reference collection specimens. The laboratory insecticide-resistant 'Sydney' strain showed a mixture of no kdr mutations (20%) and L925I (80%). The novel mutation I936F may be a kdr mutation but appeared to contribute less resistance to the pyrethroids than the V419L and L925I mutations. The detection of high frequencies of kdr mutations indicates that kdr-type resistance is widespread across Australia. Hence, there should be a reduced reliance on pyrethroid insecticides and an integrated management approach for the control of C. lectularius infestations. © 2014 Society of Chemical Industry.

Nucleic Acid Homologies Among Oxidase-Negative Moraxella Species

PubMed Central

Johnson, John L.; Anderson, Robert S.; Ordal, Erling J.

1970-01-01

The deoxyribonucleic acid (DNA) base composition and DNA homologies of more than 40 strains of oxidase-negative Moraxella species were determined. These bacteria have also been identified as belonging to the Mima-Herellea-Acinetobacter group and the Bacterium anitratum group, as well as to several other genera including Achromobacter and Alcaligenes. The DNA base content of these strains ranged from 40 to 46% guanine plus cytosine. DNA–DNA competition experiments distinguished five groups whose members were determined by showing 50% or more homology to one of the reference strains: B. anitratum type B5W, Achromobacter haemolyticus var. haemolyticus, Alcaligenes haemolysans, Achromobacter metalcaligenes, and Moraxella lwoffi. A sixth group comprised those strains showing less than 50% homology to any of the reference strains. Negligible homology was found between strains of oxidase-negative and oxidase-positive Moraxella species in DNA–DNA competition experiments. However, evidence of a distant relationship between the two groups was obtained in competition experiments by using ribosomal ribonucleic acid. PMID:5413826

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

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

Ahn, Tae-Hyuk; Chai, Juanjuan; Pan, Chongle

Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis. Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic readsmore » to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. In conclusion, the algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains. Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org.« less

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

DOE PAGES

Ahn, Tae-Hyuk; Chai, Juanjuan; Pan, Chongle

2014-09-29

Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis. Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic readsmore » to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. In conclusion, the algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains. Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org.« less

Resonant nonlinear ultrasound spectroscopy

DOEpatents

Johnson, Paul A.; TenCate, James A.; Guyer, Robert A.; Van Den Abeele, Koen E. A.

2001-01-01

Components with defects are identified from the response to strains applied at acoustic and ultrasound frequencies. The relative resonance frequency shift .vertline..DELTA..function./.function..sub.0.vertline., is determined as a function of applied strain amplitude for an acceptable component, where .function..sub.0 is the frequency of the resonance peak at the lowest amplitude of applied strain and .DELTA..function. is the frequency shift of the resonance peak of a selected mode to determine a reference relationship. Then, the relative resonance frequency shift .vertline..DELTA..function./.function..sub.0 is determined as a function of applied strain for a component under test, where fo .function..sub.0 the frequency of the resonance peak at the lowest amplitude of applied strain and .DELTA..function. is the frequency shift of the resonance peak to determine a quality test relationship. The reference relationship is compared with the quality test relationship to determine the presence of defects in the component under test.

Taxonomic study of extreme halophilic archaea isolated from the "Salar de Atacama", Chile.

PubMed

Lizama, C; Monteoliva-Sánchez, M; Prado, B; Ramos-Cormenzana, A; Weckesser, J; Campos, V

2001-11-01

A large number of halophilic bacteria were isolated in 1984-1992 from the Atacama Saltern (North of Chile). For this study 82 strains of extreme halophilic archaea were selected. The characterization was performed by using the phenotypic characters including morphological, physiological, biochemical, nutritional and antimicrobial susceptibility test. The results, together with those from reference strains, were subjected to numerical analysis, using the Simple Matching (S(SM)) coefficient and clustered by the unweighted pair group method of association (UPGMA). Fifteen phena were obtained at an 70% similarity level. The results obtained reveal a high diversity among the halophilic archaea isolated. Representative strains from the phena were chosen to determine their DNA base composition and the percentage of DNA-DNA similarity compared to reference strains. The 16S rRNA studies showed that some of these strains constitutes a new taxa of extreme halophilic archaea.

Numerical taxonomy of phenanthrene-degrading bacteria isolated from the Chesapeake Bay

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

West, P.A.; Okpokwasili, G.C.; Brayton, P.R.

1984-11-01

Phenanthrene-degrading bacteria were isolated from Chesapeake Bay samples by the use of a solid medium which had been overlaid with an ethanol solution of phenanthrene before inoculation. Eighteen representative strains of phenanthrene-degrading bacteria with 21 type and reference bacteria were examined for 123 characteristics representing physiological, biochemical, and nutritional properties. Relationships between strains were computed with several similarity coefficients. The phenogram constructed by unweighted-pair-group arithmetic average linkage and use of the simple Jaccard (S/sub J/) coefficient was used to identify seven phena. Phenanthrene-degrading bacteria were identified as Vibrio parahaemolyticus and Vibrio fluvialis by their clustering with type and reference strains.more » Several phenanthrene-degrading bacteria resembled Enterobacteriaceae family members, although some Vibrio-like phenanthrene degraders could not be identified. 22 references, 1 figure, 2 tables.« less

MALDI-TOF MS Distinctly Differentiates Nontypable Haemophilus influenzae from Haemophilus haemolyticus

PubMed Central

Zhang, Huifang; Zhang, Yongchan; Gao, Yuan; Xu, Li; Lv, Jing; Wang, Yingtong; Zhang, Jianzhong; Shao, Zhujun

2013-01-01

Nontypable Haemophilus influenzae (NTHi) and Haemophilus haemolyticus exhibit different pathogenicities, but to date, there remains no definitive and reliable strategy for differentiating these strains. In this study, we evaluated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a potential method for differentiating NTHi and H. haemolyticus. The phylogenetic analysis of concatenated 16S rRNA and recombinase A (recA) gene sequences, outer membrane protein P6 gene sequencing and single-gene PCR were used as reference methods. The original reference database (ORD, provided with the Biotyper software) and new reference database (NRD, extended with Chinese strains) were compared for the evaluation of MALDI-TOF MS. Through a search of the ORD, 76.9% of the NTHi (40/52) and none of the H. haemolyticus (0/20) strains were identified at the species level. However, all NTHi and H. haemolyticus strains used for identification were accurately recognized at the species level when searching the NRD. From the dendrogram clustering of the main spectra projections, the Chinese and foreign H. influenzae reference strains were categorized into two distinct groups, and H. influenzae and H. haemolyticus were also separated into two categories. Compared to the existing methods, MALDI-TOF MS has the advantage of integrating high throughput, accuracy and speed. In conclusion, MALDI-TOF MS is an excellent method for differentiating NTHi and H. haemolyticus. This method can be recommended for use in appropriately equipped laboratories. PMID:23457514

Natural Strain

NASA Technical Reports Server (NTRS)

Freed, Alan D.

1995-01-01

The purpose of this paper is to present a consistent and thorough development of the strain and strain-rate measures affiliated with Hencky. Natural measures for strain and strain-rate, as I refer to them, are first expressed in terms of of the fundamental body-metric tensors of Lodge. These strain and strain-rate measures are mixed tensor fields. They are mapped from the body to space in both the Eulerian and Lagrangian configurations, and then transformed from general to Cartesian fields. There they are compared with the various strain and strain-rate measures found in the literature. A simple Cartesian description for Hencky strain-rate in the Lagrangian state is obtained.

Design and quantification of an extreme winter storm scenario for emergency preparedness and planning exercises in California

USGS Publications Warehouse

Dettinger, M.D.; Martin, Ralph F.; Hughes, M.; Das, T.; Neiman, P.; Cox, D.; Estes, G.; Reynolds, D.; Hartman, R.; Cayan, D.; Jones, L.

2012-01-01

The USGS Multihazards Project is working with numerous agencies to evaluate and plan for hazards and damages that could be caused by extreme winter storms impacting California. Atmospheric and hydrological aspects of a hypothetical storm scenario have been quantified as a basis for estimation of human, infrastructure, economic, and environmental impacts for emergency-preparedness and flood-planning exercises. In order to ensure scientific defensibility and necessary levels of detail in the scenario description, selected historical storm episodes were concatentated to describe a rapid arrival of several major storms over the state, yielding precipitation totals and runoff rates beyond those occurring during the individual historical storms. This concatenation allowed the scenario designers to avoid arbitrary scalings and is based on historical occasions from the 19th and 20th Centuries when storms have stalled over the state and when extreme storms have arrived in rapid succession. Dynamically consistent, hourly precipitation, temperatures, barometric pressures (for consideration of storm surges and coastal erosion), and winds over California were developed for the so-called ARkStorm scenario by downscaling the concatenated global records of the historical storm sequences onto 6- and 2-km grids using a regional weather model of January 1969 and February 1986 storm conditions. The weather model outputs were then used to force a hydrologic model to simulate ARkStorm runoff, to better understand resulting flooding risks. Methods used to build this scenario can be applied to other emergency, nonemergency and non-California applications. ?? 2011 The Author(s).

Mammalian collection on Noah's Ark: the effects of beauty, brain and body size.

PubMed

Frynta, Daniel; Šimková, Olga; Lišková, Silvie; Landová, Eva

2013-01-01

The importance of today's zoological gardens as the so-called "Noah's Ark" grows as the natural habitat of many species quickly diminishes. Their potential to shelter a large amount of individuals from many species gives us the opportunity to reintroduce a species that disappeared in nature. However, the selection of animals to be kept in zoos worldwide is highly selective and depends on human decisions driven by both ecological criteria such as population size or vulnerability and audience-driven criteria such as aesthetic preferences. Thus we focused our study on the most commonly kept and bred animal class, the mammals, and we asked which factors affect various aspects of the mammalian collection of zoos. We analyzed the presence/absence, population size, and frequency per species of each of the 123 mammalian families kept in the worldwide zoo collection. Our aim was to explain these data using the human-perceived attractiveness of mammalian families, their body weight, relative brain size and species richness of the family. In agreement with various previous studies, we found that the body size and the attractiveness of mammals significantly affect all studied components of the mammalian collection of zoos. There is a higher probability of the large and attractive families to be kept. Once kept, these animals are presented in larger numbers in more zoos. On the contrary, the relative mean brain size only affects the primary selection whether to keep the family or not. It does not affect the zoo population size or the number of zoos that keep the family.

Radiology on Board the PLA(N) Peace Ark Hospital Ship During a Humanitarian Medical Relief Mission to the Philippines.

PubMed

Ren, Ai-Jun; Sun, Tao; Wang, Hai-Wei; Ge, He-Quan; Ye, Hong-Jun

2016-02-01

From November 24 to December 10, 2013, the Chinese People's Liberation Army Navy [PLA(N)] hospital ship Peace Ark was deployed to the Leyte Gulf in the Philippines to provide humanitarian medical relief in Tacloban after Typhoon Haiyan. The purpose of this study was to assess the radiological services aboard the ship to provide guidance for future missions. A retrospective review was performed on a cohort of 109 patients who underwent digital radiography (DR) and 59 patients who underwent computed tomography (CT) scans during a 16-day period during a humanitarian medical relief mission to the Philippines. Patient demographics, DR findings, and CT findings were analyzed. The mean age of the 109 DR patients was 39.7 years for the 64 males and 43.7 years for the 45 females. A total of 148 DR examinations were performed of the chest (n=109), extremities (n=35), and spine (n=4). The mean age of the 59 CT patients was 43.8 years for the 32 males and 49.1 years for the 27 females. A total of 72 CT scans were performed of the head and neck (n=36), thorax (n=24), abdomen (n=5), spine (n=4), and extremities (n=3). The imaging findings mainly included disaster-related and non-disaster-related fractures, pulmonary tuberculosis, pulmonary infection, acute brain infarction, intracranial hematoma, and occupying lesions. Analysis of radiological services during a humanitarian medical relief mission to the Philippines provided meaningful information for future humanitarian medical relief missions.

Selection and evaluation of Malaysian Bacillus spp. strains as potential probiotics in cultured tiger grouper (Epinephelus fuscoguttatus).

PubMed

Yasin, Ina-salwany Md; Razak, Nabilah Fatin; Natrah, F M I; Harmin, Sharr Azni

2016-07-01

A total of 58 Gram-positive bacteria strains were isolated from the marine environment and screened for potential probiotics for disease prevention and improving the productivity of tiger grouper Epinephelus fuscoguttatus larvae and juveniles. The bacteria were identified as Bacillus licheniformis, B. subtilis, B. circulans, B. sphaericus, B. cereus, Brevibacillus brevis, Corynebacterium propinquum, Leifsonia aquatica and Paenibacillus macerans. Only 24 strains showed antagonistic activities against four pathogenic strains; Vibrio alginolyticus, V. harveyi, V. parahaemolyticus and Aeromonas hydrophila, where two of the Bacillus strains, B12 and B45 demonstrated intermediate to highest level of inhibitory activity against these pathogenic strains, respectively. Further assessment by co-culture assay showed that Bacillus strain B12 exhibited a total inhibition of V. alginolyticus, while B45 strain displayed no inhibitory activity. Mixed culture of Bacillus B12 and B45 strains to outcompete V. alginolyticus was observed at a cell density of 10(7) CFU ml(-1). Molecular identification and phylogenetic tree analysis have categorized Bacillus strain B12 to the reference strains GQ340480 and JX290193 of? B. amyloliquafaciens, and Bacillus strain B45 with a reference strain JF496522 of B. subtilis. Safety tests of probionts by intraperitoneal administration of B12 and B45 strains at cell densities of 103, 105 and 10(7) CFU ml(-1) revealed no abnormalities and cent percent survival for healthy Epinephelus fuscoguttatus juveniles within 15 days of experimental period. Overall, the study revealed that Bacillus B12 strain possesses tremendous probiotic potential that could be used as a feed supplement in tiger grouper diets. ?

Current Awareness and Use of the Strain Echocardiography in Routine Clinical Practices: Result of a Nationwide Survey in Korea.

PubMed

Lee, Ju-Hee; Park, Jae-Hyeong; Park, Seung Woo; Kim, Woo-Shik; Sohn, Il Suk; Chin, Jung Yeon; Cho, Jung Sun; Youn, Ho-Joong; Jung, Hae Ok; Lee, Sun Hwa; Kim, Seong-Hwan; Chung, Wook-Jin; Shim, Chi Young; Jeong, Jin-Won; Choi, Eui-Young; Rim, Se-Joong; Kim, Jang-Young; Kim, Kye Hun; Shin, Joon-Han; Kim, Dae-Hee; Jeon, Ung; Choi, Jung Hyun; Kim, Yong-Jin; Joo, Seung Jae; Kim, Ki-Hong; Cho, Kyoung Im; Cho, Goo-Yeong

2017-09-01

Because conventional echocardiographic parameters have several limitations, strain echocardiography has often been introduced in clinical practice. However, there are also obstacles in using it in clinical practice. Therefore, we wanted to find the current status of awareness on using strain echocardiography in Korea. We conducted a nationwide survey to evaluate current use and awareness of strain echocardiography from the members of the Korean Society of Echocardiography. We gathered total 321 questionnaires from 25 cardiology centers in Korea. All participants were able to perform or interpret echocardiographic examinations. All participating institutions performed strain echocardiography. Most of our study participants (97%) were aware of speckle tracking echocardiography and 185 (58%) performed it for clinical and research purposes. Two-dimensional strain echocardiography was the most commonly used modality and left ventricle (LV) was the most commonly used cardiac chamber (99%) for clinical purposes. Most of the participants (89%) did not think LV strain can replace LV ejection fraction (LVEF) in their clinical practice. The common reasons for not performing routine use of strain echocardiography was diversity of strain measurements and lack of normal reference value. Many participants had a favorable view of the future of strain echocardiography. Most of our study participants were aware of strain echocardiography, and all institutions performed strain echocardiography for clinical and research purposes. However, they did not think the LV strain values could replace LVEF. The diversity of strain measurements and lack of normal reference values were common reasons for not using strain echocardiography in clinical practice.

Copy Number Heterogeneity, Large Origin Tandem Repeats, and Interspecies Recombination in Human Herpesvirus 6A (HHV-6A) and HHV-6B Reference Strains

PubMed Central

Roychoudhury, Pavitra; Makhsous, Negar; Hanson, Derek; Chase, Jill; Krueger, Gerhard; Xie, Hong; Huang, Meei-Li; Saunders, Lindsay; Ablashi, Dharam; Koelle, David M.; Cook, Linda; Jerome, Keith R.

2018-01-01

ABSTRACT Quantitative PCR is a diagnostic pillar for clinical virology testing, and reference materials are necessary for accurate, comparable quantitation between clinical laboratories. Accurate quantitation of human herpesvirus 6A/B (HHV-6A/B) is important for detection of viral reactivation and inherited chromosomally integrated HHV-6A/B in immunocompromised patients. Reference materials in clinical virology commonly consist of laboratory-adapted viral strains that may be affected by the culture process. We performed next-generation sequencing to make relative copy number measurements at single nucleotide resolution of eight candidate HHV-6A and seven HHV-6B reference strains and DNA materials from the HHV-6 Foundation and Advanced Biotechnologies Inc. Eleven of 17 (65%) HHV-6A/B candidate reference materials showed multiple copies of the origin of replication upstream of the U41 gene by next-generation sequencing. These large tandem repeats arose independently in culture-adapted HHV-6A and HHV-6B strains, measuring 1,254 bp and 983 bp, respectively. The average copy number measured was between 5 and 10 times the number of copies of the rest of the genome. We also report the first interspecies recombinant HHV-6A/B strain with a HHV-6A backbone and a >5.5-kb region from HHV-6B, from U41 to U43, that covered the origin tandem repeat. Specific HHV-6A reference strains demonstrated duplication of regions at U1/U2, U87, and U89, as well as deletion in the U12-to-U24 region and the U94/U95 genes. HHV-6A/B strains derived from cord blood mononuclear cells from different laboratories on different continents with fewer passages revealed no copy number differences throughout the viral genome. These data indicate that large origin tandem duplications are an adaptation of both HHV-6A and HHV-6B in culture and show interspecies recombination is possible within the Betaherpesvirinae. IMPORTANCE Anything in science that needs to be quantitated requires a standard unit of measurement. This includes viruses, for which quantitation increasingly determines definitions of pathology and guidelines for treatment. However, the act of making standard or reference material in virology can alter its very accuracy through genomic duplications, insertions, and rearrangements. We used deep sequencing to examine candidate reference strains for HHV-6, a ubiquitous human virus that can reactivate in the immunocompromised population and is integrated into the human genome in every cell of the body for 1% of people worldwide. We found large tandem repeats in the origin of replication for both HHV-6A and HHV-6B that are selected for in culture. We also found the first interspecies recombinant between HHV-6A and HHV-6B, a phenomenon that is well known in alphaherpesviruses but to date has not been seen in betaherpesviruses. These data critically inform HHV-6A/B biology and the standard selection process. PMID:29491155

Genome assemblies for 11 Yersinia pestis strains isolated in the Caucasus region

DOE PAGES

Zhgenti, Ekaterine; Johnson, Shannon L.; Davenport, Karen W.; ...

2015-09-17

Yersinia pestis, the causative agent of plague, is endemic to the Caucasus region but few reference strain genome sequences from that region are available. We present the improved draft or finished assembled genomes from 11 strains isolated in the nation of Georgia and surrounding countries.

Pico-strain multiplexed fiber optic sensor array operating down to infra-sonic frequencies.

PubMed

Littler, Ian C M; Gray, Malcolm B; Chow, Jong H; Shaddock, Daniel A; McClelland, David E

2009-06-22

An integrated sensor system is presented which displays passive long range operation to 100 km at pico-strain (pepsilon) sensitivity to low frequencies (4 Hz) in wavelength division multiplexed operation with negligible cross-talk (better than -75 dB). This has been achieved by pre-stabilizing and multiplexing all interrogation lasers for the sensor array to a single optical frequency reference. This single frequency reference allows each laser to be locked to an arbitrary wavelength and independently tuned, while maintaining suppression of laser frequency noise. With appropriate packaging, such a multiplexed strain sensing system can form the core of a low frequency accelerometer or hydrophone array.

Molecular and biological characterization of the 5 human-bovine rotavirus (WC3)-based reassortant strains of the pentavalent rotavirus vaccine, RotaTeq (registered)

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

Matthijnssens, Jelle; Joelsson, Daniel B.; Warakomski, Donald J.

RotaTeq (registered) is a pentavalent rotavirus vaccine that contains five human-bovine reassortant strains (designated G1, G2, G3, G4, and P1) on the backbone of the naturally attenuated tissue culture-adapted parental bovine rotavirus (BRV) strain WC3. The viral genomes of each of the reassortant strains were completely sequenced and compared pairwise and phylogenetically among each other and to human rotavirus (HRV) and BRV reference strains. Reassortants G1, G2, G3, and G4 contained the VP7 gene from their corresponding HRV parent strains, while reassortants G1 and G2 also contained the VP3 gene (genotype M1) from the HRV parent strain. The P1 reassortantmore » contained the VP4 gene from the HRV parent strain and all the other gene segments from the BRV WC3 strain. The human VP7s had a high level of overall amino acid identity (G1: 95-99%, G2: 94-99% G3: 96-100%, G4: 93-99%) when compared to those of representative rotavirus strains of their corresponding G serotypes. The VP4 of the P1 reassortant had a high identity (92-97%) with those of serotype P1A[8] HRV reference strains, while the BRV VP7 showed identities ranging from 91% to 94% to those of serotype G6 HRV strains. Sequence analyses of the BRV or HRV genes confirmed that the fundamental structure of the proteins in the vaccine was similar to those of the HRV and BRV references strains. Sequences analyses showed that RotaTeq (registered) exhibited a high degree of genetic stability as no mutations were identified in the material of each reassortant, which undergoes two rounds of replication cycles in cell culture during the manufacturing process, when compared to the final material used to fill the dosing tubes. The infectivity of each of the reassortant strains of RotaTeq (registered) , like HRV strains, did not require the presence of sialic acid residues on the cell surface. The molecular and biologic characterization of RotaTeq (registered) adds to the significant body of clinical data supporting the consistent efficacy, immunogenicity, and safety of RotaTeq (registered) .« less

Calibration of Nu-Instruments Noblesse multicollector mass spectrometers for argon isotopic measurements using a newly developed reference gas

USGS Publications Warehouse

Coble, M.A.; Grove, M.; Calvert, A.T.

2011-01-01

The greatest challenge limiting 40Ar/39Ar multicollection measurements is the availability of appropriate standard gasses to intercalibrate detectors. In particular, use of zoom lens ion-optics to steer and focus ion beams into a fixed detector array (i.e., Nu Instruments Noblesse) makes intercalibration of multiple detectors challenging because different ion-optic tuning conditions are required for optimal peak shape and sensitivity at different mass stations. We have found that detector efficiency and mass discrimination are affected by changes in ion-optic tuning parameters. Reliance upon an atmospheric Ar standard to calibrate the Noblesse is problematic because there is no straightforward way to relate atmospheric 40Ar and 36Ar to measurements of 40Ar and 39Ar if they are measured on separate detectors. After exploring alternative calibration approaches, we have concluded that calibration of the Noblesse is best performed using exactly the same source, detector, and ion-optic tuning settings as those used in routine 40Ar/39Ar analysis. To accomplish this, we have developed synthetic reference gasses containing 40Ar, 39Ar and 38Ar produced by mixing gasses derived from neutron-irradiated sanidine with an enriched 38Ar spike. We present a new method for calibrating the Noblesse based on use of both atmospheric Ar and the synthetic reference gasses. By combining atmospheric Ar and synthetic reference gas in different ways, we can directly measure 40Ar/39Ar, 38Ar/39Ar, and 36Ar/39Ar correction factors over ratios that vary from 0.5 to 460. These correction factors are reproducible to better than ??0.5??? (2?? standard error) over intervals spanning ~24h but can vary systematically by ~4% over 2weeks of continuous use when electron multiplier settings are held constant. Monitoring this variation requires daily calibration of the instrument. Application of the calibration method to 40Ar/39Ar multicollection measurements of widely used sanidine reference materials ACs-2, FCs-2, and TCs-2 demonstrate that calculated 40Ar*/39ArK can be accurately corrected to yield model 40Ar/39Ar ages consistent with those reported by Earthtime 40Ar/39Ar laboratories. Replicate analyses of 8-12 single-crystal sanidine ages are reproduced to within 1-2??? (2?? standard error) under optimal analytical conditions. This calibration technique is applicable over a wide range of isotopic ratios and signal sizes. Finally, the reference gas has the added advantage of facilitating straightforward characterization of electron multiplier dead time over a wide dynamic range. ?? 2011 Elsevier B.V.

High variability in strain estimation errors when using a commercial ultrasound speckle tracking algorithm on tendon tissue.

PubMed

Fröberg, Åsa; Mårtensson, Mattias; Larsson, Matilda; Janerot-Sjöberg, Birgitta; D'Hooge, Jan; Arndt, Anton

2016-10-01

Ultrasound speckle tracking offers a non-invasive way of studying strain in the free Achilles tendon where no anatomical landmarks are available for tracking. This provides new possibilities for studying injury mechanisms during sport activity and the effects of shoes, orthotic devices, and rehabilitation protocols on tendon biomechanics. To investigate the feasibility of using a commercial ultrasound speckle tracking algorithm for assessing strain in tendon tissue. A polyvinyl alcohol (PVA) phantom, three porcine tendons, and a human Achilles tendon were mounted in a materials testing machine and loaded to 4% peak strain. Ultrasound long-axis cine-loops of the samples were recorded. Speckle tracking analysis of axial strain was performed using a commercial speckle tracking software. Estimated strain was then compared to reference strain known from the materials testing machine. Two frame rates and two region of interest (ROI) sizes were evaluated. Best agreement between estimated strain and reference strain was found in the PVA phantom (absolute error in peak strain: 0.21 ± 0.08%). The absolute error in peak strain varied between 0.72 ± 0.65% and 10.64 ± 3.40% in the different tendon samples. Strain determined with a frame rate of 39.4 Hz had lower errors than 78.6 Hz as was the case with a 22 mm compared to an 11 mm ROI. Errors in peak strain estimation showed high variability between tendon samples and were large in relation to strain levels previously described in the Achilles tendon. © The Foundation Acta Radiologica 2016.

Characterization of a variant strain of Norwalk virus from a food-borne outbreak of gastroenteritis on a cruise ship in Hawaii.

PubMed Central

Herwaldt, B L; Lew, J F; Moe, C L; Lewis, D C; Humphrey, C D; Monroe, S S; Pon, E W; Glass, R I

1994-01-01

A gastroenteritis outbreak affecting at least 217 (41%) of 527 passengers on a cruise ship was caused by a variant strain of Norwalk virus (NV) that is related to but distinct from the prototype NV strain. Consumption of fresh-cut fruit served at two buffets was significantly associated with illness (P < or = 0.01), and a significant dose-response relationship was evident between illness and the number of various fresh-cut fruit items eaten. Seven (58%) of 12 paired serum specimens from ill persons demonstrated at least fourfold rises in antibody response to recombinant NV capsid antigen. A 32-nm small round-structured virus was visualized by electron microscopy in 4 (29%) of 14 fecal specimens, but none of the 8 specimens that were examined by an enzyme immunoassay for NV antigen demonstrated antigen. Four (40%) of 10 fecal specimens were positive by reverse transcriptase-PCR by using primer pairs selected from the polymerase region of NV. In a 145-bp region, the PCR product shared only 72% nucleotide sequence identity with the reference NV strain and 77% nucleotide sequence identity with Southampton virus but shared 95% nucleotide sequence identity with UK2 virus, a United Kingdom reference virus strain. In addition, the outbreak virus was serotyped as UK2 virus by solid-phase immune electron microscopy. The genetic and antigenic divergence of the outbreak strain from the reference NV strain highlights the need for more broadly reactive diagnostic assays and for improved understanding of the relatedness of the NV group of agents. Images PMID:8027335

Possibility of the real-time dynamic strain field monitoring deduced from GNSS data: case study of the 2016 Kumamoto earthquake sequence

NASA Astrophysics Data System (ADS)

Ohta, Y.; Ohzono, M.; Takahashi, H.; Kawamoto, S.; Hino, R.

2017-12-01

A large and destructive earthquake (Mjma 7.3) occurred on April 15, 2016 in Kumamoto region, southwestern Japan. This earthquake was accompanied approximately 32 s later by an M 6 earthquake in central Oita region, which hypocenter located 80 km northeast from the hypocenter of the mainshock of the Kumamoto earthquake. This triggered earthquake also had the many aftershocks in and around the Oita region. It is important to understand how to occur such chain-reacted earthquake sequences. We used the 1Hz dual-frequency phase and range data from GEONET in Kyushu island. The data were processed using GIPSY-OASIS (version 6.4). We adopoted kinematic PPP strategy for the coordinate estimation. The reference GPS satellite orbit and 5 s clock information were obtained using the CODE product. We also applied simple sidereal filter technique for the estimated time series. Based on the obtained 1Hz GNSS time series, we estimated the areal strain and principle strain field using the method of the Shen et al. (1996). For the assessment of the dynamic strain, firstly we calculated the averaged absolute value of areal strain field between 60-85s after the origin time of the mainshock of the Kumamoto earthquake which was used as the "reference" static strain field. Secondly, we estimated the absolute value of areal strain in each time step. Finally, we calculated the strain ratio in each time step relative to the "reference". Based on this procedure, we can extract the spatial and temporal characteristic of the dynamic strain in each time step. Extracted strain ratio clearly shows the spatial and temporal dynamic strain characteristic. When an attention is paid to a region of triggered Oita earthquake, the timing of maximum dynamic strain ratio in the epicenter just corresponds to the origin time of the triggered event. It strongly suggested that the large dynamic strain may trigger the Oita event. The epicenter of the triggered earthquake located within the geothermal region. In the geothermal region, the crustal materials are more sensitive to stress perturbations, and the earthquakes are more easily triggered compared with other typical regions. Our result also suggested that the real-time strain field monitoring may be useful information for the understanding of the possibility of the remotely triggered earthquake in the future.

Aeromonas aquariorum Is Widely Distributed in Clinical and Environmental Specimens and Can Be Misidentified as Aeromonas hydrophila▿†

PubMed Central

Aravena-Román, Max; Harnett, Gerald B.; Riley, Thomas V.; Inglis, Timothy J. J.; Chang, Barbara J.

2011-01-01

Genotypic characterization of 215 Aeromonas strains (143 clinical, 52 environmental, and 20 reference strains) showed that Aeromonas aquariorum (60 strains, 30.4%) was the most frequently isolated species in clinical and water samples and could be misidentified as Aeromonas hydrophila by phenotypic methods. PMID:21697316

Cluster of tick-borne infections at Fort Chaffee, Arkansas: Rickettsiae and Borrelia burgdorferi in ixodid ticks.

PubMed

Kardatzke, J T; Neidhardt, K; Dzuban, D P; Sanchez, J L; Azad, A F

1992-07-01

Human intrusion into pristine habitats increases the likelihood of acquiring infectious agents from potentially infective ticks. As part of a larger human serological investigation into tick-borne illnesses, 3,000 ixodid ticks were collected during May, August, and November 1990 at Fort Chaffee, Arkansas. Ticks were examined to determine whether they harbor rickettsiae, ehrlichiae, and Borrelia burgdorferi, and to assess relationship to human exposure to tick-borne infections at Fort Chaffee, Ark. The overall tick infection rates with SFG rickettsiae, B. burgdorferi, and ehrlichiae were 4.8, 0.1, and 0.3%, respectively.

A Vectorized ’Nearest-Neighbors’ Algorithm of Order N Using a Monotonic Logical Grid

DTIC Science & Technology

1985-05-29

Computational Phy’sics 0 4 May 29 , 1985 This work was supported by the Office of Naval Research. . ~ Q~JUN 1719851- * NAVAL RESEARCH LABORATORY * lit...YE ’.ARK:NGS UNCLASSIFIED_______________ _____ K -. A R, ~ CA7,ON 4, 71CO1, 3 :)-S7R,9U-ON AdA,.A3:L ’Y OF REPOR7Io - EC..ASi.’ CA27 ON., DOWNGAZING...Year. Month. Day) 5 PAGE COUNT Interim FROM -____ Toi__ 1985 May 29 50 𔄀 SuPPILSMENTARY NOTATION This work was supported by the Office of Naval

Science for decision making: Transmitting hazard science using catastrophic scenarios

NASA Astrophysics Data System (ADS)

Wein, A.

2010-12-01

The ShakeOut and ARkStorm scenarios are scientifically-based, multi-disciplinary efforts to describe the damages and consequences of large, but plausible, natural disasters for use in emergency management and other planning. The ShakeOut earthquake scenario, completed in 2008, posits the occurrence of a major earthquake on the southern San Andreas Fault. It was used by more than 5,000 emergency personnel in a California statewide exercise, and it underpins the Federal Emergency Management Agency’s (FEMA) Catastrophic Plan for Southern California. The ARkStorm winter storm scenario, to be completed in 2010, posits the occurrence of a statewide disaster like the storm that occurred during 1861-1862. The ARkStorm scenario will culminate with two planning summits comprised of federal and state agencies, because such an event would exceed local response and recovery capabilities. This talk will address the following questions that are critical to transmitting science for decision making with examples and observations from the two scenarios: 1) Who are the end users of the scenarios, what types of decisions can scenarios inform, and how are stakeholders engaged? 2) What forms of information and processes work best to communicate and apply the hazard science? 3) What are the challenges of using science in decision making? 4) What future directions shall we pursue? From my perspective as coordinator of economic consequences analyses for the two scenarios, I will share insights to these questions. Framing stakeholder decisions in terms of scale (e.g., household to State) and disaster phase (e.g., emergency response, recovery, and mitigation) allows us to align methods of stakeholder engagement with stakeholder decision making. For these regional-scale scenarios, the methods of engagement included stakeholder participation in project vision, scenario construction workshops, presentations, conferences, and emergency response and recovery exercises. Champions (self-motivated individuals who took on leadership roles in their communities or industrial sectors), customized and localized analyses, and workshops enhanced the use of hazard science. Examples from the two scenarios will be used to illustrate these points. We experienced several significant challenges in using science to enhance emergency management exercises and community decision making. Some of these challenges include 1) adapting scientific results to exercise format; 2) the special needs of recovery exercises, which can mimic response exercises only with limited success, because recovery is tactical while response is strategic; 3) staff turnover; and 4) limited resources. An important future direction will be to leverage our in-depth knowledge of scenarios, multi-disciplinary network, and stakeholder relations to integrate knowledge about multiple hazards to better inform risk-based decision making for all hazards.

Nonlinear Finite Element Analysis of a General Composite Shell

DTIC Science & Technology

1988-12-01

strain I Poisson’s ratio ix I I iI I I 1 Total potential energy a Normal stress rShear stress Rotational terms Distance from midsurface e ,Y ,0 Rotations...respectively 0 0 Subscript "e" indicates element reference Subscript "g" indicates global reference Superscript "o" indicates midsurface values...surface strains and rotations are small, and displacements away from the midsurface are restricted by the Kirchhoff-Love hypotheses [3]. With these

Isolation and Characterization of Lytic Properties of Bacteriophages Specific for M. haemolytica Strains.

PubMed

Urban-Chmiel, Renata; Wernicki, Andrzej; Stęgierska, Diana; Dec, Marta; Dudzic, Anna; Puchalski, Andrzej

2015-01-01

The objective of this study was isolation and morphological characterization of temperate bacteriophages obtained from M. haemolytica strains and evaluation of their lytic properties in vitro against M. haemolytica isolated from the respiratory tract of calves. The material for the study consisted of the reference strain M. haemolytica serotype 1 (ATCC®) BAA-410™, reference serotypes A1, A2, A5, A6, A7, A9 and A11, and wild-type isolates of M. haemolytica. Bacteriophages were induced from an overnight bacterial starter culture of all examined M. haemolytica strains treated with mitomycin C. The lytic properties and host ranges were determined by plaque assays. The morphology of the bacteriophages was examined in negative-stained smears with 5% uranyl acetate solution using a transmission electron microscope. The genetic analysis of the bacteriophages was followed by restriction analysis of bacteriophage DNA. This was followed by analysis of genetic material by polymerase chain reaction (PCR). Eight bacteriophages were obtained, like typical of the families Myoviridae, Siphoviridae and Podoviridae. Most of the bacteriophages exhibited lytic properties against the M. haemolytica strains. Restriction analysis revealed similarities to the P2-like phage obtained from the strain M. haemolytica BAA-410. The most similar profiles were observed in the case of bacteriophages φA1 and φA5. All of the bacteriophages obtained were characterized by the presence of additional fragments in the restriction profiles with respect to the P2-like reference phage. In the analysis of PCR products for the P2-like reference phage phi-MhaA1-PHL101 (DQ426904) and the phages of the M. haemolytica serotypes, a 734-bp phage PCR product was obtained. The primers were programmed in Primer-Blast software using the structure of the sequence DQ426904 of reference phage PHL101. The results obtained indicate the need for further research aimed at isolating and characterizing bacteriophages, including sequence analysis of selected fragments. Moreover, standardization of methods for obtaining them in order to eliminate M. haemolytica bacteria involved in the etiopathogenesis of BRDC is essential.

Changes in Central Walker Lane Strain Accommodation near Bridgeport, California; as told by the Stanislaus Group

NASA Astrophysics Data System (ADS)

Carlson, C. W.; Pluhar, C. J.; Glen, J. M.; Farner, M. J.

2012-12-01

Accommodating ~20-25% of the dextral-motion between the Pacific and North American plates the Walker Lane is represented as an elongate, NW oriented, region of active tectonics positioned between the northwesterly-translating Sierra Nevada microplate and the east-west extension of the Basin and Range. This region of transtension is being variably accommodated on regional-scale systems of predominantly strike-slip faulting. At the western edge of the central Walker Lane (ca. 38°-39°N latitude) is a region of crustal-scale blocks bounded by wedge-shaped depositional-basins and normal-fault systems, here defined as the west-central Walker Lane (WCWL). Devoid of obvious strike-slip faulting, the presence of tectonic-block vertical-axis rotations in the WCWL represents unrecognized components of dextral-shearing and/or changes of strain-accommodation over time. We use paleomagnetic reference directions for Eureka Valley Tuff (EVT) members of the late Miocene Stanislaus Group as spatial and temporal markers for documentation of tectonic-block vertical-axis rotations near Bridgeport, CA. Study-site rotations revealed discrete rotational domains of mean vertical-axis rotation ranging from ~10°-30° with heterogeneous regional distribution. Additionally, the highest measured magnitudes of vertical-axis rotation (~50°-60° CW) define a 'Region of High Strain' that includes the wedge-shaped Bridgeport Valley (Basin). This study revealed previously-unrecognized tectonic rotation of reference direction sites from prior studies for two (By-Day and Upper) of the three members of the EVT, resulting in under-estimates of regional strain accommodation by these studies. Mean remanent directions and virtual geomagnetic poles utilized in our study yielded a recalculated reference direction for the By-Day member of: Dec.=353.2°; Inc.= 43.7°; α95=10.1, in agreement with new measurements in the stable Sierra Nevada. This recalculated direction confirmed the presence of previously unrecognized reference site rotations, and provided an additional reference direction for determining vertical-axis rotation magnitudes. We present a kinematic model based on mean rotation magnitudes of ~30° CW for the Sweetwater Mountains and Bodie Hills that accounts for rotational-strain accommodation of dextral shear in the WCWL since the late Miocene. This model considers rotational magnitudes, paleostrain indicators, edge-effects, and strain-accommodating structures of rotating crustal blocks to represent changes in regional strain accommodation over time. The results and models presented here elucidate the complicated and evolving nature of the WCWL, and further understanding of variations in strain accommodation for the Walker Lane.

[Cases of menstrual toxic shock syndrome in the Czech Republic in 1997-2011].

PubMed

Petrás, P; Machová, I; Rysková, L; Prásil, P

2011-11-01

To determine toxigenicity and other basic characteristics of 47 strains of Staphylococcus aureus referred to the National Reference Laboratory for Staphylococci (NRL) as suspected causative agents of menstrual toxic shock syndrome (MTSS). S. aureus strains were collected from 11 administrative regions of the Czech Republic in 1997-2011. The diagnosis was based on phenotypic (reverse latex agglutination test) and genotypic (polymerase chain reaction) methods. Forty-four S. aureus strains were producers of toxic shock syndrome toxin 1 (TSST-1), either alone or in combination with staphylococcal enterotoxin. Three strains only produced enterotoxin (B, C, and H). MTSS is a serious multisystem disease. In this study, MTSS often had a severe course requiring intensive care. All MTSS patients used vaginal tampons that had been identified in the literature as a risk factor for MTSS. The case of MTSS in a 36-year-old woman caused by an enterotoxin H positive strain of S. aureus is probably the first to be reported in the world.

Identification and genetic characterization of unique HIV-1 A1/C recombinant strain in South Africa.

PubMed

Musyoki, Andrew M; Rakgole, Johnny N; Selabe, Gloria; Mphahlele, Jeffrey

2015-03-01

HIV isolates from South Africa are predominantly subtype C. Sporadic isolation of non-C strains has been reported mainly in cosmopolitan cities. HIV isolate j51 was recovered from a rural South African heterosexual female aged 51 years. Near full length amplification of the genome was attempted using PCR with primers targeting overlapping segments of the HIV genome. Analysis of 5593 bp (gag to vpu) at a bootstrap value greater than 70% found that all but the vpu gene was HIV-1 subtype A1. The vpu gene was assigned HIV-1 subtype C. The recombination breaking point was estimated at position 6035+/- 15 bp with reference to the beginning of the HXB2 reference strain. Isolate j51 revealed a unique genome constellation to previously reported recombinant strains with parental A/C backbones from South Africa though a common recombination with subtype C within the vpu gene. Identification of recombinant strains supports continued surveillance of HIV genetic diversity.

Mycobacterium massiliense BRA100 strain recovered from postsurgical infections: resistance to high concentrations of glutaraldehyde and alternative solutions for high level disinfection.

PubMed

Lorena, Nádia Suely de Oliveira; Pitombo, Marcos Bettini; Côrtes, Patrícia Barbur; Maya, Maria Cristina Araújo; Silva, Marlei Gomes da; Carvalho, Ana Carolina da Silva; Coelho, Fábrice Santana; Miyazaki, Neide Hiromi Tokumaru; Marques, Elizabeth Andrade; Chebabo, Alberto; Freitas, Andréa D'Avila; Lupi, Otília; Duarte, Rafael Silva

2010-10-01

To evaluate the minimum inhibitory concentration (MIC) of GTA against these microorganisms and alternative disinfectants for high-level disinfection (HLD). Reference mycobacteria and clinical M. massiliense strains were included in this study. Active cultures were submitted to susceptibility qualitative tests with GTA dilutions (ranging from 1.5% to 8%), and commercial orthophthaldehyde (OPA) and peracetic acid (PA)-based solutions, during the period of exposure as recommended by National Agency of Sanitary Surveillance for HLD. All reference and M. massiliense non-BRA100 strains, recovered from sputum, were susceptible to any GTA concentration, OPA and PA solutions. M. massiliense BRA100 strains presented MIC of 8% GTA and were susceptible to OPA and PA. M. massiliense BRA100 strain is resistant to high GTA concentrations (up to 7%), which proves that this product is non-effective against specific rapidly growing mycobacteria and should be substituted by OPA or PA-based solutions for HLD.

Genomic characterisation of Leptospira inadai serogroup Lyme isolated from captured rat in Brazil and comparative analysis with human reference strain.

PubMed

Moreno, Luisa Z; Miraglia, Fabiana; Loureiro, Ana P; Kremer, Frederico S; Eslabao, Marcus R; Dellagostin, Odir A; Lilenbaum, Walter; Vasconcellos, Silvio A; Heinemann, Marcos B; Moreno, Andrea M

2018-03-12

Leptospira inadai is classified as a species of the Leptospira intermediate group that has been poorly studied due to its apparent insignificance to human and animal health. Nevertheless, over the last two decades the species has been described in human cases in India and in carrier animals in Ecuador. Here, we present the first identification and genomic characterisation of L. inadai serogroup Lyme isolated from captured rodent in Brazil. Even though the M34/99 strain was not pathogenic for hamsters, it was able to establish renal colonisation. The M34/99 strain presented high similarity with L. inadai serogroup Lyme human reference indicating that animal strain could also infect humans, although it does not represent high risk of severe disease. An extrachromosomal sequence was also identified in M34/99 strain and presented high identity with previously described L. inadai phage LinZ_10, suggesting that phage-like extrachromosomal sequence may be another feature of this understudied species.

In Vitro Activity of the New Fluoroketolide Solithromycin (CEM-101) against a Large Collection of Clinical Neisseria gonorrhoeae Isolates and International Reference Strains, Including Those with High-Level Antimicrobial Resistance: Potential Treatment Option for Gonorrhea?

PubMed Central

Golparian, Daniel; Fernandes, Prabhavathi; Ohnishi, Makoto; Jensen, Jörgen S.

2012-01-01

Gonorrhea may become untreatable, and new treatment options are essential. We investigated the in vitro activity of the first fluoroketolide, solithromycin. Clinical Neisseria gonorrhoeae isolates and reference strains (n = 246), including the two extensively drug-resistant strains H041 and F89 and additional isolates with clinical cephalosporin resistance and multidrug resistance, were examined. The activity of solithromycin was mainly superior to that of other antimicrobials (n = 10) currently or previously recommended for gonorrhea treatment. Solithromycin might be an effective treatment option for gonorrhea. PMID:22354296

Molecular typing of Brucella melitensis endemic strains and differentiation from the vaccine strain Rev-1.

PubMed

Noutsios, Georgios T; Papi, Rigini M; Ekateriniadou, Loukia V; Minas, Anastasios; Kyriakidis, Dimitrios A

2012-03-01

In the present study forty-four Greek endemic strains of Br. melitensis and three reference strains were genotyped by Multi locus Variable Number Tandem Repeat (ML-VNTR) analysis based on an eight-base pair tandem repeat sequence that was revealed in eight loci of Br. melitensis genome. The forty-four strains were discriminated from the vaccine strain Rev-1 by Restriction Fragment Length Polymorphism (RFLP) and Denaturant Gradient Gel Electrophoresis (DGGE). The ML-VNTR analysis revealed that endemic, reference and vaccine strains are genetically closely related, while most of the loci tested (1, 2, 4, 5 and 7) are highly polymorphic with Hunter-Gaston Genetic Diversity Index (HGDI) values in the range of 0.939 to 0.775. Analysis of ML-VNTRs loci stability through in vitro passages proved that loci 1 and 5 are non stable. Therefore, vaccine strain can be discriminated from endemic strains by allele's clusters of loci 2, 4, 6 and 7. RFLP and DGGE were also employed to analyse omp2 gene and reveled different patterns among Rev-1 and endemic strains. In RFLP, Rev-1 revealed three fragments (282, 238 and 44 bp), while endemic strains two fragments (238 and 44 bp). As for DGGE, the electrophoretic mobility of Rev-1 is different from the endemic strains due to heterologous binding of DNA chains of omp2a and omp2b gene. Overall, our data show clearly that it is feasible to genotype endemic strains of Br. melitensis and differentiate them from vaccine strain Rev-1 with ML-VNTR, RFLP and DGGE techniques. These tools can be used for conventional investigations in brucellosis outbreaks.

Diversity and Antibiotic Susceptibility of Acinetobacter Strains From Milk Powder Produced in Germany

PubMed Central

Cho, Gyu-Sung; Li, Bo; Rostalsky, André; Fiedler, Gregor; Rösch, Niels; Igbinosa, Etinosa; Kabisch, Jan; Bockelmann, Wilhelm; Hammer, Philipp; Huys, Geert; Franz, Charles M. A. P.

2018-01-01

Forty-seven Acinetobacter spp. isolates from milk powder obtained from a powdered milk producer in Germany were investigated for their antibiotic resistance susceptibilities, in order to assess whether strains from food harbor multiple antibiotic resistances and whether the food route is important for dissemination of resistance genes. The strains were identified by 16S rRNA and rpoB gene sequencing, as well as by whole genome sequencing of selected isolates and their in silico DNA-DNA hybridization (DDH). Furthermore, they were genotyped by rep-PCR together with reference strains of pan-European groups I, II, and III strains of Acinetobacter baumannii. Of the 47 strains, 42 were identified as A. baumannii, 4 as Acinetobacter Pittii, and 1 as Acinetobacter calcoaceticus based on 16S rRNA gene sequencing. In silico DDH with the genome sequence data of selected strains and rpoB gene sequencing data suggested that the five non-A. baumannii strains all belonged to A. pittii, suggesting that the rpoB gene is more reliable than the 16S rRNA gene for species level identification in this genus. Rep-PCR genotyping of the A. baumannii strains showed that these could be grouped into four groups, and that some strains clustered together with reference strains of pan-European clinical group II and III strains. All strains in this study were intrinsically resistant toward chloramphenicol and oxacillin, but susceptible toward tetracycline, tobramycin, erythromycin, and ciprofloxacin. For cefotaxime, 43 strains (91.5%) were intermediate and 3 strains (6.4%) resistant, while 3 (6.4%) and 21 (44.7%) strains exhibited resistance to cefepime and streptomycin, respectively. Forty-six (97.9%) strains were susceptible to amikacin and ampicillin-sulbactam. Therefore, the strains in this study were generally not resistant to the clinically relevant antibiotics, especially tobramycin, ciprofloxacin, cefepime, and meropenem, suggesting that the food route probably poses only a low risk for multidrug resistant Acinetobacter strains or resistance genes. PMID:29636733

Phenotypic characterization and adhesive properties of vaginal Candida spp. strains provided by the CHU Farhat Hached (Sousse, Tunisia).

PubMed

Noumi, Emira; Snoussi, Mejdi; Noumi, Inès; Saghrouni, Fatma; Aouni, Mahjoub; Valentin, Eulogio

2015-01-01

Vulvovaginal candidiasis is a common infection among women worldwide, being Candida albicans the most commonly isolated species. Therefore, controlling this opportunistic yeast is one of the key factors for reducing nosocomial infection. We investigated several virulence properties of 28 vaginal strains of Candida isolated from Tunisian women suffering from vulvovaginitis. We also analyzed the virulence properties of a clinical Candida krusei strain and five Candida reference strains. Candida strains were subjected to microscopic analysis and culture in Candida ID2 chromogenic medium. The adhesive properties of these strains were estimated by the microtiter plate - the safranin-staining - and the Congo red agar (CRA) methods, for determining yeast ability to form biofilms on biomaterials used in urinary catheter manufacturing. Their potency to produce hydrolytic enzymes was also studied. Our results showed that nine out of the total studied strains produced phospholipase. In addition, very high protease activity was detected in 23 Candida strains. All Candida strains were beta-hemolytic and adhered to polystyrene microtiter plates in varying degrees. Two vaginal C. albicans strains were strongly adhesive to polystyrene and glass slides. Also, our results showed that vaginal Candida strains were more adhesive to the three tested materials than the reference strains. This study shows the presence of a range of virulence and adhesion factors in clinical isolates of vaginal Candida. Consequently, control and treatment of vaginal candidiasis as a means to prevent biofilm formation on urinary catheters is of crucial importance. Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

MALDI-TOF Mass Spectrometry for the Detection and Differentiation of Entamoeba histolytica and Entamoeba dispar

PubMed Central

Calderaro, Adriana; Piergianni, Maddalena; Buttrini, Mirko; Montecchini, Sara; Piccolo, Giovanna; Gorrini, Chiara; Rossi, Sabina; Chezzi, Carlo; Arcangeletti, Maria Cristina; Medici, Maria Cristina; De Conto, Flora

2015-01-01

Detection of Entamoeba histolytica and its differentiation from Entamoeba dispar is an important goal of the clinical parasitology laboratory. The aim of this study was the identification and differentiation of E. histolytica and E. dispar by MALDI-TOF MS, in order to evaluate the application of this technique in routine diagnostic practice. MALDI-TOF MS was applied to 3 amebic reference strains and to 14 strains isolated from feces that had been differentiated by molecular methods in our laboratory. Protein extracts from cultures of these strains (axenic cultures for the 3 reference strains and monoxenic cultures for the 14 field isolates) were analyzed by MALDI-TOF MS and the spectra obtained were analyzed by statistical software. Five peaks discriminating between E. histolytica and E. dispar reference strains were found by protein profile analysis: 2 peaks (8,246 and 8,303 Da) specific for E. histolytica and 3 (4,714; 5,541; 8,207 Da) for E. dispar. All clinical isolates except one showed the discriminating peaks expected for the appropriate species. For 2 fecal samples from which 2 strains (1 E. histolytica and 1 E. dispar) out of the 14 included in this study were isolated, the same discriminating peaks found in the corresponding isolated amebic strains were detected after only 12h (E. histolytica) and 24h (E. dispar) of incubation of the fecal samples in Robinson’s medium without serum. Our study shows that MALDI-TOF MS can be used to discriminate between E. histolytica and E. dispar using in vitro xenic cultures and it also could have potential for the detection of these species in clinical samples. PMID:25874612

Complete genome sequence analysis of novel human bocavirus reveals genetic recombination between human bocavirus 2 and human bocavirus 4.

PubMed

Khamrin, Pattara; Okitsu, Shoko; Ushijima, Hiroshi; Maneekarn, Niwat

2013-07-01

Epidemiological surveillance of human bocavirus (HBoV) was conducted on fecal specimens collected from hospitalized children with diarrhea in Chiang Mai, Thailand in 2011. By partial sequence analysis of VP1 gene, an unusual strain of HBoV (CMH-S011-11), was initially identified as HBoV4. The complete genome sequence of CMH-S011-11 was performed and analyzed further to clarify whether it was a recombinant strain or a new HBoV variant. Analysis of complete genome sequence revealed that the coding sequence starting from NS1, NP1 to VP1/VP2 was 4795 nucleotides long. Interestingly, the nucleotide sequence of NS1 gene of CMH-S011-11 was most closely related to the HBoV2 reference strains detected in Pakistan, which contradicted to the initial genotyping result of the partial VP1 region in the previous study. In addition, comparison of NP1 nucleotide sequence of CMH-S011-11 with those of other HBoV1-4 reference strains also revealed a high level of sequence identity with HBoV2. On the other hand, nucleotide sequence of VP1/VP2 gene of CMH-S011-11 was most closely related to those of HBoV4 reference strains detected in Nigeria. The overall full-length sequence analysis revealed that this CMH-S011-11 was grouped within HBoV4 species, but located in a separate branch from other HBoV4 prototype strains. Recombination analysis revealed that CMH-S011-11 was the result of recombination between HBoV2 and HBoV4 strains with the break point located near the start codon of VP2. Copyright © 2013 Elsevier B.V. All rights reserved.

High-resolution melt-curve analysis of random amplified polymorphic DNA (RAPD-HRM) for the characterisation of pathogenic leptospires: intra-serovar divergence, inter-serovar convergence, and evidence of attenuation in Leptospira reference collections.

PubMed

Tulsiani, S M; Craig, S B; Graham, G C; Cobbold, R C; Dohnt, M F; Burns, M-A; Jansen, C C; Leung, L K-P; Field, H E; Smythe, L D

2010-07-01

High-resolution melt-curve analysis of random amplified polymorphic DNA (RAPD-HRM) is a novel technology that has emerged as a possible method to characterise leptospires to serovar level. RAPD-HRM has recently been used to measure intra-serovar convergence between strains of the same serovar as well as inter-serovar divergence between strains of different serovars. The results indicate that intra-serovar heterogeneity and inter-serovar homogeneity may limit the application of RAPD-HRM in routine diagnostics. They also indicate that genetic attenuation of aged, high-passage-number isolates could undermine the use of RAPD-HRM or any other molecular technology. Such genetic attenuation may account for a general decrease seen in titres of rabbit hyperimmune antibodies over time. Before RAPD-HRM can be further advanced as a routine diagnostic tool, strains more representative of the wild-type serovars of a given region need to be identified. Further, RAPD-HRM analysis of reference strains indicates that the routine renewal of reference collections, with new isolates, may be needed to maintain the genetic integrity of the collections.

World Reference Center for Arboviruses.

DTIC Science & Technology

1981-02-01

CTF isolates including clones of the Florio strain. Representatives of the genera Rotavirus , cytoplasmic polyhedrosis virus group, and plant reovirus...group were supplied as purified virus preparations; and the virus strains respectively included a human rotavirus isolated from a fecal sample, Bom x...strain - CTF), Rotavirus (human rotavirus - HR), cytoplasmic polyhedrosis group ( Bombyx mori cytoplasmic polyhedrosis -CPV), and plant reovirus group

Genome Sequence of Actinobacillus seminis Strain ATCC 15768, a Reference Strain of Ovine Pathogens That Causes Infections in Reproductive Organs

PubMed Central

Negrete-Abascal, Erasmo; Montes-Garcia, Fernando; Vaca-Pacheco, Sergio; Leyto-Gil, Abraham M.; Fragoso-Garcia, Edgar; Carvente-Garcia, Roberto; Perez-Agueros, Sandra; Castelan-Sanchez, Hugo G.; Garcia-Molina, Alejandra; Villamar, Tomas E.; Sánchez-Alonso, Patricia

2018-01-01

ABSTRACT The draft genome sequence of Actinobacillus seminis strain ATCC 15768 is reported here. The genome comprises 22 contigs corresponding to 2.36 Mb with 40.7% G+C content and contains several genes related to virulence, including a putative RTX protein. PMID:29326222

Whole-genome sequence of Escherichia coli serotype O157:H7 strain EDL932 (ATCC 43894)

USDA-ARS?s Scientific Manuscript database

Escherichia coli serotype O157:H7 EDL 933 is a ground beef isolate associated with a 1983 hemorrhagic colitis outbreak. Considered the prototype O157:H7 strain, its derived genome sequence is a standard reference strain for comparative genomic studies of Shiga toxin-producing E. coli (STEC). Here we...

[Genetic Characterization of Hemagglutinin on Measles Virus Epidemic Strain Genotype H1a in Liaoning Province (China) from 1997 to 2014].

PubMed

Wang, Yan; Ma, Yan; Xu, Xiaoting; Hao, Shuang; Han, Yue; Yao, Wenqing; Zhao, Zhuo

2015-07-01

To wished to characterize the hemagglutinin (H) gene of the measles virus epidemic strain H1a in Liaoning Province (China) from 1997-2014 to provide a basis for the control and elimination of measles. All 63 measles virus strains were the H1a genotype. Fragments of the H gene (1854 nucleotides) and nucleoprotein (N) gene (450 nucleotides) were amplified by reverse transcription-polymerase chain reaction (RT-PCR) and the PCR products sequenced and analyzed. Phylogenetic-trees were constructed with reference strains of the genotype-H measles virus downloaded from GenBank, including Chinese measles virus strains isolated in 1993-1994 and the vaccine reference strains S-191 and C-47. Sixty-three strains of the measles virus in 1997-2014 belonged to genotype H1a. The mean evolutionary rate for gene N-450 was higher than that for the H gene. All 63 strains of the measles virus were mutated from: serine (Ser S) to asparagine (Asn N) in the 240th amino acid; arginine (Arg R) to glycine (Gly G) in the 243th; and tyrosine (Tyr Y) to Asn N in the 481th amino acid. All measles virus strains in cluster 2 were mutated from proline (Pro P) to leucine (Leu L) in the 397th amino acid. The other neutralization sites showed no apparent difference when comparing the nucleotides/amino acids of the H gene of S191 vaccine strains.

Methodology of mycobacteria tuberculosis bacteria detection by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Zyubin, A.; Lavrova, A.; Manicheva, O.; Dogonadze, M.; Tsibulnikova, A.; Samusev, I.

2018-01-01

We have developed a methodology for the study of deactivated strains of Mycobacterium tuberculosis. Strains of the Beijing species obtained from pulmonary patient secrete (XDR strain) and reference strain (H37Rv) were investigated by Raman spectrometry with He-Ne (632,8 nm) laser excitation source. As a result of the research, the optimal experimental parameters have been obtained to get spectra of mycolic acids, which are part of the cell wall of mycobacteria.

Digital antimicrobial susceptibility testing using the MilliDrop technology.

PubMed

Jiang, L; Boitard, L; Broyer, P; Chareire, A-C; Bourne-Branchu, P; Mahé, P; Tournoud, M; Franceschi, C; Zambardi, G; Baudry, J; Bibette, J

2016-03-01

We present the MilliDrop Analyzer (MDA), a droplet-based millifluidic system for digital antimicrobial susceptibility testing (D-AST), which enables us to determine minimum inhibitory concentrations (MICs) precisely and accurately. The MilliDrop technology was validated by using resazurin for fluorescence readout, for comparison with standard methodology, and for conducting reproducibility studies. In this first assessment, the susceptibility of a reference Gram-negative strain Escherichia coli ATCC 25922 to gentamicin, chloramphenicol, and nalidixic acid were tested by the MDA, VITEK®2, and broth microdilution as a reference standard. We measured the susceptibility of clinically relevant Gram-positive strains of Staphylococcus aureus to vancomycin, including vancomycin-intermediate S. aureus (VISA), heterogeneous vancomycin-intermediate S. aureus (hVISA), and vancomycin-susceptible S. aureus (VSSA) strains. The MDA provided results which were much more accurate than those of VITEK®2 and standard broth microdilution. The enhanced accuracy enabled us to reliably discriminate between VSSA and hVISA strains.

Unmet Needs of Caregivers of Patients Referred to a Dementia Care Program

PubMed Central

Jennings, Lee A.; Reuben, David B.; Evertson, Leslie Chang; Serrano, Katherine S.; Ercoli, Linda; Grill, Joshua; Chodosh, Joshua; Tan, Zaldy; Wenger, Neil S.

2014-01-01

Background/Objectives Caregiver strain and low self-efficacy for managing dementia-related problems are common among those caring for patients with dementia, but the level of unmet need and relation to provider type has not been well characterized. Design Cross-sectional observational cohort Setting Urban academic medical center Participants Caregivers of community-dwelling adults with dementia referred to the program Measurements Caregivers were surveyed and completed the Patient Health Questionnaire (PHQ-9) about themselves, the Modified Caregiver Strain Index, the Neuropsychiatric Inventory Questionnaire, which measures patient symptom severity and related caregiver distress, and a 9-item caregiver self-efficacy scale developed for the study. Results Of 307 patient and caregiver dyads surveyed over a one year period, 32% of caregivers reported confidence in managing dementia-related problems, 19% knew how to access community services to help provide care, and 28% agreed the patient’s provider helped them work through dementia care problems. Thirty-eight percent reported high levels of caregiver strain, and 15% reported moderate to severe depressive symptoms. Caregivers of patients referred by geriatricians more often reported having a healthcare professional to help work through dementia care problems than those referred by internists, family physicians, or other specialists, but self-efficacy did not differ. Low caregiver self-efficacy was associated with higher caregiver strain, more caregiver depressive symptoms, and caring for a patient with more severe behavioral symptoms. Conclusion Most caregivers perceived inadequate support from the patient’s provider in managing dementia-related problems, reported strain, and had low confidence in managing caregiving. New models of care are needed to address the complex care needs of patients with dementia and their caregivers. PMID:25688604

Right ventricular beneficial effects of beta adrenergic receptor kinase inhibitor (betaARKct) gene transfer in a rat model of severe pressure overload.

PubMed

Molina, Ezequiel J; Gupta, Dipin; Palma, Jon; Gaughan, John P; Macha, Mahender

2009-06-01

Heart failure is associated with abnormalities in betaAR cascade regulation, calcium cycling, expression of inflammatory mediators and apoptosis. Adenoviral mediated gene transfer of betaARKct has beneficial indirect effects on these pathologic processes upon the left ventricular myocardium. The concomitant biochemical changes that occur in the right ventricle have not been well characterized. Sprague-Dawley rats underwent aortic banding and were followed by echocardiography. After a decrease in fractional shortening of 25% from baseline, intracoronary injection of adenoviral-betaARKct (n=14) or adenoviral-beta-galactosidase (control, n=13) was performed. Rats were randomly euthanized on post-operative day 7, 14 or 21. Protein analysis including RV myocardial levels of betaARKct, betaARK1, SERCA(2a), inflammatory tissue mediators (IL-1, IL-6 and TNF-alpha), apoptotic markers (bax and bak), and MAP kinases (jnk, p38 and erk) was performed. ANOVA was employed for group comparison. Adenoviral-betaARKct treated animals showed increased expression of betaARKct and decreased levels of betaARK1 compared with controls. This treatment group also demonstrated normalization of SERCA(2a) expression and decreased levels of the inflammatory markers IL-1, IL-6 and TNF-alpha. The pro-apoptotic markers bax and bak were similarly improved. Ventricular levels of the MAP kinase jnk were increased. Differences were most significant 7 days after gene transfer, but the majority of these changes persisted at 21 days. These results suggest that attenuation of the pathologic mechanisms of beta adrenergic receptor desensitization, SERCA(2a) expression, inflammation and apoptosis, not only occur in the left ventricle but also in the right ventricular myocardium after intracoronary gene transfer of betaARKct during heart failure.

SAFRR AND Physics-Based Scenarios: The Power of Scientifically Credible Stories

NASA Astrophysics Data System (ADS)

Cox, D. A.; Jones, L.

2015-12-01

USGS's SAFRR (Science Application for Risk Reduction) Project and its predecessor, the Multi Hazards Demonstration Project, uses the latest earth science to develop scenarios so that communities can improve disaster resilience. SAFRR has created detailed physics-based natural-disaster scenarios of a M7.8 San Andreas earthquake in southern California (ShakeOut), atmospheric-river storms rivaling the Great California Flood of 1862 (ARkStorm), a Tohoku-sized earthquake and tsunami in the eastern Aleutians (SAFRR Tsunami), and now a M7.05 quake on the Hayward Fault in the San Francisco Bay area (HayWired), as novel ways of providing science for decision making. Each scenario is scientifically plausible, deterministic, and large enough to demand attention but not too large to be believable. The scenarios address interacting hazards, requiring involvement of multiple science disciplines and user communities. The scenarios routinely expose hitherto unknown or ignored vulnerabilities, most often in cascading effects missed when impacts are considered in isolation. They take advantage of story telling to provide decision makers with clear explanations and justifications for mitigation and preparedness actions, and have been used for national-to-local disaster response exercises and planning. Effectiveness is further leveraged by downscaling the scenarios to local levels. For example, although the ARkStorm scenario describes state-scale events and has been used that way by NASA and the Navy, SAFRR also partnered with FEMA to focus on two local areas, Ventura County in the coastal plain and the mountain setting of Lake Tahoe with downstream impacts in Reno, Sparks and Carson City. Downscaling and focused analyses increased usefulness to user communities, drawing new participants into the study. SAFRR scenarios have also motivated new research to answer questions uncovered by stakeholders, closing the circle of co-evolving disaster-science and disaster-response improvements.

Interactions between the S-domain receptor kinases and AtPUB-ARM E3 ubiquitin ligases suggest a conserved signaling pathway in Arabidopsis.

PubMed

Samuel, Marcus A; Mudgil, Yashwanti; Salt, Jennifer N; Delmas, Frédéric; Ramachandran, Shaliny; Chilelli, Andrea; Goring, Daphne R

2008-08-01

The Arabidopsis (Arabidopsis thaliana) genome encompasses multiple receptor kinase families with highly variable extracellular domains. Despite their large numbers, the various ligands and the downstream interacting partners for these kinases have been deciphered only for a few members. One such member, the S-receptor kinase, is known to mediate the self-incompatibility (SI) response in Brassica. S-receptor kinase has been shown to interact and phosphorylate a U-box/ARM-repeat-containing E3 ligase, ARC1, which, in turn, acts as a positive regulator of the SI response. In an effort to identify conserved signaling pathways in Arabidopsis, we performed yeast two-hybrid analyses of various S-domain receptor kinase family members with representative Arabidopsis plant U-box/ARM-repeat (AtPUB-ARM) E3 ligases. The kinase domains from S-domain receptor kinases were found to interact with ARM-repeat domains from AtPUB-ARM proteins. These kinase domains, along with M-locus protein kinase, a positive regulator of SI response, were also able to phosphorylate the ARM-repeat domains in in vitro phosphorylation assays. Subcellular localization patterns were investigated using transient expression assays in tobacco (Nicotiana tabacum) BY-2 cells and changes were detected in the presence of interacting kinases. Finally, potential links to the involvement of these interacting modules to the hormone abscisic acid (ABA) were investigated. Interestingly, AtPUB9 displayed redistribution to the plasma membrane of BY-2 cells when either treated with ABA or coexpressed with the active kinase domain of ARK1. As well, T-DNA insertion mutants for ARK1 and AtPUB9 lines were altered in their ABA sensitivity during germination and acted at or upstream of ABI3, indicating potential involvement of these proteins in ABA responses.

Hemiuroid trematode sporocysts are undetected by hemocytes of their intermediate host, the ark cockle Anadara trapezia: potential role of surface carbohydrates in successful parasitism.

PubMed

Kawasaki, Minami; Delamare-Deboutteville, Jerome; Dang, Cecile; Barnes, Andrew C

2013-12-01

In order to establish a successful relationship with their hosts, parasites must subvert or evade immune defences. Cockle Anadara trapezia and Sydney Rock oyster (SRO) Saccostrea glomerata live in the same location but only ark cockles are infected by sporocysts of hemiuroid trematode. This provides an opportunity to explore differing interactions between the parasite and the immune system of susceptible and refractive hosts. Rapid migration and encapsulation of sporocysts was observed by SRO hemocytes but not by cockle hemocytes. This migration/encapsulation was inhibited by N-acetylglucosamine or N-acetylgalactosamine but not by the other sugars, implicating specific surface carbohydrates in immune detection. Effector responses of hemocytes were investigated in vitro in terms of production of reactive oxygen production (ROS). Hemocytes of both species strongly reacted to Zymosan, but only SRO hemocytes responded to live sporocysts. Neither species' hemocytes produced ROS in the presence of dead/fixed sporocysts, and there was no suppression of Zymosan-induced respiratory burst by sporocysts. This suggests that immune escape is mediated by avoiding encapsulation, perhaps through molecular mimicry. Membrane-shaving with proteases indicated that sporocyst surface proteins are not a key factors in hemocytic detection. Surface carbohydrates of SRO and cockle hemocytes and of sporocysts were profiled with a panel of biotinylated lectins. This revealed substantial differences between cockle and SRO hemocytes, but greater similarity between cockle hemocytes and sporocysts. Results suggest that surface carbohydrates play an integral role in hemocyte immunorecognition and that surface carbohydrate molecular mimicry is a potential strategy for immune evasion in cockles by hemiuroid trematode sporocysts. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

A deep X-ray view of the bare AGN Ark 120. III. X-ray timing analysis and multiwavelength variability

NASA Astrophysics Data System (ADS)

Lobban, A. P.; Porquet, D.; Reeves, J. N.; Markowitz, A.; Nardini, E.; Grosso, N.

2018-03-01

We present the spectral/timing properties of the bare Seyfert galaxy Ark 120 through a deep ˜420 ks XMM-Newton campaign plus recent NuSTAR observations and a ˜6-month Swift monitoring campaign. We investigate the spectral decomposition through fractional rms, covariance and difference spectra, finding the mid- to long-time-scale (˜day-year) variability to be dominated by a relatively smooth, steep component, peaking in the soft X-ray band. Additionally, we find evidence for variable Fe K emission redward of the Fe Kα core on long time-scales, consistent with previous findings. We detect a clearly defined power spectrum which we model with a power law with a slope of α ˜ 1.9. By extending the power spectrum to lower frequencies through the inclusion of Swift and Rossi X-ray Timing Explorer data, we find tentative evidence of a high-frequency break, consistent with existing scaling relations. We also explore frequency-dependent Fourier time lags, detecting a negative (`soft') lag for the first time in this source with the 0.3-1 keV band lagging behind the 1-4 keV band with a time delay, τ, of ˜900 s. Finally, we analyse the variability in the optical and ultraviolet (UV) bands using the Optical/UV Monitor onboard XMM-Newton and the Ultra-Violet/Optical Telescope onboard Swift and search for time-dependent correlations between the optical/UV/X-ray bands. We find tentative evidence for the U-band emission lagging behind the X-rays with a time delay of τ = 2.4 ± 1.8 d, which we discuss in the context of disc reprocessing.

Microarray-based comparative genomic profiling of reference strains and selected Canadian field isolates of Actinobacillus pleuropneumoniae

PubMed Central

Gouré, Julien; Findlay, Wendy A; Deslandes, Vincent; Bouevitch, Anne; Foote, Simon J; MacInnes, Janet I; Coulton, James W; Nash, John HE; Jacques, Mario

2009-01-01

Background Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is a highly contagious respiratory pathogen that causes severe losses to the swine industry worldwide. Current commercially-available vaccines are of limited value because they do not induce cross-serovar immunity and do not prevent development of the carrier state. Microarray-based comparative genomic hybridizations (M-CGH) were used to estimate whole genomic diversity of representative Actinobacillus pleuropneumoniae strains. Our goal was to identify conserved genes, especially those predicted to encode outer membrane proteins and lipoproteins because of their potential for the development of more effective vaccines. Results Using hierarchical clustering, our M-CGH results showed that the majority of the genes in the genome of the serovar 5 A. pleuropneumoniae L20 strain were conserved in the reference strains of all 15 serovars and in representative field isolates. Fifty-eight conserved genes predicted to encode for outer membrane proteins or lipoproteins were identified. As well, there were several clusters of diverged or absent genes including those associated with capsule biosynthesis, toxin production as well as genes typically associated with mobile elements. Conclusion Although A. pleuropneumoniae strains are essentially clonal, M-CGH analysis of the reference strains of the fifteen serovars and representative field isolates revealed several classes of genes that were divergent or absent. Not surprisingly, these included genes associated with capsule biosynthesis as the capsule is associated with sero-specificity. Several of the conserved genes were identified as candidates for vaccine development, and we conclude that M-CGH is a valuable tool for reverse vaccinology. PMID:19239696

World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide

PubMed Central

Wu, Linhuan; Sun, Qinglan; Desmeth, Philippe; Sugawara, Hideaki; Xu, Zhenghong; McCluskey, Kevin; Smith, David; Alexander, Vasilenko; Lima, Nelson; Ohkuma, Moriya; Robert, Vincent; Zhou, Yuguang; Li, Jianhui; Fan, Guomei; Ingsriswang, Supawadee; Ozerskaya, Svetlana; Ma, Juncai

2017-01-01

The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of the World Federation for Culture Collections (WFCC)—Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big data technology for microbial resource centers and microbiologists all over the world. Here, we provide an overview of WDCM including all of its integrated services. Culture Collections Information Worldwide (CCINFO) provides metadata information on 708 culture collections from 72 countries and regions. Global Catalogue of Microorganism (GCM) gathers strain catalogue information and provides a data retrieval, analysis, and visualization system of microbial resources. Currently, GCM includes >368 000 strains from 103 culture collections in 43 countries and regions. Analyzer of Bioresource Citation (ABC) is a data mining tool extracting strain related publications, patents, nucleotide sequences and genome information from public data sources to form a knowledge base. Reference Strain Catalogue (RSC) maintains a database of strains listed in International Standards Organization (ISO) and other international or regional standards. RSC allocates a unique identifier to strains recommended for use in diagnosis and quality control, and hence serves as a valuable cross-platform reference. WDCM provides free access to all these services at www.wdcm.org. PMID:28053166

Identification of Medically Relevant Species of Arthroconidial Yeasts by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Kolecka, Anna; Khayhan, Kantarawee; Groenewald, Marizeth; Theelen, Bart; Arabatzis, Michael; Velegraki, Aristea; Kostrzewa, Markus; Mares, Mihai; Taj-Aldeen, Saad J.

2013-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) was used for an extensive identification study of arthroconidial yeasts, using 85 reference strains from the CBS-KNAW yeast collection and 134 clinical isolates collected from medical centers in Qatar, Greece, and Romania. The test set included 72 strains of ascomycetous yeasts (Galactomyces, Geotrichum, Saprochaete, and Magnusiomyces spp.) and 147 strains of basidiomycetous yeasts (Trichosporon and Guehomyces spp.). With minimal preparation time, MALDI-TOF MS proved to be an excellent diagnostic tool that provided reliable identification of most (98%) of the tested strains to the species level, with good discriminatory power. The majority of strains were correctly identified at the species level with good scores (>2.0) and seven of the tested strains with log score values between 1.7 and 2.0. The MALDI-TOF MS results obtained were consistent with validated internal transcribed spacer (ITS) and/or large subunit (LSU) ribosomal DNA sequencing results. Expanding the mass spectrum database by increasing the number of reference strains for closely related species, including those of nonclinical origin, should enhance the usefulness of MALDI-TOF MS-based diagnostic analysis of these arthroconidial fungi in medical and other laboratories. PMID:23678074

Isolates of viral hemorrhagic septicemia virus from North America and Europe can be detected and distinguished by DNA probes

USGS Publications Warehouse

Batts, W.N.; Arakawa, C.K.; Bernard, J.; Winton, J.R.

1993-01-01

Biotinylated DNA probes were constructed to hybndize with speclfic sequences within the messenger RNA (mRNA) of the nucleoprotein (N) gene of vlral hemorrhagic septicemia virus (VHSV) reference strains from Europe (07-71) and North Arnenca (Makah) Probes were synthesized that were complementary to (1) a 29-nucleotide sequence near the center of the N gene conlmon to both the 07-71 and Makah reference strains of the virus (2) a unique 28- nucleotide sequence that followed the open readng frame of the Makah N gene mRNA most of which was absent In the 07-71 strain, and (3) a 22-nucleobde sequence wthin the 07-71 N gene that had 6 nllsmatches \

Genomic and bioinformatics analyses of HAdV-4vac and HAdV-7vac, two human adenovirus (HAdV) strains that constituted original prophylaxis against HAdV-related acute respiratory disease, a reemerging epidemic disease.

PubMed

Purkayastha, Anjan; Su, Jing; McGraw, John; Ditty, Susan E; Hadfield, Ted L; Seto, Jason; Russell, Kevin L; Tibbetts, Clark; Seto, Donald

2005-07-01

Vaccine strains of human adenovirus serotypes 4 and 7 (HAdV-4vac and HAdV-7vac) have been used successfully to prevent adenovirus-related acute respiratory disease outbreaks. The genomes of these two vaccine strains have been sequenced, annotated, and compared with their prototype equivalents with the goals of understanding their genomes for molecular diagnostics applications, vaccine redevelopment, and HAdV pathoepidemiology. These reference genomes are archived in GenBank as HAdV-4vac (35,994 bp; AY594254) and HAdV-7vac (35,240 bp; AY594256). Bioinformatics and comparative whole-genome analyses with their recently reported and archived prototype genomes reveal six mismatches and four insertions-deletions (indels) between the HAdV-4 prototype and vaccine strains, in contrast to the 611 mismatches and 130 indels between the HAdV-7 prototype and vaccine strains. Annotation reveals that the HAdV-4vac and HAdV-7vac genomes contain 51 and 50 coding units, respectively. Neither vaccine strain appears to be attenuated for virulence based on bioinformatics analyses. There is evidence of genome recombination, as the inverted terminal repeat of HAdV-4vac is initially identical to that of species C whereas the prototype is identical to species B1. These vaccine reference sequences yield unique genome signatures for molecular diagnostics. As a molecular forensics application, these references identify the circulating and problematic 1950s era field strains as the original HAdV-4 prototype and the Greider prototype, from which the vaccines are derived. Thus, they are useful for genomic comparisons to current epidemic and reemerging field strains, as well as leading to an understanding of pathoepidemiology among the human adenoviruses.

Genomic and Bioinformatics Analyses of HAdV-4vac and HAdV-7vac, Two Human Adenovirus (HAdV) Strains That Constituted Original Prophylaxis against HAdV-Related Acute Respiratory Disease, a Reemerging Epidemic Disease

PubMed Central

Purkayastha, Anjan; Su, Jing; McGraw, John; Ditty, Susan E.; Hadfield, Ted L.; Seto, Jason; Russell, Kevin L.; Tibbetts, Clark; Seto, Donald

2005-01-01

Vaccine strains of human adenovirus serotypes 4 and 7 (HAdV-4vac and HAdV-7vac) have been used successfully to prevent adenovirus-related acute respiratory disease outbreaks. The genomes of these two vaccine strains have been sequenced, annotated, and compared with their prototype equivalents with the goals of understanding their genomes for molecular diagnostics applications, vaccine redevelopment, and HAdV pathoepidemiology. These reference genomes are archived in GenBank as HAdV-4vac (35,994 bp; AY594254) and HAdV-7vac (35,240 bp; AY594256). Bioinformatics and comparative whole-genome analyses with their recently reported and archived prototype genomes reveal six mismatches and four insertions-deletions (indels) between the HAdV-4 prototype and vaccine strains, in contrast to the 611 mismatches and 130 indels between the HAdV-7 prototype and vaccine strains. Annotation reveals that the HAdV-4vac and HAdV-7vac genomes contain 51 and 50 coding units, respectively. Neither vaccine strain appears to be attenuated for virulence based on bioinformatics analyses. There is evidence of genome recombination, as the inverted terminal repeat of HAdV-4vac is initially identical to that of species C whereas the prototype is identical to species B1. These vaccine reference sequences yield unique genome signatures for molecular diagnostics. As a molecular forensics application, these references identify the circulating and problematic 1950s era field strains as the original HAdV-4 prototype and the Greider prototype, from which the vaccines are derived. Thus, they are useful for genomic comparisons to current epidemic and reemerging field strains, as well as leading to an understanding of pathoepidemiology among the human adenoviruses. PMID:16000418

Draft Genome Sequence of Acinetobacter calcoaceticus Strain P23, a Plant Growth-Promoting Bacterium of Duckweed

PubMed Central

Hosoyama, Akira; Yamazoe, Atsushi; Morikawa, Masaaki

2015-01-01

Acinetobacter calcoaceticus strain P23 is a plant growth-promoting bacterium, which was isolated from the surface of duckweed. We report here the draft genome sequence of strain P23. The genome data will serve as a valuable reference for understanding the molecular mechanism of plant growth promotion in aquatic plants. PMID:25720680

Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria)

PubMed Central

Bendiks, Zachary A.; Lang, Jenna M.; Darling, Aaron E.; Coil, David A.

2013-01-01

Here, we present the draft genome sequence of Microbacterium sp. strain UCD-TDU, a member of the phylum Actinobacteria. The assembly contains 3,746,321 bp (in 8 scaffolds). This strain was isolated from a residential toilet as part of an undergraduate student research project to sequence reference genomes of microbes from the built environment. PMID:23516225

Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753).

PubMed

Criscuolo, Alexis; Chesneau, Olivier; Clermont, Dominique; Bizet, Chantal

2018-04-05

Flavobacterium columnare strain PH-97028 (=CIP 109753) is a genomovar III reference strain that was isolated from a diseased Ayu fish in Japan. We report here the analysis of the first available genomovar III sequence of this species to aid in identification, epidemiological tracking, and virulence studies. Copyright © 2018 Criscuolo et al.

Putative Novel Genotype of Avian Hepatitis E Virus, Hungary, 2010

PubMed Central

Bányai, Krisztián; Tóth, Ádám György; Ivanics, Éva; Glávits, Róbert; Szentpáli-Gavallér, Katalin

2012-01-01

To explore the genetic diversity of avian hepatitis E virus strains, we characterized the near-complete genome of a strain detected in 2010 in Hungary, uncovering moderate genome sequence similarity with reference strains. Public health implications related to consumption of eggs or meat contaminated by avian hepatitis E virus, or to poultry handling, require thorough investigation. PMID:22840214

Genome Sequence of Actinobacillus seminis Strain ATCC 15768, a Reference Strain of Ovine Pathogens That Causes Infections in Reproductive Organs.

PubMed

Negrete-Abascal, Erasmo; Montes-Garcia, Fernando; Vaca-Pacheco, Sergio; Leyto-Gil, Abraham M; Fragoso-Garcia, Edgar; Carvente-Garcia, Roberto; Perez-Agueros, Sandra; Castelan-Sanchez, Hugo G; Garcia-Molina, Alejandra; Villamar, Tomas E; Sánchez-Alonso, Patricia; Vazquez-Cruz, Candelario

2018-01-11

The draft genome sequence of Actinobacillus seminis strain ATCC 15768 is reported here. The genome comprises 22 contigs corresponding to 2.36 Mb with 40.7% G+C content and contains several genes related to virulence, including a putative RTX protein. Copyright © 2018 Negrete-Abascal et al.

Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1.

PubMed

Babrzadeh, Farbod; Jalili, Roxana; Wang, Chunlin; Shokralla, Shadi; Pierce, Sarah; Robinson-Mosher, Avi; Nyren, Pål; Shafer, Robert W; Basso, Luiz C; de Amorim, Henrique V; de Oliveira, Antonio J; Davis, Ronald W; Ronaghi, Mostafa; Gharizadeh, Baback; Stambuk, Boris U

2012-06-01

The Saccharomyces cerevisiae strains widely used for industrial fuel-ethanol production have been developed by selection, but their underlying beneficial genetic polymorphisms remain unknown. Here, we report the draft whole-genome sequence of the S. cerevisiae strain CAT-1, which is a dominant fuel-ethanol fermentative strain from the sugarcane industry in Brazil. Our results indicate that strain CAT-1 is a highly heterozygous diploid yeast strain, and the ~12-Mb genome of CAT-1, when compared with the reference S228c genome, contains ~36,000 homozygous and ~30,000 heterozygous single nucleotide polymorphisms, exhibiting an uneven distribution among chromosomes due to large genomic regions of loss of heterozygosity (LOH). In total, 58 % of the 6,652 predicted protein-coding genes of the CAT-1 genome constitute different alleles when compared with the genes present in the reference S288c genome. The CAT-1 genome contains a reduced number of transposable elements, as well as several gene deletions and duplications, especially at telomeric regions, some correlated with several of the physiological characteristics of this industrial fuel-ethanol strain. Phylogenetic analyses revealed that some genes were likely associated with traits important for bioethanol production. Identifying and characterizing the allelic variations controlling traits relevant to industrial fermentation should provide the basis for a forward genetics approach for developing better fermenting yeast strains.

Usefulness of the (GTG)4-PCR for typing of monophasic Salmonella enterica isolates with antigenic shame l,4,[5],12:i:-.

PubMed

Wołkowicz, Tomasz; Januszkiewicz, Aleksandra; Chróst, Anna; Wolaniuk, Natalia; Kubiak, Anna B; Majchrzak, Marta; Szych, Jolanta; Parniewski, Paweł

2015-01-01

Monophasic Salmonella enterica strains presenting the antigenic shame 1,4,[5],12:i:- are becoming more prevalent. Accurate identification of such strains is hard with routine using biochemical and serological tests. Such strains can be identified with molecular tests. In this study we have tested the usefulness of(GTG)4-PCR for the diagnostic of such monophasic strains. This usefulness of this method was previously confirmed for genoserotyping of S. Enterica, Typhimurium, Infantis, Virchow, Hadar, Newport and Anatum. 76 strains with antigenic shame l,4,[5],12:i:-, isolated in Poland in years 2007-12 were tested. Additionally (GTG)4-PCR patterns were obtained for reference strains of serotypes S. Lagos, S. Agama, S. Farsta, S. Tsevie, S. Glocester and S. Tumodi. (GTG)4-PCR was performed with DreamTaq DNA polymerase. Obtained patterns were analysed with BioNumerics software. No pattern specific for monophasic pattern was identified. Additionally it was also impossible to differentiate patterns obtained for S. Typhimurium, S. Farsta, S. Tsevie and S. Glocester. Only reference strains of serotypes S. Tumodi, Farsta and Agama has the distinguishable patterns of (GTG)4-PCR. Analysed (GTG)4-PCR method do not show the ability to distinguish S. enterica serotypes from group 04, H:i, including monophasic strains with the antigenic shame 1,4,[5],12:i:-.

[SH and HN Protein Genetic Characterization Analysis of Mumps Virus Isolated in Liaoning Province from 2008 to 2014].

PubMed

Wang, Yan; Ma, Yan; Hao, Shuang; Xu, Xiaoting; Han, Yue; Yao, Wenqing; Zhao, Zhuo

2016-03-01

To analyze the genetic characterization of epidemic mumps virus strains in Liaoning Province and provide the basis for mumps control. A total of 32 mumps viruses strains were isolated during 2008-2104. The fragment of SH genes and HN genes were amplified by RT-PCR, the PCR products were sequenced and analyzed. Basing on the 316 nucleotides of SH gene, The phylogenetic analyses were processed with the data of WHO mumps reference strains downloaded from GenBank and 32 mumps viruses strains. It showed that the 31 mumps virus strains belong to F genotype except MuVi/Liaoning. CHN/16.11 which was G genotype . Comparing to the A reference strains (Jeryl-Lynn and S-79), F genotype MuV were mutated on 12 amino acids sites and 27 amino acids siteson on HN gene. F genotype MuV added one N-glycosylation site in 464th-466th amino acids. The antigenic sites on HN were mutated on 121th, 123th, 279th, 287th, 336th, 356th and 442th. Maybe, it will influence the MuV antigenic.

DFB fiber laser static strain sensor based on beat frequency interrogation with a reference fiber laser locked to a FBG resonator.

PubMed

Huang, Wenzhu; Feng, Shengwen; Zhang, Wentao; Li, Fang

2016-05-30

We report on a high-resolution static strain sensor developed with distributed feedback (DFB) fiber laser. A reference FBG resonator is used for temperature compensation. Locking another independent fiber laser to the resonator using the Pound-Drever-Hall technique results in a strain power spectral density better than S_ε(f) = (4.6 × 10^-21) ε²/Hz in the frequency range from 1 Hz to 1 kHz, corresponding to a minimum dynamic strain resolution of 67.8 pε/√Hz. This frequency stabilized fiber laser is proposed to interrogate the sensing DFB fiber laser by the beat frequency principle. As a reasonable DFB fiber laser setup is realized, a narrow beat frequency line-width of 3.23 kHz and a high beat frequency stability of 0.036 MHz in 15 minutes are obtained in the laboratory test, corresponding to a minimum static strain resolution of 270 pε. This is the first time that a sub-0.5 nε level for static strain measurement using DFB fiber laser is demonstrated.

The new strains Brucella inopinata BO1 and Brucella species 83-210 behave biologically like classic infectious Brucella species and cause death in murine models of infection.

PubMed

Jiménez de Bagüés, María P; Iturralde, María; Arias, Maykel A; Pardo, Julián; Cloeckaert, Axel; Zygmunt, Michel S

2014-08-01

Recently, novel atypical Brucella strains isolated from humans and wild rodents have been reported. They are phenotypically close to Ochrobactrum species but belong to the genus Brucella, based on genetic relatedness, although genetic diversity is higher among the atypical Brucella strains than between the classic species. They were classified within or close to the novel species Brucella inopinata. However, with the exception of Brucella microti, the virulence of these novel strains has not been investigated in experimental models of infection. The type species B. inopinata strain BO1 (isolated from a human) and Brucella species strain 83-210 (isolated from a wild Australian rodent) were investigated. A classic infectious Brucella reference strain, B. suis 1330, was also used. BALB/c, C57BL/6, and CD1 mice models and C57BL/6 mouse bone-marrow-derived macrophages (BMDMs) were used as infection models. Strains BO1 and 83-210 behaved similarly to reference strain 1330 in all mouse infection models: there were similar growth curves in spleens and livers of mice and similar intracellular replication rates in BMDMs. However, unlike strain 1330, strains BO1 and 83-210 showed lethality in the 3 mouse models. The novel atypical Brucella strains of this study behave like classic intracellular Brucella pathogens. In addition, they cause death in murine models of infection, as previously published for B. microti, another recently described environmental and wildlife species. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Precise GPS/Acoustic Positioning of Seafloor Reference Points for Tectonic Studies

NASA Technical Reports Server (NTRS)

Spiess, F. N.; Chadwell, C.; Hildebrand, J. A.; Young, L. E.; Purcell, G. H., Jr.; Dragert, H.

1998-01-01

Global networks for crustal strain measurement provide important constraints for studies of tectonic plate motion and deformation. To date, crustal strain measurements have been possible only in terrestrial settings: on continental plates and island sites within oceanic plates.

Comparative Sequence Analysis of the Plasmid-Encoded Regulator of Enteropathogenic Escherichia coli Strains

PubMed Central

Okeke, Iruka N.; Borneman, Jade A.; Shin, Sooan; Mellies, Jay L.; Quinn, Laura E.; Kaper, James B.

2001-01-01

Enteropathogenic Escherichia coli (EPEC) strains that carry the EPEC adherence factor (EAF) plasmid were screened for the presence of different EAF sequences, including those of the plasmid-encoded regulator (per). Considerable variation in gene content of EAF plasmids from different strains was seen. However, bfpA, the gene encoding the structural subunit for the bundle-forming pilus, bundlin, and per genes were found in 96.8% of strains. Sequence analysis of the per operon and its promoter region from 15 representative strains revealed that it is highly conserved. Most of the variation occurs in the 5′ two-thirds of the perA gene. In contrast, the C-terminal portion of the predicted PerA protein that contains the DNA-binding helix-turn-helix motif is 100% conserved in all strains that possess a full-length gene. In a minority of strains including the O119:H2 and canine isolates and in a subset of O128:H2 and O142:H6 strains, frameshift mutations in perA leading to premature truncation and consequent inactivation of the gene were identified. Cloned perA, -B, and -C genes from these strains, unlike those from strains with a functional operon, failed to activate the LEE1 operon and bfpA transcriptional fusions or to complement a per mutant in reference strain E2348/69. Furthermore, O119, O128, and canine strains that carry inactive per operons were deficient in virulence protein expression. The context in which the perABC operon occurs on the EAF plasmid varies. The sequence upstream of the per promoter region in EPEC reference strains E2348/69 and B171-8 was present in strains belonging to most serogroups. In a subset of O119:H2, O128:H2, and O142:H6 strains and in the canine isolate, this sequence was replaced by an IS1294-homologous sequence. PMID:11500429

Memorandum on availability of ground water for irrigation in certain areas of eastern Arkansas

USGS Publications Warehouse

Dennis, P.E.; ,

1957-01-01

This memorandum was prepared in response to a request from the Soil Conservation Service, Little Rock, Ark., for information on the future prospects of irrigation of rice with water from wells in certain areas in the basins of the Bache, St. Francis, and L'Anguille Rivers, Big and Dials Creeks, and Bayou Meto and the Bouef-Tensas-Macon basin. It was prepared as a aprt of the Statewide ground-water investigation in cooperation with the Arkansas Geological and Conservation Commission ad the University of Arkansas. The specific areas and water requirement specified by the Soil Conservation Service are listed in the appendix.

Potentiometric maps of the Sparta Sand, northern Louisiana and southern Arkansas, 1900, 1965, 1975, and 1980

USGS Publications Warehouse

Ryals, G.N.

1980-01-01

The potentiometric surface of the Sparta Sand in northern Louisiana is shown by contours on four maps. Maps for 1900, 1965 , and spring 1975 are generalized, small-scale maps from previously published reports. The spring 1980 map (1:500,000) is based on measurements in 144 wells and includes the southern tier of counties in southern Arkansas. The map shows regional effects of pumping from the Sparta Sand and effects of local pumping centers at Magnolia and El Dorado, Ark., and at Minden, Ruston, Jonesboro-Hodge, Winnfield, Bastrop, and in the Monroe area of Louisiana. (USGS)

Elliptic Integrals in the Minkowski Plane

DTIC Science & Technology

1991-05-09

factorial Pochhammer notation F(a + k) (a)k - (a) Let F(a, b , c denote the hypergeometric function. Assume c - a - b = d , where d is a positive...integer. Then in a neighborhood of C = 1 , ((d) F(a+ b+d) d-1 (a)n (b)n )n(22) F(a , b , a + b + d , () = E~ )rb+ 0-’)n( ) r(a +d) r(b +d) n =O0( ’d’ n...axes a , b and eccentriaty e = c where c = Ta2 - b2 . Let P denote one of the foci of the ellipse. Then (26) 1 1 1 2 and(26) ar+(K, P) 2 -er F(- 1

Design and implementation of a CORBA-based genome mapping system prototype.

PubMed

Hu, J; Mungall, C; Nicholson, D; Archibald, A L

1998-01-01

CORBA (Common Object Request Broker Architecture), as an open standard, is considered to be a good solution for the development and deployment of applications in distributed heterogeneous environments. This technology can be applied in the bioinformatics area to enhance utilization, management and interoperation between biological resources. This paper investigates issues in developing CORBA applications for genome mapping information systems in the Internet environment with emphasis on database connectivity and graphical user interfaces. The design and implementation of a CORBA prototype for an animal genome mapping database are described. The prototype demonstration is available via: http://www.ri.bbsrc.ac.uk/ark_corba/. jian.hu@bbsrc.ac.uk

Strain and ferroelectric soft-mode induced superconductivity in strontium titanate

NASA Astrophysics Data System (ADS)

Dunnett, K.; Narayan, Awadhesh; Spaldin, N. A.; Balatsky, A. V.

2018-04-01

We investigate the effects of strain on superconductivity with particular reference to SrTiO3. Assuming that a ferroelectric mode that softens under tensile strain is responsible for the coupling, an increase in the critical temperature and range of carrier densities for superconductivity is predicted, while the peak of the superconducting dome shifts towards lower carrier densities. Using a Ginzburg-Landau approach in 2D, we find a linear dependence of the critical temperature on strain: if the couplings between the order parameter and strains in different directions differ while their sum is fixed, different behaviors under uniaxial and biaxial strain can be understood.

Genetic studies on reference strains of mutans streptococci.

PubMed

Ota, Fusao; Yamato, Masayuki; Hayashi, Mie; Ota, Masayuki; Koga, Tetsuro; Sherin, Ahmed; Mukai, Chiharu; Sakai, Kentaro; Yamamoto, Shigeru

2002-01-01

Twenty four reference strains (serotype a-h) belonging to the mutans group of streptococci were compared for DNA fragment patterns of rDNA after treatment with Hind III. It was shown that Streptococcus cricetus (serotype a), S. rattus (serotype b), and S. downei (serotype h) reveals comparatively homogeneous patterns while S. mutans (serotype c, e and f) exhibits differences between the different serotypes as well as within single serotypes. S. sobrinus had an intermediary diversity. These data support the previous findings that S. mutans is heterogeneous at the serological, biochemical and genetical level.

Equid herpesvirus 9 (EHV-9) isolates from zebras in Ontario, Canada, 1989 to 2007.

PubMed

Rebelo, Ana Rita; Carman, Susy; Shapiro, Jan; van Dreumel, Tony; Hazlett, Murray; Nagy, Éva

2015-04-01

The objective of this study was to identify and partially characterize 3 equid herpesviruses that were isolated postmortem from zebras in Ontario, Canada in 1989, 2002, and 2007. These 3 virus isolates were characterized by plaque morphology, restriction fragment length polymorphism (RFLP) of their genomic deoxyribonucleic acid (DNA), real-time polymerase chain reaction (PCR) assay, and sequence analyses of the full length of the glycoprotein G (gG) gene (ORF70) and a portion of the DNA polymerase gene (ORF30). The isolates were also compared to 3 reference strains of equid herpesvirus 1 (EHV-1). Using rabbit kidney cells, the plaques for the isolates from the zebras were found to be much larger in size than the EHV-1 reference strains. The RFLP patterns of the zebra viruses differed among each other and from those of the EHV-1 reference strains. Real-time PCR and sequence analysis of a portion of the DNA polymerase gene determined that the herpesvirus isolates from the zebras contained a G at nucleotide 2254 and a corresponding N at amino acid position 752, which suggested that they could be neuropathogenic EHV-1 strains. However, subsequent phylogenetic analysis of the gG gene suggested that they were EHV-9 and not EHV-1.

Automation and Job Satisfaction among Reference Librarians.

ERIC Educational Resources Information Center

Whitlatch, Jo Bell

1991-01-01

Discussion of job satisfaction and the level of job performance focuses on the effect of automation on job satisfaction among reference librarians. The influence of stress is discussed, a job strain model is explained, and examples of how to design a job to reduce the stress caused by automation are given. (12 references) (LRW)

Microscopic Electronic and Mechanical Properties of Ultra-Thin Layered Materials

DTIC Science & Technology

2016-07-25

Graphene single layers grown by chemical vapor deposition on single crystal Cu substrates are subject to nonuniform physisorption strains that...the observed highly nonuniform strains. 4. Connecting dopant bond type with electronic structure in N-doped graphene (reference [4]) Robust methods

Complete genome assemblies and methylome characterization in infectious diseases

USDA-ARS?s Scientific Manuscript database

Understanding the genetic basis of infectious diseases is a critical component to effective treatments. Because of the rapid evolution of bacterial strains and frequent horizontal transfer of DNA between them, resequencing of new isolates against known reference strains often provides an incomplete ...

Reference Ranges of Left Ventricular Strain Measures by Two-Dimensional Speckle-Tracking Echocardiography in Children: A Systematic Review and Meta-Analysis.

PubMed

Levy, Philip T; Machefsky, Aliza; Sanchez, Aura A; Patel, Meghna D; Rogal, Sarah; Fowler, Susan; Yaeger, Lauren; Hardi, Angela; Holland, Mark R; Hamvas, Aaron; Singh, Gautam K

2016-03-01

Establishment of the range of reference values and associated variations of two-dimensional speckle-tracking echocardiography (2DSTE)-derived left ventricular (LV) strain is a prerequisite for its routine clinical adoption in pediatrics. The aims of this study were to perform a meta-analysis of normal ranges of LV global longitudinal strain (GLS), global circumferential strain (GCS), and global radial strain (GRS) measurements derived by 2DSTE in children and to identify confounding factors that may contribute to variance in reported measures. A systematic review was launched in MEDLINE, Embase, Scopus, the Cumulative Index to Nursing and Allied Health Literature, and the Cochrane Library. Search hedges were created to cover the concepts of pediatrics, STE, and left-heart ventricle. Two investigators independently identified and included studies if they reported 2DSTE-derived LV GLS, GCS, or GRS. The weighted mean was estimated by using random effects models with 95% CIs, heterogeneity was assessed using the Cochran Q statistic and the inconsistency index (I(2)), and publication bias was evaluated using the Egger test. Effects of demographic (age), clinical, and vendor variables were assessed in a metaregression. The search identified 2,325 children from 43 data sets. The reported normal mean values of GLS among the studies varied from -16.7% to -23.6% (mean, -20.2%; 95% CI, -19.5% to -20.8%), GCS varied from -12.9% to -31.4% (mean, -22.3%; 95% CI, -19.9% to -24.6%), and GRS varied from 33.9% to 54.5% (mean, 45.2%; 95% CI, 38.3% to 51.7%). Twenty-six studies reported longitudinal strain only from the apical four-chamber view, with a mean of -20.4% (95% CI, -19.8% to -21.7%). Twenty-three studies reported circumferential strain (mean, -20.3%; 95% CI, -19.4% to -21.2%) and radial strain (mean, 46.7%; 95% CI, 42.3% to 51.1%) from the short-axis view at the midventricular level. A significant apex-to-base segmental longitudinal strain gradient (P < .01) was observed in the LV free wall. There was significant between-study heterogeneity and inconsistency (I(2) > 94% and P < .001 for each strain measure), which was not explained by age, gender, body surface area, blood pressure, heart rate, frame rate, frame rate/heart rate ratio, tissue-tracking methodology, location of reported strain value along the strain curve, ultrasound equipment, or software. The metaregression showed that these effects were not significant determinants of variations among normal ranges of strain values. There was no evidence of publication bias (P = .40). This study defines reference values of 2DSTE-derived LV strain in children on the basis of a meta-analysis. In healthy children, mean LV GLS was -20.2% (95% CI, -19.5% to -20.8%), mean GCS was -22.3% (95% CI, -19.9% to -24.6%), and mean GRS was 45.2% (95% CI, 38.3% to 51.7%). LV segmental longitudinal strain has a stable apex-to-base gradient that is preserved throughout maturation. Although variations among different reference ranges in this meta-analysis were not dependent on differences in demographic, clinical, or vendor parameters, age- and vendor-specific referenced ranges were established as well. Copyright © 2016 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.

Age, Sex, and Blood Pressure-Related Influences on Reference Values of Left Atrial Deformation and Mechanics From a Large-Scale Asian Population.

PubMed

Liao, Jo-Nan; Chao, Tze-Fan; Kuo, Jen-Yuan; Sung, Kuo-Tzu; Tsai, Jui-Peng; Lo, Chi-In; Lai, Yau-Huei; Su, Cheng-Huang; Hung, Chung-Lieh; Yeh, Hung-I; Chen, Shih-Ann

2017-10-01

Left atrial (LA) function is tightly linked to several cardiovascular diseases and confers key prognostic information. Speckle tracking-based deformation as a feasible and sensitive LA mechanical assessment has proven its clinical significance beyond volume measures; however, the reference values remain largely unknown. We studied 4042 participants undergoing annual cardiovascular survey. Among them, 2812 healthy participants (65% men; mean age, 47.4±9.9 years) were eligible for speckle tracking analysis. Peak atrial longitudinal systolic strain and strain rate (SR) at systolic (SRs), early diastolic (SRe), and late diastolic atrial contraction phases (SRa) were analyzed by dedicated software (EchoPAC, GE) and compared in terms of age, sex, and blood pressure. Overall, women demonstrated higher peak atrial longitudinal systolic strain (39.34±7.99% versus 37.95±7.96%; P<0.001) and showed age-dependent more pronounced peak atrial longitudinal systolic strain functional decay than those of men (P value for interaction, <0.05), with men showing higher SRs and SRa, although lower SRe (all P<0.001). Both increasing age and higher blood pressure were independently associated with deteriorated peak atrial longitudinal systolic strain, SRs, and SRe, although augmented LA SRa, even after accounting for baseline clinical covariates in multivariable models that incorporated LA volume, NT-proBNP (N-terminal pro-B-type natriuretic peptide), or left ventricular E/e' (all P<0.001). Our findings suggest LA mechanical functional decays in association with increasing age and higher blood pressure, which seem to be compensated for by augmentation of atrial pump function. We have also provided age- and sex-stratified reference values for strain and SR based on a large-scale Asian population. © 2017 American Heart Association, Inc.

Real-time sonoelastography using an external reference material: test-retest reliability of healthy Achilles tendons.

PubMed

Schneebeli, Alessandro; Del Grande, Filippo; Vincenzo, Gabriele; Cescon, Corrado; Clijsen, Ron; Biordi, Fulvio; Barbero, Marco

2016-08-01

To establish the test-retest reliability of sonoelastography (SE) on healthy Achilles tendons in contracted and relaxed states using an external reference system. Forty-eight Achilles tendons from 24 healthy volunteers were assessed using ultrasound and real-time SE with an external reference material. Tendons were analyzed under relaxed and contracted conditions. Strain ratios between the tendons and the reference material were calculated. The intraclass correlation coefficient (ICC2.k) and Bland-Altman plot were used to assess test-retest reliability. The reliability of SE measurements under relaxed conditions ranged from high to very high, with an ICC2.k of 0.84 (95 % CI: 0.64-0.92) for reference material, 0.91 (95 % CI: 0.83-0.95) for Achilles tendons and 0.95 (95 % CI: 0.91-0.97) for Kager fat pads (KFP). The ICC2.k value for skin was 0.30 (95 % CI: -0.26 to 0.61). Reliability for measurements in the contracted state ranged from high to very high, with an ICC2.k of 0.93 (95 % CI: 0.87-0.96) for reference material, 0.72 (95 % CI: 0.50-0.84) for skin, 0.93 (95 % CI: 0.87-0.96) for Achilles tendons, and 0.81 (95 % CI: 0.66-0.89) for KFP. Reliability of the strain ratio (tendon/reference) under relaxed conditions was high with an ICC2.k of 0.87 (95 % CI: 0.75-0.93), and in the contracted state, it was very high with an ICC2.k of 0.94 (95 % CI: 0.90-0.97). Sonoelastography using an external reference material is a reliable and simple technique for the assessment of the elasticity of healthy Achilles tendons. The use of an external material as a reference, along with strain ratios, could provide a quantitative measure of elasticity.

Effects of the probiotic Enterococcus faecium NCIMB 10415 on selected lactic acid bacteria and enterobacteria in co-culture.

PubMed

Starke, I C; Zentek, J; Vahjen, W

2015-01-01

Enterococcus faecium NCIMB 10415 is used as a probiotic for piglets and has been shown to modify the porcine intestinal microbiota. However, the mode of action of this probiotic modification is still unclear. One possible explanation is the direct growth inhibiting or stimulating effect of the probiotic on other indigenous bacteria. Therefore, the aim of the present study was to examine the growth interactions of the probiotic with different indigenous porcine bacteria in vitro. Reference strains were cultivated with the probiotic E. faecium strain NCIMB10415 (SF68) in a checkerboard assay with 102 to 105 cells/ml inoculum per strain. Growth kinetics were recorded for 8 h and used to determine specific growth of the co-cultures. Additionally, total DNA was extracted from the co-cultures at the end of the incubation to verify which strain in the co-culture was affected. Co-cultivation with eight Enterococcus spp. tester strains showed strain-specific growth differences. Three of four E. faecium strains were not influenced by the probiotic strain. PCR results showed reduced growth of the probiotic strain in co-culture with E. faecium DSM 6177. Three of four Enterococcus faecalis strains showed reduced specific growth in co-culture with the probiotic strain. However, E. faecalis DSM 20478 impaired growth of the probiotic E. faecium strain. The growth of Lactobacillus johnsonii DSM 10533 and Lactobacillus reuteri DSM 20016 was enhanced in co-culture with the probiotic strain, but co-cultivations with Lactobacillus mucosae DSM13345 or Lactobacillus amylovorus DSM10533 showed no differences. Co-cultures with the probiotic E. faecium showed no impact on the growth rate of four different enterobacterial reference strains (2 strains of Salmonella enterica and 2 strains of Escherichia coli), but PCR results showed reduced cell numbers for a pathogenic E. coli isolate at higher concentration of the probiotic strain. As the in vitro effect of the probiotic E. faecium on enterococci was strain specific and the growth of certain Lactobacillus spp. was enhanced by the probiotic, these results indicate a direct effect of the probiotic on certain members of the porcine gastro intestinal microbiota.

A high-precision, distributed geodetic strainmeter based on dual coaxial cable Bragg gratings

NASA Astrophysics Data System (ADS)

Fu, J.; Wei, T.; Wei, M.; Shen, Y.

2014-12-01

Observations of surface deformation are essential for understanding a wide range of geophysical problems, including earthquakes, volcanoes, landslides, and glaciers. Current geodetic technologies, such as GPS, InSAR, borehole and laser strainmeters, are costly and limited in their temporal or spatial resolution. Here we present a new type of strainmeter based on coaxial cable Bragg grating (CCBG) sensing technology that provides high-precision, distributed strain measurements at a moderate cost. The coaxial-cable-based strainmeter is designed to cover a long distance (~ km) under harsh environmental conditions such as extreme temperatures. To minimize the environmental noises, two CCBGs are introduced into the geodetic strainmeter: one is used to measure the strain applied on it, and the other acts as a reference only to detect the environmental noises. The environmental noises are removed using the inputs from the strained CCBG and the reference CCBG in a frequency mixer. The test results show that the geodetic strainmeter with dual CCBGs has micron-strain accuracy in the lab.

Comparative genomics of Vibrio cholerae El Tor strains isolated at epidemic complications in Siberia and at the Far East.

PubMed

Mironova, Liliya V; Gladkikh, Anna S; Ponomareva, Anna S; Feranchuk, Sergey I; Bochalgin, Nikita О; Basov, Evgenii A; Yu Khunkheeva, Zhanna; Balakhonov, Sergey V

2018-06-01

The territory of Siberia and the Far East of Russia is classified as epidemically safe for cholera; however, in the 1970s and 1990s a number of infection importation cases and acute outbreaks associated with the cholera importation were reported. Here, we analyze genomes of four Vibrio cholerae El Tor strains isolated from humans during epidemic complications (imported cases, an outbreak) in the 1990s. The analyzed strains harbor the classical allele of the cholera toxin subunit B gene (ctxB1); thus, belong to genetically altered variants of the El Tor biotype. Analysis of the genomes revealed their high homology with the V. cholerae N16961 reference strain: 85-93 SNPs were identified in the core genome as compared to the reference. The determined features of SNPs in the CTX prophage made it possible to propose the presence of a new subtype - CTX-2a in two strains; the other two strains carried the prophage of CTX-3 type. Results of phylogenetic analysis based on SNP-typing demonstrated that two strains belonged to the second wave, and two - to the early third wave of cholera dissemination in the world. Phylogenetic reconstruction in combination with epidemiological data permitted to trace the origin of the strains and the way of their importation to the Russian Federation directly or through temporary cholera foci. Copyright © 2018 Elsevier B.V. All rights reserved.

Interactions between Candida albicans and Candida glabrata in biofilms: Influence of the strain type, culture medium and glucose supplementation.

PubMed

Hosida, Thayse Yumi; Cavazana, Thamires Priscila; Henriques, Mariana; Pessan, Juliano Pelim; Delbem, Alberto Carlos Botazzo; Monteiro, Douglas Roberto

2018-04-01

The relationship among Candida species may be influenced by several factors. Thus, this study evaluated the interactions between Candida albicans and Candida glabrata in biofilms, varying the strain type, culture medium and glucose supplementation. Biofilms were formed for 48 hours in Sabouraud dextrose broth (SDB) or RPMI 1640, supplemented with 0%, 1% or 5% glucose. Each strain of C. albicans was combined with two strains of C. glabrata, generating four biofilm associations, which were quantified by colony-forming units (CFUs), total biomass and metabolic activity. Data were analysed by ANOVA and Tukey's HSD test (α = 0.05). For CFUs, all associations were classified as indifferent for biofilms formed in RPMI 1640, while for SDB the interactions were antagonistic for C. albicans and indifferent for C. glabrata. The association of reference strains resulted in a dual-species biofilm with biomass significantly higher than that observed for each single biofilm developed in SDB. The metabolic activity of dual-species biofilms did not significantly differ from that found for single ones, except for co-culture of the reference strains. Glucose supplementation and culture media had a significant influence on all parameters. In conclusion, the strain type, culture medium and glucose supplementation influenced the interactions between C. albicans and C. glabrata. © 2017 Blackwell Verlag GmbH.

Assessment of Mycosphaerella graminicola resistance to azoxystrobin.

PubMed

Siah, A; Deweer, C; Morand, E; Reignault, Ph; Halama, P

2008-01-01

Azoxystrobin resistance levels of twenty two strains sampled from ten French locations and two reference isolates (IPO323 and IPO94269) of the wheat pathogen Mycosphaerella graminicola were investigated in vitro. French strains assayed were selected from twenty two genetic groups determined from three hundred sixty three strains previously characterised using microsatellites, actine and beta-tubuline markers. For the first time, the evaluation was carried out using four distinct methods: spotting on PDA medium, spore germination on PDA medium and using microtitre plates with and without Alamar blue, a growth indicator. From dose-response curve, half maximal inhibitory concentration (IC50) was determined for each strain. The results obtained using microtitre plates with the addition of Alamar blue displayed high standard deviations from the growth averages observed. Therefore, we suggest that this method is inadequate to assess M. graminicolo resistance to fungicides. However, a good correlation was observed between the rankings of strains according to their IC50 values with the three other methods used. The two reference isolates, as expected, were inhibited by low azoxystrobin concentrations. On the other hand, the IC50 values obtained showed presence of a threshold between sensitive and resistant strains that corroborates the disruptive resistance of M. graminicola against strobilurin fungicides. In addition, the strains showing resistance were those sampled mainly from northern France, where a high frequency of strobilurin resistant isolates among M. graminicola populations was reported by several studies.

Probiotic lactobacilli interfere with Streptococcus mutans biofilm formation in vitro.

PubMed

Söderling, Eva M; Marttinen, Aino M; Haukioja, Anna L

2011-02-01

In clinical studies, probiotic bacteria have decreased the counts of salivary mutans streptococci (MS). We compared the effects of probiotic Lactobacillus strains on the biofilm formation of Streptococcus mutans. The bacterial strains used included four S. mutans strains (reference strains NCTC 10449 and Ingbritt and clinical isolates 2366 and 195) and probiotic strains Lactobacillus rhamnosus GG, L. plantarum 299v, and L. reuteri strains PTA 5289 and SD2112. The ability of MS to adhere and grow on a glass surface, reflecting biofilm formation, was studied in the presence of the lactobacilli (LB). The effect of LB culture supernatants on the viability of the MS was studied as well. All of the LB inhibited the biofilm formation of the clinical isolates of MS (P < 0.001). The biofilm formation of the reference strains of MS was also inhibited by the LB, but L. plantarum and L. reuteri PTA 5289 showed a weaker inhibition when compared to L. reuteri SD2112 and L. rhamnosus GG. Viable S. mutans cells could be detected in the biofilms and culture media only when the experiments were performed with the L. reuteri strains. The L. reuteri strains were less efficient in killing the MS also in the tests performed with the culture supernatants. The pHs of the supernatants of L. reuteri were higher compared to those of L. rhamnosus GG and L. plantarum; P < 0.001. In conclusion, our results demonstrated that four commonly used probiotics interfered with S. mutans biofilm formation in vitro, and that the antimicrobial activity against S. mutans was pH-dependent.

Whole-genome mapping reveals a large chromosomal inversion on Iberian Brucella suis biovar 2 strains.

PubMed

Ferreira, Ana Cristina; Dias, Ricardo; de Sá, Maria Inácia Corrêa; Tenreiro, Rogério

2016-08-30

Optical mapping is a technology able to quickly generate high resolution ordered whole-genome restriction maps of bacteria, being a proven approach to search for diversity among bacterial isolates. In this work, optical whole-genome maps were used to compare closely-related Brucella suis biovar 2 strains. This biovar is the unique isolated in domestic pigs and wild boars in Portugal and Spain and most of the strains share specific molecular characteristics establishing an Iberian clonal lineage that can be differentiated from another lineage mainly isolated in several Central European countries. We performed the BamHI whole-genome optical maps of five B. suis biovar 2 field strains, isolated from wild boars in Portugal and Spain (three from the Iberian lineage and two from the Central European one) as well as of the reference strain B. suis biovar 2 ATCC 23445 (Central European lineage, Denmark). Each strain showed a distinct, highly individual configuration of 228-231 BamHI fragments. Nevertheless, a low divergence was globally observed in chromosome II (1.6%) relatively to chromosome I (2.4%). Optical mapping also disclosed genomic events associated with B. suis strains in chromosome I, namely one indel (3.5kb) and one large inversion (944kb). By using targeted-PCR in a set of 176 B. suis strains, including all biovars and haplotypes, the indel was found to be specific of the reference strain ATCC 23445 and the large inversion was shown to be an exclusive genomic marker of the Iberian clonal lineage of biovar 2. Copyright © 2016 Elsevier B.V. All rights reserved.

[Analysis on the antimicrobial resistance of lactic acid bacteria isolated from the yogurt sold in China].

PubMed

Fan, Qin; Liu, Shuliang; Li, Juan; Huang, Tingting

2012-05-01

To analyze the antimicrobial susceptibility of lactic acid bacteria (LAB) from yogurt, and to provide references for evaluating the safety of LAB and screening safe strains. The sensitivity of 43 LAB strains, including 14 strains of Streptococcus thermophilus, 12 strains of Lactobacillus acidophilus, 9 strains of Lactobacillus bulgaricus and 8 strains of Bifidobacterium, to 22 antibiotics were tested by agar plate dilution method. All 43 LAB strains were resistant to trimethoprim, nalidixic acid, ciprofloxacin, lomefloxacin, danofloxacin and polymyxin E. Their resistances to kanamycin, tetracycline, clindamycin, doxycycline and cephalothin were varied. The sensitivity to other antibiotics were sensitive or moderate. All isolates were multidrug-resistant. The antimicrobial resistance of tested LAB strains was comparatively serious, and continuously monitoring their antimicrobial resistance and evaluating their safety should be strengthened.

In vitro effectiveness of triterpenoids and their synergistic effect with antibiotics against Staphylococcus aureus strains.

PubMed

Hamza, Muhammad; Nadir, Maha; Mehmood, Nadir; Farooq, Adeel

2016-01-01

The aim of this study is to evaluate the effect of four triterpenoids such as oleanolic acid, ursolic acid, cycloastragenol, and beta-boswellic acid alone and in combination with antibiotics against Staphylococcus aureus strains. Sixteen clinical strains of S. aureus from infected wounds were isolated. Eight were methicillin-sensitive S. aureus (MSSA), and the other eight were methicillin-resistant S. aureus (MRSA). The activity was also seen in reference S. aureus American Type Culture Collection ™ strains. The activity of all the triterpenoids and antibiotics against S. aureus was evaluated by broth microdilution method. The effectiveness was judged by comparing the minimum inhibitory concentrations (MICs) of the compounds with antibiotics. The combination of antibiotics with compounds was evaluated by their fractional inhibitory concentrations (FIC). Against both clinical and reference MSSA strains, none of the compounds exhibited comparable activity to antibiotics vancomycin or cefradine except for ursolic acid (MIC 7.8 μg/ml). Against MRSA, all compounds (MIC 16-128 μg/ml) showed lesser activity than vancomycin (MIC 5.8 μg/ml). Among triterpenoid-antibiotic combinations, the most effective were ursolic acid and vancomycin against clinical strain MSSA (FIC S 0.17). However, overall, different combinations between triterpenoids and antibiotics showed 95%-46% ( P < 0.05) reduction in MICs of antibiotics compared to when antibiotics were used alone. Cefradine, a drug not suitable for treating MRSA (MIC = 45 μg/ml), showed a remarkable decrease in its MIC (87% P< 0.01) when it was used in combination with oleanolic acid or ursolic acid in both clinical and reference strains. The tested triterpenoids are relatively weaker than antibiotics. However, when used in combination with antibiotics, they showed remarkable synergistic effect and thus can help in prolonging the viability of these antibiotics against S. aureus infections. Furthermore, reduction in MIC of cefradine with oleanolic acid indicates their potential use against MRSA.

Radiation from Directional Seismic Sources in Laterally Stratified Media with Application to Arctic Ice Cracking Noise

DTIC Science & Technology

1989-05-22

Stress- Strain Relation . . . . . . . . . . . . . . . . . . . . . . . . 88 5.3 Equivalent Transversely Isotropic Elastic Constants for Periodi- cally...a vertical wavenumber parameters for compressional waves. # : vertical wavenumber parameters for shear waves. 6 dip angle, refer to Fig 3.2. E strain ...been pursued along two different lines[1] : First, in terms of body forces ; second, in terms of disconti- nuities in displacement or strain across a

Insecticide Resistance and Metabolic Mechanisms Involved in Larval and Adult Stages of Aedes aegypti Insecticide-Resistant Reference Strains from Cuba.

PubMed

Bisset, Juan Andrés; Rodríguez, María Magdalena; French, Leydis; Severson, David W; Gutiérrez, Gladys; Hurtado, Daymi; Fuentes, Ilario

2014-12-01

Studies were conducted to compare levels of insecticide resistance and to determine the metabolic resistance mechanisms in larval and adult stages of Aedes aegypti from Cuba. Three insecticide-resistant reference strains of Ae. aegypti from Cuba were examined. These strains were derived from a Santiago de Cuba strain isolated in 1997; it was previously subjected to a strong selection for resistance to temephos (SAN-F6), deltamethrin (SAN-F12), and propoxur (SAN-F13) and routinely maintained in the laboratory under selection pressure up to the present time, when the study was carried out. In addition, an insecticide-susceptible strain was used for comparison. The insecticide resistance in larvae and adults was determined using standard World Health Organization methodologies. Insecticide resistance mechanisms were determined by biochemical assays. The esterases (α EST and β EST) and mixed function oxidase (MFO) activities were significantly higher in adults than in the larvae of the three resistant strains studied. The association of resistance level with the biochemical mechanism for each insecticide was established for each stage. The observed differences between larval and adult stages of Ae. aegypti in their levels of insecticide resistance and the biochemical mechanisms involved should be included as part of monitoring and surveillance activities in Ae. aegypti vector control programs.

Antibacterial activity of different honeys against pathogenic bacteria.

PubMed

Voidarou, C; Alexopoulos, A; Plessas, S; Karapanou, A; Mantzourani, I; Stavropoulou, E; Fotou, K; Tzora, A; Skoufos, I; Bezirtzoglou, E

2011-12-01

To study the antimicrobial activity of honey, 60 samples of various botanical origin were evaluated for their antimicrobial activities against 16 clinical pathogens and their respective reference strains. The microbiological quality of honeys and the antibiotic susceptibility of the various isolates were also examined. The bioassay applied for determining the antimicrobial effect employs the well-agar diffusion method and the estimation of minimum active dilution which produces a 1mm diameter inhibition zone. All honey samples, despite their origin (coniferous, citrus, thyme or polyfloral), showed antibacterial activity against the pathogenic and their respective reference strains at variable levels. Coniferous and thyme honeys showed the highest activity with an average minimum dilution of 17.4 and 19.2% (w/v) followed by citrus and polyfloral honeys with 20.8 and 23.8% respectively. Clinical isolates of Staphylococcus aureus subsp. aureus, Escherichia coli, Salmonella enterica subsp. Enterica, Streptococcus pyogenes, Bacillus cereus and Bacillus subtilis were proven to be up to 60% more resistant than their equal reference strains thus emphasizing the variability in the antibacterial effect of honey and the need for further research. Copyright © 2011 Elsevier Ltd. All rights reserved.

Antimicrobial Sensitivity of Avibacterium paragallinarum Isolates from Four Latin American Countries.

PubMed

Luna-Galaz, G A; Morales-Erasto, V; Peñuelas-Rivas, C G; Blackall, P J; Soriano-Vargas, E

2016-09-01

The antimicrobial sensitivity of 11 reference strains and 66 Avibacterium paragallinarum isolates from four Latin American countries was investigated. All 11 reference strains were sensitive to amoxicillin-clavulanic acid, ampicillin, fosfomycin, gentamicin, kanamycin, neomycin, penicillin, tetracycline, and trimethoprim-sulfamethoxazole. The 11 reference strains were all resistant to lincomycin. All isolates (100%) from Mexico, Panama, and Peru were sensitive to amoxicillin-clavulanic acid, ampicillin, and fosfomycin. The Ecuadorian isolates showed some level of resistance to all 16 agents tested. The Ecuadorian isolates were significantly more sensitive to erythromycin, lincomycin, and streptomycin, and significantly more resistant to gentamicin, kanamycin, penicillin, and tetracycline, than the Mexican isolates. A total of 57.5% (38/66) of tested isolates were multi-drug resistant (MDR), with 16 MDR patterns detected in 88.4% (23/26) of the antimicrobial-resistant isolates from Ecuador, and 8 MDR patterns detected in 42.8% (15/35) of the antimicrobial-resistant isolates from Mexico. In conclusion, the variation in antimicrobial sensitivity patterns between isolates from Ecuador and Mexico emphasizes the importance of active, ongoing monitoring of A. paragallinarum isolates.

Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains.

PubMed

Han, Mee-Jung; Kim, Jin Young; Kim, Jung A

2014-04-01

Escherichia coli typically secretes many proteins into the periplasmic space, and the periplasmic proteins have been used for the secretory production of various proteins by the biotechnology industry. However, the identity of all of the E. coli periplasmic proteins remains unknown. Here, high-resolution periplasmic proteome reference maps of the E. coli K-12 and B strains were constructed and compared. Of the 145 proteins identified by tandem mass spectrometry, 61 proteins were conserved in the two strains, whereas 11 and 12 strain-specific proteins were identified for the E. coli K-12 and B strains, respectively. In addition, 27 proteins exhibited differences in intensities greater than 2-fold between the K-12 and B strains. The periplasmic proteins MalE and OppA were the most abundant proteins in the two E. coli strains. Distinctive differences between the two strains included several proteins that were caused by genetic variations, such as CybC, FliC, FliY, KpsD, MglB, ModA, and Ybl119, hydrolytic enzymes, particularly phosphatases, glycosylases, and proteases, and many uncharacterized proteins. Compared to previous studies, the localization of many proteins, including 30 proteins for the K-12 strain and 53 proteins for the B strain, was newly identified as periplasmic. This study identifies the largest number of proteins in the E. coli periplasm as well as the dynamics of these proteins. Additionally, these findings are summarized as reference proteome maps that will be useful for studying protein secretion and may provide new strategies for the enhanced secretory production of recombinant proteins. Copyright © 2013. Published by Elsevier B.V.

Delineation of the Species Haemophilus influenzae by Phenotype, Multilocus Sequence Phylogeny, and Detection of Marker Genes▿ †

PubMed Central

Nørskov-Lauritsen, Niels; Overballe, Merete D.; Kilian, Mogens

2009-01-01

To obtain more information on the much-debated definition of prokaryotic species, we investigated the borders of Haemophilus influenzae by comparative analysis of H. influenzae reference strains with closely related bacteria including strains assigned to Haemophilus haemolyticus, cryptic genospecies biotype IV, and the never formally validated species “Haemophilus intermedius”. Multilocus sequence phylogeny based on six housekeeping genes separated a cluster encompassing the type and the reference strains of H. influenzae from 31 more distantly related strains. Comparison of 16S rRNA gene sequences supported this delineation but was obscured by a conspicuously high number of polymorphic sites in many of the strains that did not belong to the core group of H. influenzae strains. The division was corroborated by the differential presence of genes encoding H. influenzae adhesion and penetration protein, fuculokinase, and Cu,Zn-superoxide dismutase, whereas immunoglobulin A1 protease activity or the presence of the iga gene was of limited discriminatory value. The existence of porphyrin-synthesizing strains (“H. intermedius”) closely related to H. influenzae was confirmed. Several chromosomally encoded hemin biosynthesis genes were identified, and sequence analysis showed these genes to represent an ancestral genotype rather than recent transfers from, e.g., Haemophilus parainfluenzae. Strains previously assigned to H. haemolyticus formed several separate lineages within a distinct but deeply branching cluster, intermingled with strains of “H. intermedius” and cryptic genospecies biotype IV. Although H. influenzae is phenotypically more homogenous than some other Haemophilus species, the genetic diversity and multicluster structure of strains traditionally associated with H. influenzae make it difficult to define the natural borders of that species. PMID:19060144

Hoof position during limb loading affects dorsoproximal bone strains on the equine proximal phalanx.

PubMed

Singer, Ellen; Garcia, Tanya; Stover, Susan

2015-07-16

Sagittal fractures of the proximal phalanx (P1) in the racehorse appear to be associated with turf racing surfaces, which are known to restrict forward slide of the foot at impact. We hypothesized that restriction of forward foot slip would result in higher P1 bone strains during metacarpophalangeal joint (MCPJ) hyperextension. Unilateral limbs from six equine cadavers were instrumented with strain gauges and bone reference markers to measure dorsoproximal P1 bone strains and MCPJ extension, collateromotion and axial rotation during in vitro limb loading to 10,500 N. By limiting movement of the distal actuator platform, three different foot conditions (forward, free, and restricted) were applied in a randomised block design. Bone reference markers, recorded by video, were analyzed to determine motion of P1 relative to MC3. Rosette strain data were reduced to principal and shear magnitudes and directions. A mixed model ANOVA determined the effect of foot position on P1 bone strains and MCPJ angles. At 10,000 N load, the restricted condition resulted in higher P1 axial compressive (p=0.015), maximum shear (p=0.043) and engineering shear (p=0.046) strains compared to the forward condition. The restricted condition had higher compressive (p=0.025) and lower tensile (p=0.043) principal strains compared to the free condition. For the same magnitude of principal or shear strains, axial rotation and collateromotion angles were greatest for the restricted condition. Therefore, the increase in P1 principal compressive and shear bone strains associated with restricted foot slip indicate that alterations in foot:ground interaction may play a role in fracture occurrence in horses. Copyright © 2015 Elsevier Ltd. All rights reserved.

Laser Induced Damage in Optical Materials: 1980.

DTIC Science & Technology

1981-10-01

is used to describe microplastic strain resulting from short duration loading, and the term microcreep refers to time dependent strains of small...effectively, and the maximum temperature rise will thus be at the Work supported by Naval Sea Systems Command, PflS-405, and Naval Weapons Center

[Behavior of different strains of Staphylococcus aureus against root canal filling cements].

PubMed

Pumarola, J; Berástegui, E; Canalda, C; Brau, E

1991-01-01

The mean goal of this study is the determination of the conduct of 120 strains of Staphylococcus aureus against seven root canal sealers: Traitement Spad, Endométhasone, N2 Universal, AH26 with silver, Diaket-A, Tubli Seal and Sealapex. The agar diffusion test was employed in the determination of its bacterial growth inhibition. The results obtained have demonstrated values very different between the tested strains. Therefore we recommended to employ strains with reference in the investigation of the bacterial growth inhibition in order to repeat equal experimentation conditions.

Factors associated with quality of life and caregiver strain amongst frail older adults referred to a community rehabilitation service: implications for service delivery.

PubMed

Comans, Tracy A; Currin, Michelle L; Brauer, Sandra G; Haines, Terry P

2011-01-01

To identify factors contributing to reduced quality of life and increased caregiver strain in an older population referred to a community rehabilitation team and to recommend service delivery models. Analytical cross-sectional study arising from baseline assessments from 107 subjects drawn from a randomised controlled trial of community rehabilitation service delivery models. A community rehabilitation team based in Brisbane, Queensland, Australia. Primary outcome variables include quality of life (EQ-5D & VAS) and Carer Strain Index. Predictor variables include participation in functional activities, history of falls, number of medications, number of co-morbidities, depression, environmental hazards, physical function and nutrition. Association between variables assessed using linear regression. Major factors contributing to reduced quality of life were having reduced participation in daily activities, depression, and having poor vision. Having poor nutrition and no longer driving also contributed to poor quality of life. The major factor contributing to increased caregiver strain was reduced participation in daily activities by the older person. Community rehabilitation services working with older populations must adopt models of care that screen for and address a wide range of factors that contribute to poor quality of life and caregiver strain.

Development of two real-time polymerase chain reaction assays to detect Actinobacillus pleuropneumoniae serovars 1-9-11 and serovar 2.

PubMed

Marois-Créhan, Corinne; Lacouture, Sonia; Jacques, Mario; Fittipaldi, Nahuel; Kobisch, Marylène; Gottschalk, Marcelo

2014-01-01

Two real-time, or quantitative, polymerase chain reaction (qPCR) assays were developed to detect Actinobacillus pleuropneumoniae serovars 1-9-11 (highly related serovars with similar virulence potential) and serovar 2, respectively. The specificity of these assays was verified on a collection of 294 strains, which included all 16 reference A. pleuropneumoniae strains (including serovars 5a and 5b), 263 A. pleuropneumoniae field strains isolated between 1992 and 2009 in different countries, and 15 bacterial strains other than A. pleuropneumoniae. The detection levels of both qPCR tests were evaluated using 10-fold dilutions of chromosomal DNA from reference strains of A. pleuropneumoniae serovars 1 and 2, and the detection limit for both assays was 50 fg per assay. The analytical sensitivities of the qPCR tests were also estimated by using pure cultures and tonsils experimentally spiked with A. pleuropneumoniae. The detection threshold was 2.5 × 10(4) colony forming units (CFU)/ml and 2.9 × 10(5) CFU/0.1 g of tonsil, respectively, for both assays. These specific and sensitive tests can be used for the serotyping of A. pleuropneumoniae in diagnostic laboratories to control porcine pleuropneumonia.

Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations.

PubMed

Leitwein, M; Gagnaire, P-A; Desmarais, E; Guendouz, S; Rohmer, M; Berrebi, P; Guinand, B

2016-12-01

A genome-wide assessment of diversity is provided for wild Mediterranean brown trout Salmo trutta populations from headwater tributaries of the Orb River and from Atlantic and Mediterranean hatchery-reared strains that have been used for stocking. Double-digest restriction-site-associated DNA sequencing (dd-RADseq) was performed and the efficiency of de novo and reference-mapping approaches to obtain individual genotypes was compared. Large numbers of single nucleotide polymorphism (SNP) markers with similar genome-wide distributions were discovered using both approaches (196 639 v. 121 016 SNPs, respectively), with c. 80% of the loci detected de novo being also found with reference mapping, using the Atlantic salmon Salmo salar genome as a reference. Lower mapping density but larger nucleotide diversity (π) was generally observed near extremities of linkage groups, consistent with regions of residual tetrasomic inheritance observed in salmonids. Genome-wide diversity estimates revealed reduced polymorphism in hatchery strains (π = 0·0040 and π = 0·0029 in Atlantic and Mediterranean strains, respectively) compared to wild populations (π = 0·0049), a pattern that was congruent with allelic richness estimated from microsatellite markers. Finally, pronounced heterozygote deficiency was found in hatchery strains (Atlantic F IS = 0·18; Mediterranean F IS = 0·42), indicating that stocking practices may affect the genetic diversity in wild populations. These new genomic resources will provide important tools to define better conservation strategies in S. trutta. © 2016 The Fisheries Society of the British Isles.

Reassortment and evolution of current human influenza A and B viruses.

PubMed

Xu, Xiyan; Lindstrom, Stephen E; Shaw, Michael W; Smith, Catherine B; Hall, Henrietta E; Mungall, Bruce A; Subbarao, Kanta; Cox, Nancy J; Klimov, Alexander

2004-07-01

During the 2001-2002 influenza season, human influenza A (H1N2) reassortant viruses were detected globally. The hemagglutinin (HA) of these H1N2 viruses was similar to that of the A/New Caledonia/20/99 (H1N1) vaccine strain both antigenically and genetically, while their neuraminidase (NA) was antigenically and genetically related to that of recent human influenza H3N2 reference viruses such as A/Moscow/10/99. All six internal genes of the H1N2 reassortants originated from an H3N2 virus. After being detected only in eastern Asia during the past 10 years, Influenza B/Victoria/2/87 lineage viruses reappeared in many countries outside of Asia in 2001. Additionally, reassortant influenza B viruses possessing an HA similar to that of B/Shandong/7/97, a recent B/Victoria/2/87 lineage reference strain, and an NA closely related to that of B/Sichuan/379/99, a recent B/Yamagata/16/88 lineage reference strain, were isolated globally and became the predominant influenza B epidemic strain. The current influenza vaccine is expected to provide good protection against H1N2 viruses because it contains A/New Caledonia/20/99 (H1N1) and A/Panama/2007/99 (H3N2) like viruses whose H1 HA or N2 NA are antigenically similar to those of recent circulating H1N2 viruses. On the other hand, widespread circulation of influenza B Victoria lineage viruses required inclusion of a strain from this lineage in influenza vaccines for the 2002-2003 season.

Cis and Trans Isomers of Cycloalkenes

ERIC Educational Resources Information Center

Barrows, Susan E.; Eberlein, Thomas H.

2005-01-01

A study investigates the strain in medium-sized cycloalkenes and the geometric and electronic distortions through which alkenes can relieve that strain. Literature data is summarized and results are presented with the aim of providing a concise reference for those interested in addressing the topic in an introductory organic chemistry curriculum.

Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

PubMed

Vuilleumier, Stéphane; Chistoserdova, Ludmila; Lee, Ming-Chun; Bringel, Françoise; Lajus, Aurélie; Zhou, Yang; Gourion, Benjamin; Barbe, Valérie; Chang, Jean; Cruveiller, Stéphane; Dossat, Carole; Gillett, Will; Gruffaz, Christelle; Haugen, Eric; Hourcade, Edith; Levy, Ruth; Mangenot, Sophie; Muller, Emilie; Nadalig, Thierry; Pagni, Marco; Penny, Christian; Peyraud, Rémi; Robinson, David G; Roche, David; Rouy, Zoé; Saenampechek, Channakhone; Salvignol, Grégory; Vallenet, David; Wu, Zaining; Marx, Christopher J; Vorholt, Julia A; Olson, Maynard V; Kaul, Rajinder; Weissenbach, Jean; Médigue, Claudine; Lidstrom, Mary E

2009-01-01

Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid). These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.

Clinical Chemistry Reference Intervals for C57BL/6J, C57BL/6N, and C3HeB/FeJ Mice (Mus musculus)

PubMed Central

Otto, Gordon P; Rathkolb, Birgit; Oestereicher, Manuela A; Lengger, Christoph J; Moerth, Corinna; Micklich, Kateryna; Fuchs, Helmut; Gailus-Durner, Valérie; Wolf, Eckhard; de Angelis, Martin Hrabě

2016-01-01

Although various mouse inbred strains are widely used to investigate disease mechanisms and to establish new therapeutic strategies, sex-specific reference intervals for laboratory diagnostic analytes that are generated from large numbers of animals have been unavailable. In this retrospective study, we screened data from more than 12,000 mice phenotyped in the German Mouse Clinic from January 2006 through June 2014 and selected animals with the genetic background of C57BL/6J, C57BL/6N, or C3HeB/FeJ. In addition, we distinguished between the C57BL/6NTac substrain and C57BL/6N mice received from other vendors. The corresponding data sets of electrolytes (sodium, potassium, calcium, chloride, inorganic phosphate), lipids (cholesterol, triglyceride), and enzyme activities (ALT, AST, ALP, α-amylase) and urea, albumin, and total protein levels were analyzed. Significant effects of age and sex on these analytes were identified, and strain- or substrain- and sex-specific reference intervals for 90- to 135-d-old mice were calculated. In addition, we include an overview of the literature that reports clinical chemistry values for wild-type mice of different strains. Our results support researchers interpreting clinical chemistry values from various mouse mutants and corresponding wild-type controls based on the examined strains and substrains. PMID:27423143

Clinical Chemistry Reference Intervals for C57BL/6J, C57BL/6N, and C3HeB/FeJ Mice (Mus musculus).

PubMed

Otto, Gordon P; Rathkolb, Birgit; Oestereicher, Manuela A; Lengger, Christoph J; Moerth, Corinna; Micklich, Kateryna; Fuchs, Helmut; Gailus-Durner, Valérie; Wolf, Eckhard; Hrabě de Angelis, Martin

2016-01-01

Although various mouse inbred strains are widely used to investigate disease mechanisms and to establish new therapeutic strategies, sex-specific reference intervals for laboratory diagnostic analytes that are generated from large numbers of animals have been unavailable. In this retrospective study, we screened data from more than 12,000 mice phenotyped in the German Mouse Clinic from January 2006 through June 2014 and selected animals with the genetic background of C57BL/6J, C57BL/6N, or C3HeB/FeJ. In addition, we distinguished between the C57BL/6NTac substrain and C57BL/6N mice received from other vendors. The corresponding data sets of electrolytes (sodium, potassium, calcium, chloride, inorganic phosphate), lipids (cholesterol, triglyceride), and enzyme activities (ALT, AST, ALP, α-amylase) and urea, albumin, and total protein levels were analyzed. Significant effects of age and sex on these analytes were identified, and strain- or substrain- and sex-specific reference intervals for 90- to 135-d-old mice were calculated. In addition, we include an overview of the literature that reports clinical chemistry values for wild-type mice of different strains. Our results support researchers interpreting clinical chemistry values from various mouse mutants and corresponding wild-type controls based on the examined strains and substrains.

Antibiotic susceptibility of bifidobacterial strains distributed in the Japanese market.

PubMed

Xiao, Jin-Zhong; Takahashi, Sachiko; Odamaki, Toshitaka; Yaeshima, Tomoko; Iwatsuki, Keiji

2010-01-01

The aim of the present study was to analyze the antibiotic susceptibility of bifidobacterial strains distributed in the Japanese market. A total of 23 strains, including probiotic isolates from foods, supplements, pharmaceuticals and reference strains of each species (or subspecies), were tested for susceptibility to 15 antibiotics by the broth microdilution method and examined for the presence of possible resistant determinants. The strains were susceptible overall to chloramphenicol, ampicillin, vancomycin and linezolid, and were intrinsically resistant to aminoglycoside group agents. Susceptibility to erythromycin, clindamycin, rifampicin, tetracycline and trimethoprim varied among the strains. All strains of Bifidobacterium animalis subsp. lactis were resistant to tetracycline and appeared to harbor tet(W) genes. No risk factor for safety was found for bifidobacterial strains distributed in the Japanese market in respect of their antimicrobial resistance, although the presence of the tet(W) gene in some strains stresses the need for future evaluation.

Sex- and Method-Specific Reference Values for Right Ventricular Strain by 2-Dimensional Speckle-Tracking Echocardiography.

PubMed

Muraru, Denisa; Onciul, Sebastian; Peluso, Diletta; Soriani, Nicola; Cucchini, Umberto; Aruta, Patrizia; Romeo, Gabriella; Cavalli, Giacomo; Iliceto, Sabino; Badano, Luigi P

2016-02-01

Despite the fact that assessment of right ventricular longitudinal strain (RVLS) carries important implications for patient diagnosis, prognosis, and treatment, its implementation in clinical settings has been hampered by the limited reference values and the lack of uniformity in software, method, and definition used for measuring RVLS. Accordingly, this study was designed to establish (1) the reference values for RVLS by 2-dimensional speckle-tracking echocardiography; and (2) their relationship with demographic, hemodynamic, and cardiac factors. In 276 healthy volunteers (55% women; age, 18-76 years), free wall and septum RVLS (6 segments) and free wall RVLS (3 segments) using both 6- and 3-segment regions of interest were obtained. Feasibility of 6-segment RVLS was 92%. Free wall RVLS from 3- versus 6-segment regions of interest had similar values, yet 6-segment region of interest was more feasible (86% versus 73%; P<0.001) and reproducible. Reference values (lower limits of normality) were as follows: 6-segment RVLS, -24.7±2.6% (-20.0%) for men and -26.7±3.1% (-20.3%) for women; 3-segment RVLS, -29.3±3.4% (-22.5%) for men and -31.6±4.0% (-23.3%) for women (P<0.001). Free wall RVLS was 5±2 strain units (%) larger in magnitude than 6-segment RVLS, 10±4% larger than septal RVLS, and 2±4% larger in women than in men (P<0.001). At multivariable analysis, age, sex, pulmonary systolic pressure, right atrial minimal volume, as well as right atrial and left ventricular longitudinal strain resulted as correlates of RVLS values. This is the largest study providing sex- and method-specific reference values for RVLS. Our data may foster the implementation of 2-dimensional speckle-tracking echocardiography-derived RV analysis in clinical practice. © 2016 American Heart Association, Inc.

Application of recombinant hemagglutinin proteins as alternative antigen standards for pandemic influenza vaccines.

PubMed

Choi, Yejin; Kwon, Seong Yi; Oh, Ho Jung; Shim, Sunbo; Chang, Seokkee; Chung, Hye Joo; Kim, Do Keun; Park, Younsang; Lee, Younghee

2017-09-01

The single radial immunodiffusion (SRID) assay, used to quantify hemagglutinin (HA) in influenza vaccines, requires reference reagents; however, because centralized production of reference reagents may slow the emergency deployment of vaccines, alternatives are needed. We investigated the production of HA proteins using recombinant DNA technology, rather than a traditional egg-based production process. The HA proteins were then used in an SRID assay as a reference antigen. We found that HA can be quantified in both egg-based and cell-based influenza vaccines when recombinant HAs (rHAs) are used as the reference antigen. Furthermore, we confirmed that rHAs obtained from strains with pandemic potential, such as H5N1, H7N3, H7N9, and H9N2 strains, can be utilized in the SRID assay. The rHA production process takes just one month, in contrast to the traditional process that takes three to four months. The use of rHAs may reduce the time required to produce reference reagents and facilitate timely introduction of vaccines during emergencies.

Unique strain history during ejection in canine left ventricle.

PubMed

Douglas, A S; Rodriguez, E K; O'Dell, W; Hunter, W C

1991-05-01

Understanding the relationship between structure and function in the heart requires a knowledge of the connection between the local behavior of the myocardium (e.g., shortening) and the pumping action of the left ventricle. We asked the question, how do changes in preload and afterload affect the relationship between local myocardial deformation and ventricular volume? To study this, a set of small radiopaque beads was implanted in approximately 1 cm3 of the isolated canine heart left ventricular free wall. Using biplane cineradiography, we tracked the motion of these markers through various cardiac cycles (controlling pre- and afterload) using the relative motion of six markers to quantify the local three dimensional Lagrangian strain. Two different reference states (used to define the strains) were considered. First, we used the configuration of the heart at end diastole for that particular cardiac cycle to define the individual strains (which gave the local "shortening fraction") and the ejection fraction. Second, we used a single reference state for all cardiac cycles i.e., the end-diastolic state at maximum volume, to define absolute strains (which gave local fractional length) and the volume fraction. The individual strain versus ejection fraction trajectories were dependent on preload and afterload. For any one heart, however, each component of absolute strain was more tightly correlated to volume fraction. Around each linear regression, the individual measurements of absolute strain scattered with standard errors that averaged less than 7% of their range. Thus the canine hearts examined had a preferred kinematic (shape) history during ejection, different from the kinematics of filling and independent or pre-or afterload and of stroke volume.

Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade.

PubMed

López, M; Rueda, A; Florido, J P; Blasco, L; Fernández-García, L; Trastoy, R; Fernández-Cuenca, F; Martínez-Martínez, L; Vila, J; Pascual, A; Bou, G; Tomas, M

2018-02-06

In this study, we compared eighteen clinical strains of A. baumannii belonging to the ST-2 clone and isolated from patients in the same intensive care unit (ICU) in 2000 (9 strains referred to collectively as Ab_GEIH-2000) and 2010 (9 strains referred to collectively as Ab_GEIH-2010), during the GEIH-REIPI project (Umbrella BioProject PRJNA422585). We observed two main molecular differences between the Ab_GEIH-2010 and the Ab_GEIH-2000 collections, acquired over the course of the decade long sampling interval and involving the mobilome: i) a plasmid harbouring genes for bla OXA 24/40 ß-lactamase and abKA/abkB proteins of a toxin-antitoxin system; and ii) two temperate bacteriophages, Ab105-1ϕ (63 proteins) and Ab105-2ϕ (93 proteins), containing important viral defence proteins. Moreover, all Ab_GEIH-2010 strains contained a Quorum functional network of Quorum Sensing (QS) and Quorum Quenching (QQ) mechanisms, including a new QQ enzyme, AidA, which acts as a bacterial defence mechanism against the exogenous 3-oxo-C12-HSL. Interestingly, the infective capacity of the bacteriophages isolated in this study (Ab105-1ϕ and Ab105-2ϕ) was higher in the Ab_GEIH-2010 strains (carrying a functional Quorum network) than in the Ab_GEIH-2000 strains (carrying a deficient Quorum network), in which the bacteriophages showed little or no infectivity. This is the first study about the evolution of the Quorum network and the mobilome in clinical strains of Acinetobacter baumannii during a decade.

Comparative analysis of biofilm formation by Bacillus cereus reference strains and undomesticated food isolates and the effect of free iron.

PubMed

Hayrapetyan, Hasmik; Muller, Lisette; Tempelaars, Marcel; Abee, Tjakko; Nierop Groot, Masja

2015-05-04

Biofilm formation of Bacillus cereus reference strains ATCC 14579 and ATCC 10987 and 21 undomesticated food isolates was studied on polystyrene and stainless steel as contact surfaces. For all strains, the biofilm forming capacity was significantly enhanced when in contact with stainless steel (SS) as a surface as compared to polystyrene (PS). For a selection of strains, the total CFU and spore counts in biofilms were determined and showed a good correlation between CFU counts and total biomass of these biofilms. Sporulation was favoured in the biofilm over the planktonic state. To substantiate whether iron availability could affect B. cereus biofilm formation, the free iron availability was varied in BHI by either the addition of FeCl3 or by depletion of iron with the scavenger 2,2-Bipyridine. Addition of iron resulted in increased air-liquid interface biofilm on polystyrene but not on SS for strain ATCC 10987, while the presence of Bipyridine reduced biofilm formation for both materials. Biofilm formation was restored when excess FeCl3 was added in combination with the scavenger. Further validation of the iron effect for all 23 strains in microtiter plate showed that fourteen strains (including ATCC10987) formed a biofilm on PS. For eight of these strains biofilm formation was enhanced in the presence of added iron and for eleven strains it was reduced when free iron was scavenged. Our results show that stainless steel as a contact material provides more favourable conditions for B. cereus biofilm formation and maturation compared to polystyrene. This effect could possibly be linked to iron availability as we show that free iron availability affects B. cereus biofilm formation. Copyright © 2015 Elsevier B.V. All rights reserved.

First complete genome sequence of infectious laryngotracheitis virus

PubMed Central

2011-01-01

Background Infectious laryngotracheitis virus (ILTV) is an alphaherpesvirus that causes acute respiratory disease in chickens worldwide. To date, only one complete genomic sequence of ILTV has been reported. This sequence was generated by concatenating partial sequences from six different ILTV strains. Thus, the full genomic sequence of a single (individual) strain of ILTV has not been determined previously. This study aimed to use high throughput sequencing technology to determine the complete genomic sequence of a live attenuated vaccine strain of ILTV. Results The complete genomic sequence of the Serva vaccine strain of ILTV was determined, annotated and compared to the concatenated ILTV reference sequence. The genome size of the Serva strain was 152,628 bp, with a G + C content of 48%. A total of 80 predicted open reading frames were identified. The Serva strain had 96.5% DNA sequence identity with the concatenated ILTV sequence. Notably, the concatenated ILTV sequence was found to lack four large regions of sequence, including 528 bp and 594 bp of sequence in the UL29 and UL36 genes, respectively, and two copies of a 1,563 bp sequence in the repeat regions. Considerable differences in the size of the predicted translation products of 4 other genes (UL54, UL30, UL37 and UL38) were also identified. More than 530 single-nucleotide polymorphisms (SNPs) were identified. Most SNPs were located within three genomic regions, corresponding to sequence from the SA-2 ILTV vaccine strain in the concatenated ILTV sequence. Conclusions This is the first complete genomic sequence of an individual ILTV strain. This sequence will facilitate future comparative genomic studies of ILTV by providing an appropriate reference sequence for the sequence analysis of other ILTV strains. PMID:21501528

[Genetic diversity and phylogeny of rhizobia isolated from peanut (Arachis hypogaea)].

PubMed

Yang, Jiang-Ke; Xie, Fu-Li; Zhou, Jun-Chu

2002-12-01

Forty three rhizobium strains isolated from peanut (Arachis hypogaea) and 15 reference strains from other genus and species were analyzed by the method of 16S rRNA RFLP, 16S rRNA sequencing and 16S-23S IGS PCR RFLP. The results of the 16S rRNA RFLP shown that 43 strains tested were all ascribed to the genus of Bradyrhizobium phylogenetically. Strains tested were adjacent to the B. japonicum and far from B. elkanii 16S rRNA genotype. The genotypes generated by the 4 restriction endonucleases, Mbo I, Dde I, Hae III and Msp I, were same as the representatives of B. japonicum. The dendrogram generated by 16S rRNA sequence and Neighbor-joining method shown that peanut rhizobia clustered into the subcluster represented by B. japonicum and B. liaoningense, were more close to B. liaoningense genetically, and the sequence difference between them was less than 1%. High sequence similarity was also determined between B. liaoningense and B. japonicum. JZ1, representative strain of peanut rhizobia were systematically far from the B. elkanii, and the sequence divergence about 2%. The results from IGS RFLP analysis indicated that although they were phylogenetically close to B. japonicum and B. elkanii, peanut rhizobia forming an independent group at the similarity of 71% could be further divided into four subgroups, A, B, C and D. Subgroup A consisted of strains from different region, subgroup B was composed of strains from Wuchang, Qianjiang and Jingzhou, subgroup C was mainly composed of strains from Jingzhou and starins of subgroup D mainly from Neijiang. Reference strains from B. japonicum and B. elkanii were independently clustered into the subgroup E at the similarity of 71%. The geographical factor effect on genetic diversity of rhizobia was found.

Broadband Two-Photon Absorption Characteristics of Highly Photostable Fluorenyl-Dicyanoethylenylated [60] Fullerene Dyads (Postprint)

DTIC Science & Technology

2016-05-14

practical use. It is crucial since a i 1. ( ) i it il tauto eri resonances at the bridging C61Hα- [ ( ) ] t t f - j t - ( ) f ll r l s - r ri e si i l... i , lea i t t e f r ati f a f ll -c j ate f r f 6 acce t r ( ) a r ( ), as arke in purple. This resulted in an extended A–D conjugation length a d...absorbing properties. Scheme 1. Synthesis of C60(>CPAF-Cn) 1-Cn (n = 4, 9, 12, or 18) dyads. Reagents and conditions: i . C60, DBU, toluene, rt, 5.0 h; ii

Verification of Empirical Method for Determining Riverbank Stability. Report 19. Report 12-24 - 1974 through 1977 Data.

DTIC Science & Technology

1981-02-01

Cairo, Ill. Blaker Towhead, Tenn. Wolf Island, Vy. Obion-Tamm, Tenn. Hickman- Reelfoot , Ky. Kate Aubrey, Tenn. Island No. 8, Ky. Harbert Point, Miss...MEfIPI S DkISTRICI 20 Porter Lake , Ark., Failur. was first repo 701 mA P I-ft blufI bank 276+00 to 278+00 1966 May Jun 5 12-4 20 28+ 0.71...and La., 447 MAHP R-4-U to R-2-Uj 1955 0 R-2-U to R-0 one boring location** 1956 0 40 39 1.02 R-3-U 1958 150 Lake Karnac, Miss., 419 MAHP R-111-D to

Does the Army Need to Better Define Missions in Terms of Resources to More Effectively Manage in a Resource-Constrained Environment?

DTIC Science & Technology

1988-06-03

Consolidation L evelI Lev/el CPITICAL REVIEW 1- CR I T CL F~ 7-; -,1 V Li st *and R’ev iew and r ark - Ll S t Aft te1 i eu 1i spl av mis- tooether j*il i...SEP 0 6 1988SD. A thesis presented to the Faculty of the U.S. Army’ Command and General Staff College in partial S fulfillment of the requirements for...the d e g r -e C 0 MASTER OF MILITARY ART AND SCIENCE dr 0) by THOMAS E. ROBERTS, MAJ, USA , S . , University of Alabama, 1976 M.B.A. , University of

Embankment of Criteria and Performance Report, Red River Watershed, Gillham Lake, Cossatot River Arkansas

DTIC Science & Technology

1987-10-01

34Gunite" to D/S face of C.O.T. in left abutment. Note gunite machine mounted on the flatbed trailer. B-17 Photo No. 35. "Gunite" being applied to D/S...GRAY, MOD. HARD. IN THIN BEDDED OR LAMINATED . A FL 52’a,9 S107 S1t’hIGERS El 524 8 a/ " 41/1 !J ! / / // / / / / / / / / ///."/// / // / A. 54-35.75B...82171LEGEND / ~I2 -PHOTOGRAPHS A=’ / 1 AULT MOVEMENT E502.3 _no 0 - DI aj STRIKE ARK GRAY, LAMINATED IIFC QUARTZ SEAMS I7 -cRIA FAC 700 Do~ 4 Zz1 1 C4-0 RE:RV

Development of Retardation and Automatic Flotation System (R.A.F.T.)

DTIC Science & Technology

1980-07-07

recovery search Category I Hazard -i ’tationE is necessary. Detailed assembly operations inhibited. Classification eck list must be implemented...VW.KIDD=E CYL.NDER.A AH2)SPRcDS 6IEE AH4 I -86 54 3 2 ECK SIR DESO!fr4VA mr= . . z -i * - = Ik r 075 i AITZ~~ R__ roARK:8 .L,,I CE AI FITTSKE Ew Eb~I A \\t...INER VOWE5 .-...... U-...... 13 1 N5ERT DOWEL F~~INE, FLUSH WITH To FITM1 SET3t INER DWE 6I LSHWT 5 REVISIONS Eck SYM DESCR-PtM DT AO A EAEL..Y RELE-A

Selecting and validating reference genes for quantitative real-time PCR in Plutella xylostella (L.).

PubMed

You, Yanchun; Xie, Miao; Vasseur, Liette; You, Minsheng

2018-05-01

Gene expression analysis provides important clues regarding gene functions, and quantitative real-time PCR (qRT-PCR) is a widely used method in gene expression studies. Reference genes are essential for normalizing and accurately assessing gene expression. In the present study, 16 candidate reference genes (ACTB, CyPA, EF1-α, GAPDH, HSP90, NDPk, RPL13a, RPL18, RPL19, RPL32, RPL4, RPL8, RPS13, RPS4, α-TUB, and β-TUB) from Plutella xylostella were selected to evaluate gene expression stability across different experimental conditions using five statistical algorithms (geNorm, NormFinder, Delta Ct, BestKeeper, and RefFinder). The results suggest that different reference genes or combinations of reference genes are suitable for normalization in gene expression studies of P. xylostella according to the different developmental stages, strains, tissues, and insecticide treatments. Based on the given experimental sets, the most stable reference genes were RPS4 across different developmental stages, RPL8 across different strains and tissues, and EF1-α across different insecticide treatments. A comprehensive and systematic assessment of potential reference genes for gene expression normalization is essential for post-genomic functional research in P. xylostella, a notorious pest with worldwide distribution and a high capacity to adapt and develop resistance to insecticides.

Identification of Cronobacter species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with an optimized analysis method.

PubMed

Wang, Qi; Zhao, Xiao-Juan; Wang, Zi-Wei; Liu, Li; Wei, Yong-Xin; Han, Xiao; Zeng, Jing; Liao, Wan-Jin

2017-08-01

Rapid and precise identification of Cronobacter species is important for foodborne pathogen detection, however, commercial biochemical methods can only identify Cronobacter strains to genus level in most cases. To evaluate the power of mass spectrometry based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF MS) for Cronobacter species identification, 51 Cronobacter strains (eight reference and 43 wild strains) were identified by both MALDI-TOF MS and 16S rRNA gene sequencing. Biotyper RTC provided by Bruker identified all eight reference and 43 wild strains as Cronobacter species, which demonstrated the power of MALDI-TOF MS to identify Cronobacter strains to genus level. However, using the Bruker's database (6903 main spectra products) and Biotyper software, the MALDI-TOF MS analysis could not identify the investigated strains to species level. When MALDI-TOF MS analysis was performed using the combined in-house Cronobacter database and Bruker's database, bin setting, and unweighted pair group method with arithmetic mean (UPGMA) clustering, all the 51 strains were clearly identified into six Cronobacter species and the identification accuracy increased from 60% to 100%. We demonstrated that MALDI-TOF MS was reliable and easy-to-use for Cronobacter species identification and highlighted the importance of establishing a reliable database and improving the current data analysis methods by integrating the bin setting and UPGMA clustering. Copyright © 2017. Published by Elsevier B.V.

Lymphocyte proliferative responses of goats vaccinated with Brucella melitensis 16M or a delta purE201 strain.

PubMed Central

Olsen, S C; Cheville, N F; Stevens, M G; Houng, H H; Drazek, E S; Hadfield, T L; Warren, R L; Hoover, D L

1997-01-01

The response to a Brucella melitensis purEK deletion mutant, delta purE201 (referred to as strain 201), was compared with the response to its parental strain, 16M, in juvenile goats. Proliferative responses to gamma-irradiated bacteria were detected earlier in strain 201-infected goats. Lymphocytes from strain 16M- or 201-infected goats proliferated in response to one-dimensional polyacrylamide gel electrophoresis-separated proteins of similar mass isolated from strain 16M or Brucella abortus RB51. Data from this study suggest that some antigens stimulating cell-mediated responses are conserved among Brucella species, as 201- and 16M-infected goats recognized similar proteins expressed by RB51 and 16M. PMID:9199478

Rapid identification of Burkholderia mallei and Burkholderia pseudomallei by intact cell Matrix-assisted Laser Desorption/Ionisation mass spectrometric typing.

PubMed

Karger, Axel; Stock, Rüdiger; Ziller, Mario; Elschner, Mandy C; Bettin, Barbara; Melzer, Falk; Maier, Thomas; Kostrzewa, Markus; Scholz, Holger C; Neubauer, Heinrich; Tomaso, Herbert

2012-10-10

Burkholderia (B.) pseudomallei and B. mallei are genetically closely related species. B. pseudomallei causes melioidosis in humans and animals, whereas B. mallei is the causative agent of glanders in equines and rarely also in humans. Both agents have been classified by the CDC as priority category B biological agents. Rapid identification is crucial, because both agents are intrinsically resistant to many antibiotics. Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS) has the potential of rapid and reliable identification of pathogens, but is limited by the availability of a database containing validated reference spectra. The aim of this study was to evaluate the use of MALDI-TOF MS for the rapid and reliable identification and differentiation of B. pseudomallei and B. mallei and to build up a reliable reference database for both organisms. A collection of ten B. pseudomallei and seventeen B. mallei strains was used to generate a library of reference spectra. Samples of both species could be identified by MALDI-TOF MS, if a dedicated subset of the reference spectra library was used. In comparison with samples representing B. mallei, higher genetic diversity among B. pseudomallei was reflected in the higher average Eucledian distances between the mass spectra and a broader range of identification score values obtained with commercial software for the identification of microorganisms. The type strain of B. pseudomallei (ATCC 23343) was isolated decades ago and is outstanding in the spectrum-based dendrograms probably due to massive methylations as indicated by two intensive series of mass increments of 14 Da specifically and reproducibly found in the spectra of this strain. Handling of pathogens under BSL 3 conditions is dangerous and cumbersome but can be minimized by inactivation of bacteria with ethanol, subsequent protein extraction under BSL 1 conditions and MALDI-TOF MS analysis being faster than nucleic amplification methods. Our spectra demonstrated a higher homogeneity in B. mallei than in B. pseudomallei isolates. As expected for closely related species, the identification process with MALDI Biotyper software (Bruker Daltonik GmbH, Bremen, Germany) requires the careful selection of spectra from reference strains. When a dedicated reference set is used and spectra of high quality are acquired, it is possible to distinguish both species unambiguously. The need for a careful curation of reference spectra databases is stressed.

Rapid identification of Burkholderia mallei and Burkholderia pseudomallei by intact cell Matrix-assisted Laser Desorption/Ionisation mass spectrometric typing

PubMed Central

2012-01-01

Background Burkholderia (B.) pseudomallei and B. mallei are genetically closely related species. B. pseudomallei causes melioidosis in humans and animals, whereas B. mallei is the causative agent of glanders in equines and rarely also in humans. Both agents have been classified by the CDC as priority category B biological agents. Rapid identification is crucial, because both agents are intrinsically resistant to many antibiotics. Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS) has the potential of rapid and reliable identification of pathogens, but is limited by the availability of a database containing validated reference spectra. The aim of this study was to evaluate the use of MALDI-TOF MS for the rapid and reliable identification and differentiation of B. pseudomallei and B. mallei and to build up a reliable reference database for both organisms. Results A collection of ten B. pseudomallei and seventeen B. mallei strains was used to generate a library of reference spectra. Samples of both species could be identified by MALDI-TOF MS, if a dedicated subset of the reference spectra library was used. In comparison with samples representing B. mallei, higher genetic diversity among B. pseudomallei was reflected in the higher average Eucledian distances between the mass spectra and a broader range of identification score values obtained with commercial software for the identification of microorganisms. The type strain of B. pseudomallei (ATCC 23343) was isolated decades ago and is outstanding in the spectrum-based dendrograms probably due to massive methylations as indicated by two intensive series of mass increments of 14 Da specifically and reproducibly found in the spectra of this strain. Conclusions Handling of pathogens under BSL 3 conditions is dangerous and cumbersome but can be minimized by inactivation of bacteria with ethanol, subsequent protein extraction under BSL 1 conditions and MALDI-TOF MS analysis being faster than nucleic amplification methods. Our spectra demonstrated a higher homogeneity in B. mallei than in B. pseudomallei isolates. As expected for closely related species, the identification process with MALDI Biotyper software (Bruker Daltonik GmbH, Bremen, Germany) requires the careful selection of spectra from reference strains. When a dedicated reference set is used and spectra of high quality are acquired, it is possible to distinguish both species unambiguously. The need for a careful curation of reference spectra databases is stressed. PMID:23046611

Immunoelectrophoretic study of cell surface antigens from different Streptococcus mutans serotypes and Streptococcus sanguis.

PubMed

Ogier, J A; Klein, J P; Niddam, R; Frank, R M

1985-06-01

Antigens prepared from culture supernatants or whole cells of several cariogenic strains were examined by immunoelectrophoresis for their crossed antigenicity, with reference to Streptococcus mutans OMZ175, serotype f. Crossed immunoelectrophoresis revealed a crossreactivity between soluble extracellular and wall associated antigens of six strains of Streptococcus mutans and one strain of Streptococcus sanguis. Protease destroyed the immunoreactivity of crossreactive antigens. One of them was shown to be localized on the bacterial surface.

Measures of Bulk and Grain Strain in Deformation Processes(PREPRINT)

DTIC Science & Technology

2007-04-01

the process and a similar measure of the flow stress of the material. The effective , or equivalent, strain, based on an analogous definition for...The conjugate effective stress in this case is the uniaxial tensile stress . Based on equations (12) and (13), expressions for effective bulk strains...t |L(t)| in the reference state deformed to an image, x′ = t′ | L′(t′)|, in the deformed state . In both cases an equation of the form of

Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines

PubMed Central

Romano, Andrea; Trip, Hein; Campbell-Sills, Hugo; Bouchez, Olivier; Sherman, David; Lolkema, Juke S.

2013-01-01

Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines histamine, putrescine, and cadaverine by decarboxylating their amino acid precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C content) and the principal findings from its annotation, which might shed light onto the enzymatic machineries that are involved in its production of biogenic amines. PMID:23405290

Echocardiographic reference ranges for normal left atrial function parameters: results from the EACVI NORRE study.

PubMed

Sugimoto, Tadafumi; Robinet, Sébastien; Dulgheru, Raluca; Bernard, Anne; Ilardi, Federica; Contu, Laura; Addetia, Karima; Caballero, Luis; Kacharava, George; Athanassopoulos, George D; Barone, Daniele; Baroni, Monica; Cardim, Nuno; Hagendorff, Andreas; Hristova, Krasimira; Lopez, Teresa; de la Morena, Gonzalo; Popescu, Bogdan A; Penicka, Martin; Ozyigit, Tolga; Rodrigo Carbonero, Jose David; van de Veire, Nico; Von Bardeleben, Ralph Stephan; Vinereanu, Dragos; Zamorano, Jose Luis; Go, Yun Yun; Marchetta, Stella; Nchimi, Alain; Rosca, Monica; Calin, Andreea; Moonen, Marie; Cimino, Sara; Magne, Julien; Cosyns, Bernard; Galli, Elena; Donal, Erwan; Habib, Gilbert; Esposito, Roberta; Galderisi, Maurizio; Badano, Luigi P; Lang, Roberto M; Lancellotti, Patrizio

2018-06-01

To obtain the normal ranges for echocardiographic measurements of left atrial (LA) function from a large group of healthy volunteers accounting for age and gender. A total of 371 (median age 45 years) healthy subjects were enrolled at 22 collaborating institutions collaborating in the Normal Reference Ranges for Echocardiography (NORRE) study of the European Association of Cardiovascular Imaging (EACVI). Left atrial data sets were analysed with a vendor-independent software (VIS) package allowing homogeneous measurements irrespective of the echocardiographic equipment used to acquire data sets. The lowest expected values of LA function were 26.1%, 48.7%, and 41.4% for left atrial strain (LAS), 2D left atrial emptying fraction (LAEF), and 3D LAEF (reservoir function); 7.7%, 24.2%, and -0.53/s for LAS-active, LAEF-active, and LA strain rate during LA contraction (SRa) (pump function) and 12.0% and 21.6% for LAS-passive and LAEF-passive (conduit function). Left atrial reservoir and conduit function were decreased with age while pump function was increased. All indices of reservoir function and all LA strains had no difference in both gender and vendor. However, inter-vendor differences were observed in LA SRa despite the use of VIS. The NORRE study provides contemporary, applicable echocardiographic reference ranges for LA function. Our data highlight the importance of age-specific reference values for LA functions.

Proteome Analysis of the Penicillin Producer Penicillium chrysogenum

PubMed Central

Jami, Mohammad-Saeid; Barreiro, Carlos; García-Estrada, Carlos; Martín, Juan-Francisco

2010-01-01

Proteomics is a powerful tool to understand the molecular mechanisms causing the production of high penicillin titers by industrial strains of the filamentous fungus Penicillium chrysogenum as the result of strain improvement programs. Penicillin biosynthesis is an excellent model system for many other bioactive microbial metabolites. The recent publication of the P. chrysogenum genome has established the basis to understand the molecular processes underlying penicillin overproduction. We report here the proteome reference map of P. chrysogenum Wisconsin 54-1255 (the genome project reference strain) together with an in-depth study of the changes produced in three different strains of this filamentous fungus during industrial strain improvement. Two-dimensional gel electrophoresis, peptide mass fingerprinting, and tandem mass spectrometry were used for protein identification. Around 1000 spots were visualized by “blue silver” colloidal Coomassie staining in a non-linear pI range from 3 to 10 with high resolution, which allowed the identification of 950 proteins (549 different proteins and isoforms). Comparison among the cytosolic proteomes of the wild-type NRRL 1951, Wisconsin 54-1255 (an improved, moderate penicillin producer), and AS-P-78 (a penicillin high producer) strains indicated that global metabolic reorganizations occurred during the strain improvement program. The main changes observed in the high producer strains were increases of cysteine biosynthesis (a penicillin precursor), enzymes of the pentose phosphate pathway, and stress response proteins together with a reduction in virulence and in the biosynthesis of other secondary metabolites different from penicillin (pigments and isoflavonoids). In the wild-type strain, we identified enzymes to utilize cellulose, sorbitol, and other carbon sources that have been lost in the high penicillin producer strains. Changes in the levels of a few specific proteins correlated well with the improved penicillin biosynthesis in the high producer strains. These results provide useful information to improve the production of many other bioactive secondary metabolites. PMID:20154335

'Candidatus Phytoplasma solani', a novel taxon associated with stolbur- and bois noir-related diseases of plants.

PubMed

Quaglino, Fabio; Zhao, Yan; Casati, Paola; Bulgari, Daniela; Bianco, Piero Attilio; Wei, Wei; Davis, Robert Edward

2013-08-01

Phytoplasmas classified in group 16SrXII infect a wide range of plants and are transmitted by polyphagous planthoppers of the family Cixiidae. Based on 16S rRNA gene sequence identity and biological properties, group 16SrXII encompasses several species, including 'Candidatus Phytoplasma australiense', 'Candidatus Phytoplasma japonicum' and 'Candidatus Phytoplasma fragariae'. Other group 16SrXII phytoplasma strains are associated with stolbur disease in wild and cultivated herbaceous and woody plants and with bois noir disease in grapevines (Vitis vinifera L.). Such latter strains have been informally proposed to represent a separate species, 'Candidatus Phytoplasma solani', but a formal description of this taxon has not previously been published. In the present work, stolbur disease strain STOL11 (STOL) was distinguished from reference strains of previously described species of the 'Candidatus Phytoplasma' genus based on 16S rRNA gene sequence similarity and a unique signature sequence in the 16S rRNA gene. Other stolbur- and bois noir-associated ('Ca. Phytoplasma solani') strains shared >99 % 16S rRNA gene sequence similarity with strain STOL11 and contained the signature sequence. 'Ca. Phytoplasma solani' is the only phytoplasma known to be transmitted by Hyalesthes obsoletus. Insect vectorship and molecular characteristics are consistent with the concept that diverse 'Ca. Phytoplasma solani' strains share common properties and represent an ecologically distinct gene pool. Phylogenetic analyses of 16S rRNA, tuf, secY and rplV-rpsC gene sequences supported this view and yielded congruent trees in which 'Ca. Phytoplasma solani' strains formed, within the group 16SrXII clade, a monophyletic subclade that was most closely related to, but distinct from, that of 'Ca. Phytoplasma australiense'-related strains. Based on distinct molecular and biological properties, stolbur- and bois noir-associated strains are proposed to represent a novel species level taxon, 'Ca. Phytoplasma solani'; STOL11 is designated the reference strain.

[Susceptibility of Aedes aegypti (L.) strains from Havana to a Bacillus thuringiensis var. israelensis].

PubMed

Menéndez Díaz, Zulema; Rodríguez Rodríguez, Jinnay; Gato Armas, René; Companioni Ibañez, Ariamys; Díaz Pérez, Manuel; Bruzón Aguila, Rosa Yirian

2012-01-01

the integration of chemical and biological methods is one of the strategies for the vector control, due to the existing environmental problems and the concerns of the community as a result of the synthetic organic insecticide actions. The bacterium called Bacillus thuringiensis var. israelensis in liquid formulation has been widely used in the vector control programs in several countries and has shown high efficacy at lab in Cuba. to determine the susceptibility of Aedes aegypti collected in the municipalities of La Habana province to Bacillus thuringiensis var. israelensis. fifteen Aedes aegypti strains, one from each municipality, were used including larvae and pupas collected in 2010 and one reference strain known as Rockefeller. The aqueous formulation of Bacillus thuringiensis var. israelensis (Bactivec, Labiofam, Cuba) was used. The bioassays complied with the World Health Organization guidelines for use of bacterial larvicides in the public health sector. The larval mortality was read after 24 hours and the results were processed by the statistical system SPSS (11.0) through Probit analysis. the evaluated mosquito strains showed high susceptibility to biolarvicide, there were no significant differences in LC50 values of Ae. aegypti strains, neither in the comparison of these values with those of the reference strain. the presented results indicate that the use of Bacillus thuringiensis var. israelensis continues to be a choice for the control of Aedes aegypti larval populations in La Habana province.

Molecular typing of Escherichia coli strains associated with threatened sea ducks and near-shore marine habitats of south-west Alaska

USGS Publications Warehouse

Hollmén, Tuula E.; DebRoy, Chitrita; Flint, Paul L.; Safine, David E.; Schamber, Jason L.; Riddle, Ann E.; Trust, Kimberly A.

2011-01-01

In Alaska, sea ducks winter in coastal habitats at remote, non-industrialized areas, as well as in proximity to human communities and industrial activity. We evaluated prevalence and characteristics of Escherichia coli strains in faecal samples of Steller's eiders (Polysticta stelleri; n = 122) and harlequin ducks (Histrionicus histrionicus; n = 21) at an industrialized site and Steller's eiders (n = 48) at a reference site, and compared these strains with those isolated from water samples from near-shore habitats of ducks. The overall prevalence of E. coli was 16% and 67% in Steller's eiders and harlequin ducks, respectively, at the industrialized study site, and 2% in Steller's eiders at the reference site. Based on O and H antigen subtyping and genetic characterization by enterobacterial repetitive intergenic consensus polymerase chain reaction and pulsed-field gel electrophoresis, we found evidence of avian pathogenic E. coli (APEC) strains associated with both species and detected E. coli strains carrying virulence genes associated with mammals in harlequin ducks. Steller's eiders that carried APEC had lower serum total protein and albumin concentrations, providing further evidence of pathogenicity. The genetic profile of two E. coli strains from water matched an isolate from a Steller's eider providing evidence of transmission between near-shore habitats and birds.

Genome Sequencing and Analysis of Yersina pestis KIM D27, an Avirulent Strain Exempt from Select Agent Regulation

PubMed Central

Losada, Liliana; Varga, John J.; Hostetler, Jessica; Radune, Diana; Kim, Maria; Durkin, Scott; Schneewind, Olaf; Nierman, William C.

2011-01-01

Yersinia pestis is the causative agent of the plague. Y. pestis KIM 10+ strain was passaged and selected for loss of the 102 kb pgm locus, resulting in an attenuated strain, KIM D27. In this study, whole genome sequencing was performed on KIM D27 in order to identify any additional differences. Initial assemblies of 454 data were highly fragmented, and various bioinformatic tools detected between 15 and 465 SNPs and INDELs when comparing both strains, the vast majority associated with A or T homopolymer sequences. Consequently, Illumina sequencing was performed to improve the quality of the assembly. Hybrid sequence assemblies were performed and a total of 56 validated SNP/INDELs and 5 repeat differences were identified in the D27 strain relative to published KIM 10+ sequence. However, further analysis showed that 55 of these SNP/INDELs and 3 repeats were errors in the KIM 10+ reference sequence. We conclude that both 454 and Illumina sequencing were required to obtain the most accurate and rapid sequence results for Y. pestis KIMD27. SNP and INDELS calls were most accurate when both Newbler and CLC Genomics Workbench were employed. For purposes of obtaining high quality genome sequence differences between strains, any identified differences should be verified in both the new and reference genomes. PMID:21559501

Genome sequencing and analysis of Yersina pestis KIM D27, an avirulent strain exempt from select agent regulation.

PubMed

Losada, Liliana; Varga, John J; Hostetler, Jessica; Radune, Diana; Kim, Maria; Durkin, Scott; Schneewind, Olaf; Nierman, William C

2011-04-29

Yersinia pestis is the causative agent of the plague. Y. pestis KIM 10+ strain was passaged and selected for loss of the 102 kb pgm locus, resulting in an attenuated strain, KIM D27. In this study, whole genome sequencing was performed on KIM D27 in order to identify any additional differences. Initial assemblies of 454 data were highly fragmented, and various bioinformatic tools detected between 15 and 465 SNPs and INDELs when comparing both strains, the vast majority associated with A or T homopolymer sequences. Consequently, Illumina sequencing was performed to improve the quality of the assembly. Hybrid sequence assemblies were performed and a total of 56 validated SNP/INDELs and 5 repeat differences were identified in the D27 strain relative to published KIM 10+ sequence. However, further analysis showed that 55 of these SNP/INDELs and 3 repeats were errors in the KIM 10+ reference sequence. We conclude that both 454 and Illumina sequencing were required to obtain the most accurate and rapid sequence results for Y. pestis KIMD27. SNP and INDELS calls were most accurate when both Newbler and CLC Genomics Workbench were employed. For purposes of obtaining high quality genome sequence differences between strains, any identified differences should be verified in both the new and reference genomes.

Molecular typing of Escherichia coli strains associated with threatened sea ducks and near-shore marine habitats of south-west Alaska.

PubMed

Hollmén, Tuula E; Debroy, Chitrita; Flint, Paul L; Safine, David E; Schamber, Jason L; Riddle, Ann E; Trust, Kimberly A

2011-04-01

In Alaska, sea ducks winter in coastal habitats at remote, non-industrialized areas, as well as in proximity to human communities and industrial activity. We evaluated prevalence and characteristics of Escherichia coli strains in faecal samples of Steller's eiders (Polysticta stelleri; n = 122) and harlequin ducks (Histrionicus histrionicus; n = 21) at an industrialized site and Steller's eiders (n = 48) at a reference site, and compared these strains with those isolated from water samples from near-shore habitats of ducks. The overall prevalence of E. coli was 16% and 67% in Steller's eiders and harlequin ducks, respectively, at the industrialized study site, and 2% in Steller's eiders at the reference site. Based on O and H antigen subtyping and genetic characterization by enterobacterial repetitive intergenic consensus polymerase chain reaction and pulsed-field gel electrophoresis, we found evidence of avian pathogenic E. coli (APEC) strains associated with both species and detected E. coli strains carrying virulence genes associated with mammals in harlequin ducks. Steller's eiders that carried APEC had lower serum total protein and albumin concentrations, providing further evidence of pathogenicity. The genetic profile of two E. coli strains from water matched an isolate from a Steller's eider providing evidence of transmission between near-shore habitats and birds. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

Origanum vulgare subsp. hirtum essential oil prevented biofilm formation and showed antibacterial activity against planktonic and sessile bacterial cells.

PubMed

Schillaci, Domenico; Napoli, Edoardo Marco; Cusimano, Maria Grazia; Vitale, Maria; Ruberto, Andgiuseppe

2013-10-01

Essential oils from six different populations of Origanum vulgare subsp. hirtum were compared for their antibiofilm properties. The six essential oils (A to F) were characterized by a combination of gas chromatography with flame ionization detector and gas chromatography with mass spectrometer detector analyses. All oils showed weak activity against the planktonic form of a group of Staphylococcus aureus strains and against a Pseudomonas aeruginosa ATCC 15442 reference strain. The ability to inhibit biofilm formation was investigated at sub-MIC levels of 200, 100, and 50 m g/ml by staining sessile cells with safranin. Sample E showed the highest average effectiveness against all tested strains at 50 m g/ml and had inhibition percentages ranging from 30 to 52%. In the screening that used preformed biofilm from the reference strain P. aeruginosa, essential oils A through E were inactive at 200 m g/ml; F was active with a percentage of inhibition equal to 53.2%. Oregano essential oil can inhibit the formation of biofilms of various food pathogens and food spoilage organisms.

Optimal Reference Strain Structure for Studying Dynamic Responses of Flexible Rockets

NASA Technical Reports Server (NTRS)

Tsushima, Natsuki; Su, Weihua; Wolf, Michael G.; Griffin, Edwin D.; Dumoulin, Marie P.

2017-01-01

In the proposed paper, the optimal design of reference strain structures (RSS) will be performed targeting for the accurate observation of the dynamic bending and torsion deformation of a flexible rocket. It will provide the detailed description of the finite-element (FE) model of a notional flexible rocket created in MSC.Patran. The RSS will be attached longitudinally along the side of the rocket and to track the deformation of the thin-walled structure under external loads. An integrated surrogate-based multi-objective optimization approach will be developed to find the optimal design of the RSS using the FE model. The Kriging method will be used to construct the surrogate model. For the data sampling and the performance evaluation, static/transient analyses will be performed with MSC.Natran/Patran. The multi-objective optimization will be solved with NSGA-II to minimize the difference between the strains of the launch vehicle and RSS. Finally, the performance of the optimal RSS will be evaluated by checking its strain-tracking capability in different numerical simulations of the flexible rocket.

Geographical distribution of genetic polymorphism of the pathogen Histoplasma capsulatum isolated from infected bats, captured in a central zone of Mexico.

PubMed

Taylor, Maria Lucia; Chávez-Tapia, Catalina B; Rojas-Martínez, Alberto; del Rocio Reyes-Montes, Maria; del Valle, Mirian Bobadilla; Zúñiga, Gerardo

2005-09-01

Fourteen Histoplasma capsulatum isolates recovered from infected bats captured in Mexican caves and two human H. capsulatum reference strains were analyzed using random amplification of polymorphic DNA PCR-based and partial DNA sequences of four genes. Cluster analysis of random amplification of polymorphic DNA-patterns revealed differences for two H. capsulatum isolates of one migratory bat Tadarida brasiliensis. Three groups were identified by distance and maximum-parsimony analyses of arf, H-anti, ole, and tub1 H. capsulatum genes. Group I included most isolates from infected bats and one clinical strain from central Mexico; group II included the two isolates from T. brasiliensis; the human G-217B reference strain from USA formed an independent group III. Isolates from group II showed diversity in relation to groups I and III, suggesting a different H. capsulatum population.

Identification of Reference Genes for Quantitative Real Time PCR Assays in Aortic Tissue of Syrian Hamsters with Bicuspid Aortic Valve

PubMed Central

Rueda-Martínez, Carmen; Fernández, M. Carmen; Soto-Navarrete, María Teresa; Jiménez-Navarro, Manuel; Durán, Ana Carmen; Fernández, Borja

2016-01-01

Bicuspid aortic valve (BAV) is the most frequent congenital cardiac malformation in humans, and appears frequently associated with dilatation of the ascending aorta. This association is likely the result of a common aetiology. Currently, a Syrian hamster strain with a relatively high (∼40%) incidence of BAV constitutes the only spontaneous animal model of BAV disease. The characterization of molecular alterations in the aorta of hamsters with BAV may serve to identify pathophysiological mechanisms and molecular markers of disease in humans. In this report, we evaluate the expression of ten candidate reference genes in aortic tissue of hamsters in order to identify housekeeping genes for normalization using quantitative real time PCR (RT-qPCR) assays. A total of 51 adult (180–240 days old) and 56 old (300–440 days old) animals were used. They belonged to a control strain of hamsters with normal, tricuspid aortic valve (TAV; n = 30), or to the affected strain of hamsters with TAV (n = 45) or BAV (n = 32). The expression stability of the candidate reference genes was determined by RT-qPCR using three statistical algorithms, GeNorm, NormFinder and Bestkeeper. The expression analyses showed that the most stable reference genes for the three algorithms employed were Cdkn1β, G3pdh and Polr2a. We propose the use of Cdkn1β, or both Cdkn1β and G3pdh as reference genes for mRNA expression analyses in Syrian hamster aorta. PMID:27711171

Identification of Reference Genes for Quantitative Real Time PCR Assays in Aortic Tissue of Syrian Hamsters with Bicuspid Aortic Valve.

PubMed

Rueda-Martínez, Carmen; Fernández, M Carmen; Soto-Navarrete, María Teresa; Jiménez-Navarro, Manuel; Durán, Ana Carmen; Fernández, Borja

2016-01-01

Bicuspid aortic valve (BAV) is the most frequent congenital cardiac malformation in humans, and appears frequently associated with dilatation of the ascending aorta. This association is likely the result of a common aetiology. Currently, a Syrian hamster strain with a relatively high (∼40%) incidence of BAV constitutes the only spontaneous animal model of BAV disease. The characterization of molecular alterations in the aorta of hamsters with BAV may serve to identify pathophysiological mechanisms and molecular markers of disease in humans. In this report, we evaluate the expression of ten candidate reference genes in aortic tissue of hamsters in order to identify housekeeping genes for normalization using quantitative real time PCR (RT-qPCR) assays. A total of 51 adult (180-240 days old) and 56 old (300-440 days old) animals were used. They belonged to a control strain of hamsters with normal, tricuspid aortic valve (TAV; n = 30), or to the affected strain of hamsters with TAV (n = 45) or BAV (n = 32). The expression stability of the candidate reference genes was determined by RT-qPCR using three statistical algorithms, GeNorm, NormFinder and Bestkeeper. The expression analyses showed that the most stable reference genes for the three algorithms employed were Cdkn1β, G3pdh and Polr2a. We propose the use of Cdkn1β, or both Cdkn1β and G3pdh as reference genes for mRNA expression analyses in Syrian hamster aorta.

A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies.

PubMed

Ramos, Vitor; Morais, João; Vasconcelos, Vitor M

2017-04-25

The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies.

A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies

PubMed Central

Ramos, Vitor; Morais, João; Vasconcelos, Vitor M.

2017-01-01

The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies. PMID:28440791

[Detection and Analysis of Human Parainfluenza Virus Infection in Hospitalized Adults with Acute Respiratory Tract Infections].

PubMed

Li, Xing-Qiao; Liu, Xue-Wei; Zhou, Tao; Pei, Xiao-Fang

2017-11-01

To investigate the prevalence and gene characteristics of different groups of human parainfluenza virus (HPIV) infection in hospitalized adults with acute respiratory tract infections (ARI). RT-PCR was used to detect HPIV hemagglutinin (HA) DNA,which was extracted from sputum samples of 1 039 adult patients with ARI from March,2014 to June,2016. The HA gene amplified from randomly selected positive samples were sequenced to analyze the homology and variation. 10.6% (110/1 039) of these samples were positive for HPIV,including 8 cases of HPIV-1,22 cases of HPIV-2,46 cases of HPIV-3 and 34 cases of HPIV-4. Detectable rate varied among different groups of HPIV according to seasons of the year and ages of patients. No significant differences were found between the positive samples and the reference sequences. Compared with different reference strains of different regions,the genetic distance of nucleotide is the smallest between the strains tested in this study and the reference strains of other provinces and cities in China. In Chengdu region,HPIV virus is highly detected in ARI,all subtypes were detected with HPIV-3 being the main subtype.

Establishment of the first international repository for transfusion-relevant bacteria reference strains: ISBT working party transfusion-transmitted infectious diseases (WP-TTID), subgroup on bacteria.

PubMed

Störmer, M; Arroyo, A; Brachert, J; Carrero, H; Devine, D; Epstein, J S; Gabriel, C; Gelber, C; Goodrich, R; Hanschmann, K-M; Heath, D G; Jacobs, M R; Keil, S; de Korte, D; Lambrecht, B; Lee, C-K; Marcelis, J; Marschner, S; McDonald, C; McGuane, S; McKee, M; Müller, T H; Muthivhi, T; Pettersson, A; Radziwon, P; Ramirez-Arcos, S; Reesink, H W; Rojo, J; Rood, I; Schmidt, M; Schneider, C K; Seifried, E; Sicker, U; Wendel, S; Wood, E M; Yomtovian, R A; Montag, T

2012-01-01

Bacterial contamination of platelet concentrates (PCs) still remains a significant problem in transfusion with potential important clinical consequences, including death. The International Society of Blood Transfusion Working Party on Transfusion-Transmitted Infectious Diseases, Subgroup on Bacteria, organised an international study on Transfusion-Relevant Bacteria References to be used as a tool for development, validation and comparison of both bacterial screening and pathogen reduction methods. Four Bacteria References (Staphylococcus epidermidis PEI-B-06, Streptococcus pyogenes PEI-B-20, Klebsiella pneumoniae PEI-B-08 and Escherichia coli PEI-B-19) were selected regarding their ability to proliferate to high counts in PCs and distributed anonymised to 14 laboratories in 10 countries for identification, enumeration and bacterial proliferation in PCs after low spiking (0·3 and 0·03 CFU/ml), to simulate contamination occurring during blood donation. Bacteria References were correctly identified in 98% of all 52 identifications. S. pyogenes and E. coli grew in PCs in 11 out of 12 laboratories, and K. pneumoniae and S. epidermidis replicated in all participating laboratories. The results of bacterial counts were very consistent between laboratories: the 95% confidence intervals were for S. epidermidis: 1·19-1·32 × 10(7) CFU/ml, S. pyogenes: 0·58-0·69 × 10(7) CFU/ml, K. pneumoniae: 18·71-20·26 × 10(7) CFU/ml and E. coli: 1·78-2·10 × 10(7) CFU/ml. The study was undertaken as a proof of principle with the aim to demonstrate (i) the quality, stability and suitability of the bacterial strains for low-titre spiking of blood components, (ii) the property of donor-independent proliferation in PCs, and (iii) their suitability for worldwide shipping of deep frozen, blinded pathogenic bacteria. These aims were successfully fulfilled. The WHO Expert Committee Biological Standardisation has approved the adoption of these four bacteria strains as the first Repository for Transfusion-Relevant Bacteria Reference Strains and, additionally, endorsed as a project the addition of six further bacteria strain preparations suitable for control of platelet contamination as the next step of enlargement of the repository. © 2011 The Author(s). Vox Sanguinis © 2011 International Society of Blood Transfusion.

Draft Genome Sequence of the Serratia rubidaea CIP 103234T Reference Strain, a Human-Opportunistic Pathogen.

PubMed

Bonnin, Rémy A; Girlich, Delphine; Imanci, Dilek; Dortet, Laurent; Naas, Thierry

2015-11-19

We provide here the first genome sequence of a Serratia rubidaea isolate, a human-opportunistic pathogen. This reference sequence will permit a comparison of this species with others of the Serratia genus. Copyright © 2015 Bonnin et al.

MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria.

PubMed

Li, Yang; Gu, Bing; Liu, Genyan; Xia, Wenying; Fan, Kun; Mei, Yaning; Huang, Peijun; Pan, Shiyang

2014-05-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an accurate, rapid and inexpensive technique that has initiated a revolution in the clinical microbiology laboratory for identification of pathogens. The Vitek 2 anaerobe and Corynebacterium (ANC) identification card is a newly developed method for identification of corynebacteria and anaerobic species. The aim of this study was to evaluate the effectiveness of the ANC card and MALDI-TOF MS techniques for identification of clinical anaerobic isolates. Five reference strains and a total of 50 anaerobic bacteria clinical isolates comprising ten different genera and 14 species were identified and analyzed by the ANC card together with Vitek 2 identification system and Vitek MS together with version 2.0 database respectively. 16S rRNA gene sequencing was used as reference method for accuracy in the identification. Vitek 2 ANC card and Vitek MS provided comparable results at species level for the five reference strains. Of 50 clinical strains, the Vitek MS provided identification for 46 strains (92%) to the species level, 47 (94%) to genus level, one (2%) low discrimination, two (4%) no identification and one (2%) misidentification. The Vitek 2 ANC card provided identification for 43 strains (86%) correct to the species level, 47 (94%) correct to the genus level, three (6%) low discrimination, three (6%) no identification and one (2%) misidentification. Both Vitek MS and Vitek 2 ANC card can be used for accurate routine clinical anaerobe identification. Comparing to the Vitek 2 ANC card, Vitek MS is easier, faster and more economic for each test. The databases currently available for both systems should be updated and further developed to enhance performance.

Evaluation of reference genes in mouse preimplantation embryos for gene expression studies using real-time quantitative RT-PCR (RT-qPCR).

PubMed

Jeong, Jae-Kyo; Kang, Min-Hee; Gurunathan, Sangiliyandi; Cho, Ssang-Goo; Park, Chankyu; Seo, Han Geuk; Kim, Jin-Hoi

2014-09-25

Real-time quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) is the most sensitive, and valuable technique for rare mRNA detection. However, the expression profiles of reference genes under different experimental conditions, such as different mouse strains, developmental stage, and culture conditions have been poorly studied. mRNA stability of the actb, gapdh, sdha, ablim, ywhaz, sptbn, h2afz, tgfb1, 18 s and wrnip genes was analyzed. Using the NormFinder program, the most stable genes are as follows: h2afz for the B6D2F-1 and C57BL/6 strains; sptbn for ICR; h2afz for KOSOM and CZB cultures of B6D2F-1 and C57BL/6 strain-derived embryos; wrnip for M16 culture of B6D2F-1 and C57BL/6 strain-derived embryos; ywhaz, tgfb1, 18 s, 18 s, ywhaz, and h2afz for zygote, 2-cell, 4-cell, 8-cell, molular, and blastocyst embryonic stages cultured in KSOM medium, respectively; h2afz, wrnip, wrnip, h2afz, ywhaz, and ablim for zygote, 2-cell, 4-cell, 8-cell, molular, and blastocyst stage embryos cultured in CZB medium, respectively; 18 s, h2afz, h2afz, actb, h2afz, and wrnip for zygote, 2-cell, 4-cell, 8-cell, molular, and blastocyst stage embryos cultured in M16 medium, respectively. These results demonstrated that candidate reference genes for normalization of target gene expression using RT-qPCR should be selected according to mouse strains, developmental stage, and culture conditions.

Use of phylogenetic and phenotypic analyses to identify nonhemolytic streptococci isolated from bacteremic patients.

PubMed

Hoshino, Tomonori; Fujiwara, Taku; Kilian, Mogens

2005-12-01

The aim of this study was to evaluate molecular and phenotypic methods for the identification of nonhemolytic streptococci. A collection of 148 strains consisting of 115 clinical isolates from cases of infective endocarditis, septicemia, and meningitis and 33 reference strains, including type strains of all relevant Streptococcus species, were examined. Identification was performed by phylogenetic analysis of nucleotide sequences of four housekeeping genes, ddl, gdh, rpoB, and sodA; by PCR analysis of the glucosyltransferase (gtf) gene; and by conventional phenotypic characterization and identification using two commercial kits, Rapid ID 32 STREP and STREPTOGRAM and the associated databases. A phylogenetic tree based on concatenated sequences of the four housekeeping genes allowed unequivocal differentiation of recognized species and was used as the reference. Analysis of single gene sequences revealed deviation clustering in eight strains (5.4%) due to homologous recombination with other species. This was particularly evident in S. sanguinis and in members of the anginosus group of streptococci. The rate of correct identification of the strains by both commercial identification kits was below 50% but varied significantly between species. The most significant problems were observed with S. mitis and S. oralis and 11 Streptococcus species described since 1991. Our data indicate that identification based on multilocus sequence analysis is optimal. As a more practical alternative we recommend identification based on sodA sequences with reference to a comprehensive set of sequences that is available for downloading from our server. An analysis of the species distribution of 107 nonhemolytic streptococci from bacteremic patients showed a predominance of S. oralis and S. anginosus with various underlying infections.

In vitro effect of bergamot (Citrus bergamia) juice against cagA-positive and-negative clinical isolates of Helicobacter pylori.

PubMed

Filocamo, Angela; Bisignano, Carlo; Ferlazzo, Nadia; Cirmi, Santa; Mandalari, Giuseppina; Navarra, Michele

2015-07-30

Helicobacter pylori infection has been associated with chronic gastritis, peptic ulcer and gastric carcinoma as over half of the world's population is colonized with this gram-negative bacterium. Due to the increasing antibiotic resistance, its eradication rates fails in a great portion of patients. A number of studies showed that molecules largely distributed in commonly consumed fruits and vegetables may have antimicrobial activity. The aim of the present study was to investigate the effect of bergamot juice (BJ) against Helicobacter pylori in vitro. The potential therapeutic combination between BJ and the antibiotics amoxicillin (AMX), clarithromycin (CLA) and metronidazole (MTZ) has also been evaluated. The minimum inhibitory concentration (MIC) of BJ, AMX, CLA and MTZ against 2 ATCC and 32 clinical isolates of H. pylori was assayed according to CLSI. The checkerboard method was used to determine the efficacy of the association BJ with the three reference antibiotics. Killing curves were performed on the two cagA-positive ATCC strains of H. pylori (ATCC 43504 and ATCC 49503), on the clinical isolate cagA-positive HP6 strain of H. pylori and on the clinical isolate cagA-negative HP61 strain of H. pylori. BJ (2.5%, v/v) inhibited the growth of 50% of the H. pylori clinical isolates, whereas 5% (v/v) inhibited 90%. AMX was the most effective antibiotic against the reference strains and the clinical isolates, followed by CLA and MTZ. In the combination assays, synergism was observed between BJ and AMX and between BJ and MTZ against both the reference strains and the clinical isolates. Indifference was observed between BJ and CLA. BJ was effective in vitro against H. pylori and the genotype status of the clinical strains may have an impact on its susceptibility. The synergistic combination of BJ and antibiotics could be used to prevent or treat resistance.

Susceptibility patterns for amoxicillin/clavulanate tests mimicking the licensed formulations and pharmacokinetic relationships: do the MIC obtained with 2:1 ratio testing accurately reflect activity against beta-lactamase-producing strains of Haemophilus influenzae and Moraxella catarrhalis?

PubMed

Pottumarthy, Sudha; Sader, Helio S; Fritsche, Thomas R; Jones, Ronald N

2005-11-01

Amoxicillin/clavulanate has recently undergone formulation changes (XR and ES-600) that represent 14:1 and 16:1 ratios of amoxicillin/clavulanate. These ratios greatly differ from the 2:1 ratio used in initial formulations and in vitro susceptibility testing. The objective of this study was to determine if the reference method using a 2:1 ratio accurately reflects the susceptibility to the various clinically used amoxicillin/clavulanate formulations and their respective serum concentration ratios. A collection of 330 Haemophilus influenzae strains (300 beta-lactamase-positive and 30 beta-lactamase-negative) and 40 Moraxella catarrhalis strains (30 beta-lactamase-positive and 10 beta-lactamase-negative) were tested by the broth microdilution method against eight amoxicillin/clavulanate combinations (4:1, 5:1, 7:1, 9:1, 14:1, and 16:1 ratios; 0.5 and 2 microg/mL fixed clavulanate concentrations) and the minimum inhibitory concentration (MIC) results were compared with those obtained with the reference 2:1 ratio testing. For the beta-lactamase-negative strains of both genera, there was no demonstrable change in the MIC values obtained for all ratios analyzed (2:1 to 16:1). For the beta-lactamase-positive strains of H. influenzae and M. catarrhalis, at ratios >or=4:1 there was a shift in the central tendency of the MIC scatterplot compared with the results of testing 2:1 ratio. As a result, there was a 2-fold dilution increase in the MIC(50) and MIC(90) values, most evident for H. influenzae and BRO-1-producing M. catarrhalis strains. For beta-lactamase-positive strains of H. influenzae, the shift resulted in a change in the interpretive result for 3 isolates (1.0%) from susceptible using the reference method (2:1 ratio) to resistant (8/4 microg/mL; very major error) at the 16:1 ratio. In addition, the number of isolates with MIC values at or 1 dilution lower than the breakpoint (4/2 microg/mL) increased from 5% at 2:1 ratio to 32-33% for ratios 14:1 and 16:1. Our results indicate that, for the beta-lactamase-positive strains of H. influenzae and M. catarrhalis, the results of the amoxicillin/clavulanate reference 2:1 ratio testing do not accurately represent all the currently licensed formulations. Pharmacokinetic/pharmacodynamic (PK/PD) target attainment might be compromised when higher amoxicillin/clavulanate ratios are used clinically. With a better understanding of PK/PD parameters, reevaluation of the amoxicillin/clavulanate in vitro susceptibility testing should be considered by the standardizing authorities to reflect the licensed formulations and accurately predict clinical outcomes.

Screening of Metagenomic and Genomic Libraries Reveals Three Classes of Bacterial Enzymes That Overcome the Toxicity of Acrylate

PubMed Central

Curson, Andrew R. J.; Burns, Oliver J.; Voget, Sonja; Daniel, Rolf; Todd, Jonathan D.; McInnis, Kathryn; Wexler, Margaret; Johnston, Andrew W. B.

2014-01-01

Acrylate is produced in significant quantities through the microbial cleavage of the highly abundant marine osmoprotectant dimethylsulfoniopropionate, an important process in the marine sulfur cycle. Acrylate can inhibit bacterial growth, likely through its conversion to the highly toxic molecule acrylyl-CoA. Previous work identified an acrylyl-CoA reductase, encoded by the gene acuI, as being important for conferring on bacteria the ability to grow in the presence of acrylate. However, some bacteria lack acuI, and, conversely, many bacteria that may not encounter acrylate in their regular environments do contain this gene. We therefore sought to identify new genes that might confer tolerance to acrylate. To do this, we used functional screening of metagenomic and genomic libraries to identify novel genes that corrected an E. coli mutant that was defective in acuI, and was therefore hyper-sensitive to acrylate. The metagenomic libraries yielded two types of genes that overcame this toxicity. The majority encoded enzymes resembling AcuI, but with significant sequence divergence among each other and previously ratified AcuI enzymes. One other metagenomic gene, arkA, had very close relatives in Bacillus and related bacteria, and is predicted to encode an enoyl-acyl carrier protein reductase, in the same family as FabK, which catalyses the final step in fatty-acid biosynthesis in some pathogenic Firmicute bacteria. A genomic library of Novosphingobium, a metabolically versatile alphaproteobacterium that lacks both acuI and arkA, yielded vutD and vutE, two genes that, together, conferred acrylate resistance. These encode sequential steps in the oxidative catabolism of valine in a pathway in which, significantly, methacrylyl-CoA is a toxic intermediate. These findings expand the range of bacteria for which the acuI gene encodes a functional acrylyl-CoA reductase, and also identify novel enzymes that can similarly function in conferring acrylate resistance, likely, again, through the removal of the toxic product acrylyl-CoA. PMID:24848004

Interactions between the S-Domain Receptor Kinases and AtPUB-ARM E3 Ubiquitin Ligases Suggest a Conserved Signaling Pathway in Arabidopsis1[W][OA

PubMed Central

Samuel, Marcus A.; Mudgil, Yashwanti; Salt, Jennifer N.; Delmas, Frédéric; Ramachandran, Shaliny; Chilelli, Andrea; Goring, Daphne R.

2008-01-01

The Arabidopsis (Arabidopsis thaliana) genome encompasses multiple receptor kinase families with highly variable extracellular domains. Despite their large numbers, the various ligands and the downstream interacting partners for these kinases have been deciphered only for a few members. One such member, the S-receptor kinase, is known to mediate the self-incompatibility (SI) response in Brassica. S-receptor kinase has been shown to interact and phosphorylate a U-box/ARM-repeat-containing E3 ligase, ARC1, which, in turn, acts as a positive regulator of the SI response. In an effort to identify conserved signaling pathways in Arabidopsis, we performed yeast two-hybrid analyses of various S-domain receptor kinase family members with representative Arabidopsis plant U-box/ARM-repeat (AtPUB-ARM) E3 ligases. The kinase domains from S-domain receptor kinases were found to interact with ARM-repeat domains from AtPUB-ARM proteins. These kinase domains, along with M-locus protein kinase, a positive regulator of SI response, were also able to phosphorylate the ARM-repeat domains in in vitro phosphorylation assays. Subcellular localization patterns were investigated using transient expression assays in tobacco (Nicotiana tabacum) BY-2 cells and changes were detected in the presence of interacting kinases. Finally, potential links to the involvement of these interacting modules to the hormone abscisic acid (ABA) were investigated. Interestingly, AtPUB9 displayed redistribution to the plasma membrane of BY-2 cells when either treated with ABA or coexpressed with the active kinase domain of ARK1. As well, T-DNA insertion mutants for ARK1 and AtPUB9 lines were altered in their ABA sensitivity during germination and acted at or upstream of ABI3, indicating potential involvement of these proteins in ABA responses. PMID:18552232

Role of Scd5, a protein phosphatase-1 targeting protein, in phosphoregulation of Sla1 during endocytosis

PubMed Central

Chi, Richard J.; Torres, Onaidy T.; Segarra, Verónica A.; Lansley, Tanya; Chang, Ji Suk; Newpher, Thomas M.; Lemmon, Sandra K.

2012-01-01

Summary Phosphorylation regulates assembly and disassembly of proteins during endocytosis. In yeast, Prk1 and Ark1 phosphorylate factors after vesicle internalization leading to coat disassembly. Scd5, a protein phosphatase-1 (PP1)-targeting subunit, is proposed to regulate dephosphorylation of Prk1/Ark1 substrates to promote new rounds of endocytosis. In this study we analyzed scd5-PP1Δ2, a mutation causing impaired PP1 binding. scd5-PP1Δ2 caused hyperphosphorylation of several Prk1 endocytic targets. Live-cell imaging of 15 endocytic components in scd5-PP1Δ2 revealed that most factors arriving before the invagination/actin phase of endocytosis had delayed lifetimes. Severely affected were early factors and Sla2 (Hip1R homolog), whose lifetime was extended nearly fourfold. In contrast, the lifetime of Sla1, a Prk1 target, was extended less than twofold, but its cortical recruitment was significantly reduced. Delayed Sla2 dynamics caused by scd5-PP1Δ2 were suppressed by SLA1 overexpression. This was dependent on the LxxQxTG repeats (SR) of Sla1, which are phosphorylated by Prk1 and bind Pan1, another Prk1 target, in the dephosphorylated state. Without the SR, Sla1ΔSR was still recruited to the cell surface, but was less concentrated in cortical patches than Pan1. sla1ΔSR severely impaired endocytic progression, but this was partially suppressed by overexpression of LAS17, suggesting that without the SR region the SH3 region of Sla1 causes constitutive negative regulation of Las17 (WASp). These results demonstrate that Scd5/PP1 is important for recycling Prk1 targets to initiate new rounds of endocytosis and provide new mechanistic information on the role of the Sla1 SR domain in regulating progression to the invagination/actin phase of endocytosis. PMID:22825870

Heterologous live infectious bronchitis virus vaccination in day-old commercial broiler chicks: clinical signs, ciliary health, immune responses and protection against variant infectious bronchitis viruses.

PubMed

Awad, Faez; Hutton, Sally; Forrester, Anne; Baylis, Matthew; Ganapathy, Kannan

2016-01-01

Groups of one-day-old broiler chicks were vaccinated via the oculo-nasal route with different live infectious bronchitis virus (IBV) vaccines: Massachusetts (Mass), 793B, D274 or Arkansas (Ark). Clinical signs and gross lesions were evaluated. Five chicks from each group were humanely killed at intervals and their tracheas collected for ciliary activity assessment and for the detection of CD4+, CD8+ and IgA-bearing B cells by immunohistochemistry (IHC). Blood samples were collected at intervals for the detection of anti-IBV antibodies. At 21 days post-vaccination (dpv), protection conferred by different vaccination regimes against virulent M41, QX and 793B was assessed. All vaccination programmes were able to induce high levels of CD4+, CD8+ and IgA-bearing B cells in the trachea. Significantly higher levels of CD4+ and CD8+ expression were observed in the Mass2 + 793B2-vaccinated group compared to the other groups (subscripts indicate different manufacturers). Protection studies showed that the group of chicks vaccinated with Mass2 + 793B2 produced 92% ciliary protection against QX challenge; compared to 53%, 68% and 73% ciliary protection against the same challenge virus by Mass1 + D274, Mass1 + 793B1 and Mass3 + Ark, respectively. All vaccination programmes produced more than 85% ciliary protection against M41 and 793B challenges. It appears that the variable levels of protection provided by different heterologous live IBV vaccinations are dependent on the levels of local tracheal immunity induced by the respective vaccine combination. The Mass2 + 793B2 group showed the worst clinical signs, higher mortality and severe lesions following vaccination, but had the highest tracheal immune responses and demonstrated the best protection against all three challenge viruses.

Wire-Strain-Gage Hinge-Moment Indicators for Use in Tests of Airplane Models

NASA Technical Reports Server (NTRS)

Edwards, Howard B.

1944-01-01

The design and construction of various forms of strain-gage spring units and hinge-moment assemblies are discussed with particular reference to wind-tunnel test, although the indicators may be used equally well in flight tests. Strain-gage specifications are given, and the techniques of their application and use are described briefly. Testing, calibration and operation of hinge-moment indicators are discussed and precautions necessary for successful operation are stressed. Difficulties that may be encountered are summarized along with the possible causes.

Application of high-resolution melting curve analysis for typing of fowl adenoviruses in field cases of inclusion body hepatitis.

PubMed

Steer, P A; O'Rourke, D; Ghorashi, S A; Noormohammadi, A H

2011-05-01

Fowl adenoviruses (FAdVs) cause inclusion body hepatitis (IBH) in chickens. In this study, clinical cases of IBH from Australian broiler flocks were screened for the presence and genotype of FAdVs. Twenty-six IBH cases from commercial poultry farms were screened. Polymerase chain reaction (PCR) coupled with high-resolution melt (HRM) curve analysis (PCR/HRM genotyping) was used to determine the presence and genotype of FAdVs. For comparison, field isolates were also assessed by virus microneutralisation and nucleotide sequence analysis of the hexon loop 1 (Hex L1) gene. PCR detection of chicken anaemia virus (CAV) and infectious bursal disease virus (IBDV) was also employed. FAdV-8b and FAdV-11 were identified in 13 cases each. In one case, FAdV-1 was also identified. Cross-neutralisation was observed between the FAdV-11 field strain and the reference FAdV-2 and 11 antisera, a result also seen with the type 2 and 11 reference FAdVs. Field strains 1 and 8b were neutralised only by their respective type antisera. The FAdV-8b field strain was identical to the Australian FAdV vaccine strain (type 8b) in the Hex L1 region. The Hex L1 sequence of the FAdV-11 field strain had the highest identity to FAdV-11 (93.2%) and FAdV-2 (92.7%) reference strains. In the five cases tested for CAV and IBDV, neither virus was detected. The evidence suggested the presence of sufficient antibodies against CAV and IBD in the parent flocks and there was no indication of immunosuppression caused by these viruses. These results indicate that PCR/HRM genotyping is a reliable diagnostic method for FAdV identification and is more rapid than virus neutralisation and direct sequence analysis. Furthermore, they suggest that IBH in Australian broiler flocks is a primary disease resulting from two alternative FAdV strains from different species. © 2011 The Authors. Australian Veterinary Journal © 2011 Australian Veterinary Association.

Systematic study of the genus Acetobacter with descriptions of Acetobacter indonesiensis sp. nov., Acetobacter tropicalis sp. nov., Acetobacter orleanensis (Henneberg 1906) comb. nov., Acetobacter lovaniensis (Frateur 1950) comb. nov., and Acetobacter estunensis (Carr 1958) comb. nov.

PubMed

Lisdiyanti, Puspita; Kawasaki, Hiroko; Seki, Tatsuji; Yamada, Yuzo; Uchimura, Tai; Komagata, Kazuo

2000-06-01

Thirty-one Acetobacter strains obtained from culture collections and 45 Acetobacter strains isolated from Indonesian sources were investigated for their phenotypic characteristics, ubiquinone systems, DNA base compositions, and levels of DNA-DNA relatedness. Of 31 reference strains, six showed the presence of ubiquinone 10 (Q-10). These strains were eliminated from the genus Acetobacter. The other 25 reference strains and 45 Indonesian isolates were subjected to a systematic study and separated into 8 distinct groups on the basis of DNA-DNA relatedness. The known species, Acetobacter aceti, A. pasteurianus, and A. peroxydans are retained for three of these groups. New combinations, A. orleanensis (Henneberg 1906) comb. nov., A. lovaniensis (Frateur 1950) comb. nov., and A. estunensis (Carr 1958) comb. nov. are proposed for three other groups. Two new species, A. indonesiensis sp. nov. and A. tropicalis sp. nov. are proposed for the remaining two. No Indonesian isolates were identified as A. aceti, A. estunensis, and A. peroxydans. Phylogenetic analysis on the basis of 16S rDNA sequences was carried out for representative strains from each of the groups. This supported that the eight species belonged to the genus Acetobacter. Several strains previously assigned to the species of A. aceti and A. pasteurianus were scattered over the different species. It is evident that the value of DNA-DNA relatedness between strains comprising a new species should be determined for the establishment of the species. Thus current bacterial species without data of DNA-DNA relatedness should be reexamined for the stability of bacterial nomenclature.

Effect of bovine apo-lactoferrin on the growth and virulence of Actinobacillus pleuropneumoniae.

PubMed

Luna-Castro, Sarahí; Aguilar-Romero, Francisco; Samaniego-Barrón, Luisa; Godínez-Vargas, Delfino; de la Garza, Mireya

2014-10-01

Actinobacillus pleuropneumoniae (App) is a Gram-negative bacterium that causes porcine pleuropneumonia, leading to economic losses in the swine industry. Due to bacterial resistance to antibiotics, new treatments for this disease are currently being sought. Lactoferrin (Lf) is an innate immune system glycoprotein of mammals that is microbiostatic and microbicidal and affects several bacterial virulence factors. The aim of this study was to investigate whether bovine iron-free Lf (BapoLf) has an effect on the growth and virulence of App. Two serotype 1 strains (reference strain S4074 and the isolate BC52) and a serotype 7 reference strain (WF83) were analyzed. First, the ability of App to grow in iron-charged BLf was discarded because in vivo, BapoLf sequesters iron and could be a potential source of this element favoring the infection. The minimum inhibitory concentration of BapoLf was 14.62, 11.78 and 10.56 µM for the strain BC52, S4074 and WF83, respectively. A subinhibitory concentration (0.8 µM) was tested by assessing App adhesion to porcine buccal epithelial cells, biofilm production, and the secretion and function of toxins and proteases. Decrease in adhesion (24-42 %) was found in the serotype 1 strains. Biofilm production decreased (27 %) for only the strain 4074 of serotype 1. Interestingly, biofilm was decreased (60-70 %) in the three strains by BholoLf. Hemolysis of erythrocytes and toxicity towards HeLa cells were not affected by BapoLf. In contrast, proteolytic activity in all strains was suppressed in the presence of BapoLf. Finally, oxytetracycline produced synergistic effect with BapoLf against App. Our results suggest that BapoLf affects the growth and several of the virulence factors in App.

[Genetic characterization analysis on epidemic rubella virus strains isolated in Liaoning from 2007 to 2012].

PubMed

Wang, Yan; Ma, Yan; Xu, Xiao-Ting; Fan, Xue-Song; Lin, Qian; Sui, Dan; Yin, Ye; Wu, Feng-Tong; Pan, Bai-Ling; Liu, Guang-Yuan; Wang, Ji-Jian; Han, Yue; Guo, Jun-Qiao; Zhao, Zhuo

2013-11-01

To analyze the genetic characterization of epidemic rubella virus strains isolated in Liaoning from 2007-2012, a total of 145 rubella virus strains were isolated using Vero/Slam cell line from the patients' throat swabs during rubella outbreaks and sporadics cases in Liaoning Province from 2007 to 2012. Fragments of 945 nucleotides containing 1E gene from 145 rubella virus isolates were amplified by RT-PCR, the PCR products were sequenced and analyzed. Based on the 739 nucleotides of 1E gene, the phylogenetic trees were constructed with 32 WHO rubella reference strains of 13 genotypes downloaded from GenBank and 145 rubella virus strains. The results showed that the 145 rubella virus strains in 2007 -2012 belonged to genotype 1E, nucleotide acids and amino acids similarities were 97.2%-100.0% and 97.6%-100.0%, respectively. Compared to the 1E reference strains(Rvi/ Dezhou.CHN/02, RVi/MYS/01), the nucleotide acids and amino acids similarities were 96.6%-99.2% and 98.2%-100.0%, respectively except for one amino acid change (Val246-Ala246) of RVi/Shenyang. Liaoning. CHN/13.11/13, and Asp262-Asn262 of RVi/Shenyang. Liaoning. CHN/13.11/4 and RVi/Liaoyang. Liaoning. CHN/26. 11/2. there had no change found in the important antigenic epitope sites, the hemagglutination inhibition and neutralization epitopes of the other rubella viruses. All the 145 strains isolated had the same amino acid change (Leu338--Phe338) in E1 protein. These findings suggested that genotype 1E of rubella virus was the predominant genotype in Liaoning province. the rubella prevailed in recent six years was mainly caused by rubella viruses genotype 1E with multi-transmission routes.

Monomeric and gemini surfactants as antimicrobial agents - influence on environmental and reference strains.

PubMed

Koziróg, Anna; Brycki, Bogumił

2015-01-01

Quaternary ammonium salts (QAS) belong to surfactant commonly used both, in the household and in different branches of industry, primarily in the process of cleaning and disinfection. They have several positive features inter alia effectively limiting the development of microorganisms on many surfaces. In the present work, two compounds were used as biocides: hexamethylene-1,6-bis-(N,N-dimethyl-N-dodecylammonium bromide) that belongs to the gemini surfactant (GS), and its single analogue - dodecyl(trimethyl)ammonium bromide (DTAB). Two fold dilution method was used to determine the minimum concentration of compounds (MIC) which inhibit the growth of bacteria: Staphylococcus aureus (ATCC 6538 and an environmental strain), Pseudomonas aeruginosa (ATCC 85327 and an environmental strain), and yeast Candida albicans (ATCC 11509 and an environmental strain). The viability of cells in liquid cultures with addition of these substances at ¼ MIC, ½ MIC and MIC concentrations were also determined. The obtained results show that DTAB inhibits the growth of bacteria at the concentration of 0.126-1.010 µM/ml, and gemini surfactant is active at 0.036-0.029 µM/ml. Therefore, GS is active at more than 17-70-fold lower concentrations than its monomeric analogue. Strains isolated from natural environment are less sensitive upon testing biocides than the references strains. Both compounds at the MIC value reduced the number of cells of all strains. The use of too low concentration of biocides can limit the growth of microorganisms, but often only for a short period of time in case of special environmental strains. Later on, they can adapt to adverse environmental conditions and begin to evolve defence mechanisms.

Genome variations associated with viral susceptibility and calcification in Emiliania huxleyi.

PubMed

Kegel, Jessica U; John, Uwe; Valentin, Klaus; Frickenhaus, Stephan

2013-01-01

Emiliania huxleyi, a key player in the global carbon cycle is one of the best studied coccolithophores with respect to biogeochemical cycles, climatology, and host-virus interactions. Strains of E. huxleyi show phenotypic plasticity regarding growth behaviour, light-response, calcification, acidification, and virus susceptibility. This phenomenon is likely a consequence of genomic differences, or transcriptomic responses, to environmental conditions or threats such as viral infections. We used an E. huxleyi genome microarray based on the sequenced strain CCMP1516 (reference strain) to perform comparative genomic hybridizations (CGH) of 16 E. huxleyi strains of different geographic origin. We investigated the genomic diversity and plasticity and focused on the identification of genes related to virus susceptibility and coccolith production (calcification). Among the tested 31940 gene models a core genome of 14628 genes was identified by hybridization among 16 E. huxleyi strains. 224 probes were characterized as specific for the reference strain CCMP1516. Compared to the sequenced E. huxleyi strain CCMP1516 variation in gene content of up to 30 percent among strains was observed. Comparison of core and non-core transcripts sets in terms of annotated functions reveals a broad, almost equal functional coverage over all KOG-categories of both transcript sets within the whole annotated genome. Within the variable (non-core) genome we identified genes associated with virus susceptibility and calcification. Genes associated with virus susceptibility include a Bax inhibitor-1 protein, three LRR receptor-like protein kinases, and mitogen-activated protein kinase. Our list of transcripts associated with coccolith production will stimulate further research, e.g. by genetic manipulation. In particular, the V-type proton ATPase 16 kDa proteolipid subunit is proposed to be a plausible target gene for further calcification studies.

Genome Variations Associated with Viral Susceptibility and Calcification in Emiliania huxleyi

PubMed Central

Kegel, Jessica U.; John, Uwe; Valentin, Klaus; Frickenhaus, Stephan

2013-01-01

Emiliania huxleyi, a key player in the global carbon cycle is one of the best studied coccolithophores with respect to biogeochemical cycles, climatology, and host-virus interactions. Strains of E. huxleyi show phenotypic plasticity regarding growth behaviour, light-response, calcification, acidification, and virus susceptibility. This phenomenon is likely a consequence of genomic differences, or transcriptomic responses, to environmental conditions or threats such as viral infections. We used an E. huxleyi genome microarray based on the sequenced strain CCMP1516 (reference strain) to perform comparative genomic hybridizations (CGH) of 16 E. huxleyi strains of different geographic origin. We investigated the genomic diversity and plasticity and focused on the identification of genes related to virus susceptibility and coccolith production (calcification). Among the tested 31940 gene models a core genome of 14628 genes was identified by hybridization among 16 E. huxleyi strains. 224 probes were characterized as specific for the reference strain CCMP1516. Compared to the sequenced E. huxleyi strain CCMP1516 variation in gene content of up to 30 percent among strains was observed. Comparison of core and non-core transcripts sets in terms of annotated functions reveals a broad, almost equal functional coverage over all KOG-categories of both transcript sets within the whole annotated genome. Within the variable (non-core) genome we identified genes associated with virus susceptibility and calcification. Genes associated with virus susceptibility include a Bax inhibitor-1 protein, three LRR receptor-like protein kinases, and mitogen-activated protein kinase. Our list of transcripts associated with coccolith production will stimulate further research, e.g. by genetic manipulation. In particular, the V-type proton ATPase 16 kDa proteolipid subunit is proposed to be a plausible target gene for further calcification studies. PMID:24260453

Role of the pks15/1 gene in the biosynthesis of phenolglycolipids in the Mycobacterium tuberculosis complex. Evidence that all strains synthesize glycosylated p-hydroxybenzoic methyl esters and that strains devoid of phenolglycolipids harbor a frameshift mutation in the pks15/1 gene.

PubMed

Constant, Patricia; Perez, Esther; Malaga, Wladimir; Lanéelle, Marie-Antoinette; Saurel, Olivier; Daffé, Mamadou; Guilhot, Christophe

2002-10-11

Diesters of phthiocerol and phenolphthiocerol are important virulence factors of Mycobacterium tuberculosis and Mycobacterium leprae, the two main mycobacterial pathogens in humans. They are both long-chain beta-diols, and their biosynthetic pathway is beginning to be elucidated. Although the two classes of molecules share a common lipid core, phthiocerol diesters have been found in all the strains of the M. tuberculosis complex examined although phenolphthiocerol diesters are produced by only a few groups of strains. To address the question of the origin of this diversity 8 reference strains and 10 clinical isolates of M. tuberculosis were analyzed. We report the presence of glycosylated p-hydroxybenzoic acid methyl esters, structurally related to the type-specific phenolphthiocerol glycolipids, in the culture media of all reference strains of M. tuberculosis, suggesting that the strains devoid of phenolphthiocerol derivatives are unable to elongate the putative p-hydroxybenzoic acid precursor. We also show that all the strains of M. tuberculosis examined and deficient in the production of phenolphthiocerol derivatives are natural mutants with a frameshift mutation in pks15/1 whereas a single open reading frame for pks15/1 is found in Mycobacterium bovis BCG, M. leprae, and strains of M. tuberculosis that produce phenolphthiocerol derivatives. Complementation of the H37Rv strain of M. tuberculosis, which is devoid of phenolphthiocerol derivatives, with the fused pks15/1 gene from M. bovis BCG restored phenolphthiocerol glycolipids production. Conversely, disruption of the pks15/1 gene in M. bovis BCG led to the abolition of the synthesis of type-specific phenolphthiocerol glycolipid. These data indicate that Pks15/1 is involved in the elongation of p-hydroxybenzoic acid to give p-hydroxyphenylalkanoates, which in turn are converted, presumably by the PpsA-E synthase, to phenolphthiocerol derivatives.

Membrane potential independent transport of NH3 in the absence of ammonium permeases in Saccharomyces cerevisiae.

PubMed

Cueto-Rojas, Hugo F; Milne, Nicholas; van Helmond, Ward; Pieterse, Mervin M; van Maris, Antonius J A; Daran, Jean-Marc; Wahl, S Aljoscha

2017-04-17

Microbial production of nitrogen containing compounds requires a high uptake flux and assimilation of the N-source (commonly ammonium), which is generally coupled with ATP consumption and negatively influences the product yield. In the industrial workhorse Saccharomyces cerevisiae, ammonium (NH 4 + ) uptake is facilitated by ammonium permeases (Mep1, Mep2 and Mep3), which transport the NH 4 + ion, resulting in ATP expenditure to maintain the intracellular charge balance and pH by proton export using the plasma membrane-bound H + -ATPase. To decrease the ATP costs for nitrogen assimilation, the Mep genes were removed, resulting in a strain unable to uptake the NH 4 + ion. Subsequent analysis revealed that growth of this ∆mep strain was dependent on the extracellular NH 3 concentrations. Metabolomic analysis revealed a significantly higher intracellular NH X concentration (3.3-fold) in the ∆mep strain than in the reference strain. Further proteomic analysis revealed significant up-regulation of vacuolar proteases and genes involved in various stress responses. Our results suggest that the uncharged species, NH 3 , is able to diffuse into the cell. The measured intracellular/extracellular NH X ratios under aerobic nitrogen-limiting conditions were consistent with this hypothesis when NH x compartmentalization was considered. On the other hand, proteomic analysis indicated a more pronounced N-starvation stress response in the ∆mep strain than in the reference strain, which suggests that the lower biomass yield of the ∆mep strain was related to higher turnover rates of biomass components.

Damage Detection of CFRP Plates by Full-Spectral Analysis of a Fibre Bragg Grating Sensor Signal

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

Mizutani, Yoshihiro; Solid and Structures Engineering Laboratory, Department of Mechanical Sciences and Engineering, Tokyo Institute of Technology, Japan, 2-12-1-I1-70, Ookayama, Meguro-ku, Tokyo 152-8552; Groves, Roger M.

2010-05-28

This paper describes the measurement of average strain, strain distribution and vibration of cantilever beam made of Carbon Fiber Reinforced Plastics (CFRP), using a single Fibre Bragg Grating (FBG) sensor mounted on the beam surface. Average strain is determined from the displacement of the peak wavelength of reflected light from the FBG sensor. Unstrained reference FBG sensors were used to compensate for temperature drift and the photoelastic coefficient (P{sub e}), which was used to calculate the gauge factor. Measured strains agree with those measured by a resistance foil strain gauge attached to the sample. Stress distributions are measured by monitoringmore » the variation in the full width half maximum (FWHM) values of the reflected spectrum, using a proposed optical analytical model, described in the paper. FWHM values were measured for both the cantilever test beam and a for a reference beam, loaded using a four-point bending rig. The trend of the stress distribution for the test beam matches with our analytical model, however with a relatively large noise present in the experimentally determined data. The vibration of cantilever beam was measured by temporal analysis of the peak reflection wavelength. This technique is very stable as measurements are not affected by variations in the signal amplitude. Finally an application of FBG sensors for damage detection of CFRP plates is demonstrated, by measuring the average strain and natural frequency. With small defects of different sizes applied to the CFRP plate, average strains were seen to increase with damage size and the natural frequency decreased with damage size.« less

Clinical Trichophyton rubrum Strain Exhibiting Primary Resistance to Terbinafine

PubMed Central

Mukherjee, Pranab K.; Leidich, Steven D.; Isham, Nancy; Leitner, Ingrid; Ryder, Neil S.; Ghannoum, Mahmoud A.

2003-01-01

The in vitro antifungal susceptibilities of six clinical Trichophyton rubrum isolates obtained sequentially from a single onychomycosis patient who failed oral terbinafine therapy (250 mg/day for 24 weeks) were determined by broth microdilution and macrodilution methodologies. Strain relatedness was examined by random amplified polymorphic DNA (RAPD) analyses. Data obtained from both broth micro- and macrodilution assays were in agreement and revealed that the six clinical isolates had greatly reduced susceptibilities to terbinafine. The MICs of terbinafine for these strains were >4 μg/ml, whereas they were <0.0002 μg/ml for the susceptible reference strains. Consistent with these findings, the minimum fungicidal concentrations (MFCs) of terbinafine for all six strains were >128 μg/ml, whereas they were 0.0002 μg/ml for the reference strain. The MIC of terbinafine for the baseline strain (cultured at the initial screening visit and before therapy was started) was already 4,000-fold higher than normal, suggesting that this is a case of primary resistance to terbinafine. The results obtained by the broth macrodilution procedure revealed that the terbinafine MICs and MFCs for sequential isolates apparently increased during the course of therapy. RAPD analyses did not reveal any differences between the isolates. The terbinafine-resistant isolates exhibited normal susceptibilities to clinically available antimycotics including itraconazole, fluconazole, and griseofulvin. However, these isolates were fully cross resistant to several other known squalene epoxidase inhibitors, including naftifine, butenafine, tolnaftate, and tolciclate, suggesting a target-specific mechanism of resistance. This is the first confirmed report of terbinafine resistance in dermatophytes. PMID:12499173

Identification of Motile Aeromonas Strains with the MicroScan WalkAway System in Conjunction with the Combo Negative Type 1S Panels

PubMed Central

Vivas, J.; Sáa, A. I.; Tinajas, A.; Barbeyto, L.; Rodríguez, L. A.

2000-01-01

This study was performed to compare the MicroScan WalkAway automated identification system in conjunction with the new MicroScan Combo Negative type 1S panels with conventional biochemical methods for identifying 85 environmental, clinical, and reference strains of eight Aeromonas species. PMID:10742279

Genome Sequencing Identifies Two Nearly Unchanged Strains of Persistent Listeria monocytogenes Isolated at Two Different Fish Processing Plants Sampled 6 Years Apart

PubMed Central

Holch, Anne; Webb, Kristen; Lukjancenko, Oksana; Ussery, David; Rosenthal, Benjamin M.

2013-01-01

Listeria monocytogenes is a food-borne human-pathogenic bacterium that can cause infections with a high mortality rate. It has a remarkable ability to persist in food processing facilities. Here we report the genome sequences for two L. monocytogenes strains (N53-1 and La111) that were isolated 6 years apart from two different Danish fish processers. Both strains are of serotype 1/2a and belong to a highly persistent DNA subtype (random amplified polymorphic DNA [RAPD] type 9). We demonstrate using in silico analyses that both strains belong to the multilocus sequence typing (MLST) type ST121 that has been isolated as a persistent subtype in several European countries. The purpose of this study was to use genome analyses to identify genes or proteins that could contribute to persistence. In a genome comparison, the two persistent strains were extremely similar and collectively differed from the reference lineage II strain, EGD-e. Also, they differed markedly from a lineage I strain (F2365). On the proteome level, the two strains were almost identical, with a predicted protein homology of 99.94%, differing at only 2 proteins. No single-nucleotide polymorphism (SNP) differences were seen between the two strains; in contrast, N53-1 and La111 differed from the EGD-e reference strain by 3,942 and 3,471 SNPs, respectively. We included a persistent L. monocytogenes strain from the United States (F6854) in our comparisons. Compared to nonpersistent strains, all three persistent strains were distinguished by two genome deletions: one, of 2,472 bp, typically contains the gene for inlF, and the other, of 3,017 bp, includes three genes potentially related to bacteriocin production and transport (lmo2774, lmo2775, and the 3′-terminal part of lmo2776). Further studies of highly persistent strains are required to determine if the absence of these genes promotes persistence. While the genome comparison did not point to a clear physiological explanation of the persistent phenotype, the remarkable similarity between the two strains indicates that subtypes with specific traits are selected for in the food processing environment and that particular genetic and physiological factors are responsible for the persistent phenotype. PMID:23435887

Selection of reliable reference genes for gene expression studies in Trichoderma afroharzianum LTR-2 under oxalic acid stress.

PubMed

Lyu, Yuping; Wu, Xiaoqing; Ren, He; Zhou, Fangyuan; Zhou, Hongzi; Zhang, Xinjian; Yang, Hetong

2017-10-01

An appropriate reference gene is required to get reliable results from gene expression analysis by quantitative real-time reverse transcription PCR (qRT-PCR). In order to identify stable and reliable reference genes in Trichoderma afroharzianum under oxalic acid (OA) stress, six commonly used housekeeping genes, i.e., elongation factor 1, ubiquitin, ubiquitin-conjugating enzyme, glyceraldehyde-3-phosphate dehydrogenase, α-tubulin, actin, from the effective biocontrol isolate T. afroharzianum strain LTR-2 were tested for their expression during growth in liquid culture amended with OA. Four in silico programs (comparative ΔCt, NormFinder, geNorm and BestKeeper) were used to evaluate the expression stabilities of six candidate reference genes. The elongation factor 1 gene EF-1 was identified as the most stably expressed reference gene, and was used as the normalizer to quantify the expression level of the oxalate decarboxylase coding gene OXDC in T. afroharzianum strain LTR-2 under OA stress. The result showed that the expression of OXDC was significantly up-regulated as expected. This study provides an effective method to quantify expression changes of target genes in T. afroharzianum under OA stress. Copyright © 2017 Elsevier B.V. All rights reserved.

Numerical approach to reference identification of Staphylococcus, Stomatococcus, and Micrococcus spp.

PubMed

Rhoden, D L; Hancock, G A; Miller, J M

1993-03-01

A numerical-code system for the reference identification of Staphylococcus species, Stomatococcus mucilaginosus, and Micrococcus species was established by using a selected panel of conventional biochemicals. Results from 824 cultures (289 eye isolate cultures, 147 reference strains, and 388 known control strains) were used to generate a list of 354 identification code numbers. Each six-digit code number was based on results from 18 conventional biochemical reactions. Seven milliliters of purple agar base with 1% sterile carbohydrate solution added was poured into 60-mm-diameter agar plates. All biochemical tests were inoculated with 1 drop of a heavy broth suspension, incubated at 35 degrees C, and read daily for 3 days. All reactions were read and interpreted by the method of Kloos et al. (G. A. Hebert, C. G. Crowder, G. A. Hancock, W. R. Jarvis, and C. Thornsberry, J. Clin. Microbiol. 26:1939-1949, 1988; W. E. Kloos and D. W. Lambe, Jr., P. 222-237, in A. Balows, W. J. Hansler, Jr., K. L. Herrmann, H. D. Isenberg, and H. J. Shadomy, ed., Manual of Clinical Microbiology, 5th ed., 1991). This modified reference identification method was 96 to 98% accurate and could have value in reference and public health laboratory settings.

Molecular differentiation and pathogenicity of Aviadenoviruses isolated during an outbreak of inclusion body hepatitis in South Africa.

PubMed

Joubert, Hilda W; Aitchison, Henry; Maartens, Louis H; Venter, Estelle H

2014-11-05

Fowl adenovirus (FAdV) is a member of the genus Aviadenovirus and causes a number of economically important poultry diseases. One of these diseases, inclusion body hepatitis (IBH), has a worldwide distribution and is characterised by acute mortality (5% - 20%) in production chickens. The disease was first described in the United States of America in 1963 and has also been reported in Canada, the United Kingdom, Australia, France and Ireland, but until now, not in South Africa. Adenoviruses isolated from the first outbreak of IBH in South Africa were able to reproduce the disease in chicken embryo livers. The aim of the present study was to characterise the viruses and determine the pathogenicity of the FAdV strains responsible for the first reported case of IBH in South Africa. Polymerase chain reaction (PCR) amplification of the L1 loop region of the fowl adenovirus hexon gene using degenerate primer pair hexon A/B was used to identify the viruses that were isolated. Restriction fragment length polymorphism (RFLP) of the amplification products was used for the differentiation of 14 isolates of fowl adenovirus. Sequencing of the PCR products followed by amino acid comparison and phylogenetic analysis using the L1 loop region of the hexon protein was done to determine the identity of the isolates. Amino acid sequences of the hexon genes of all the South African isolates were compared with those of reference strains representing FAdV species. Amino acid comparison of 12 South Africa field isolates to FAdV reference strains revealed a high sequence identity (> 93.33%) with reference strains T8-A and 764. Two of the isolates had high sequence identity (93.40%) with reference strains P7-A, C2B and SR48. Phylogenetic analysis of the L1 loop region of the hexon protein of all 14 South African isolates was consistent with their RFLP clusters. The mortality rates of embryos challenged with 106 egg infective doses (EID50) FAdV 2 were 80% - 87% and mortality rates for embryos challenged with 105.95 (EID50) FAdV 8b were 65% - 80%.

Sequencing and phylogenetic analysis of the coding region of six common rotavirus strains: evidence for intragenogroup reassortment among co-circulating G1P[8] and G2P[4] strains from the United States.

PubMed

Bányai, K; Mijatovic-Rustempasic, S; Hull, J J; Esona, M D; Freeman, M M; Frace, A M; Bowen, M D; Gentsch, J R

2011-03-01

The segmented genome of rotaviruses provides an opportunity for rotavirus strains to generate a large genetic diversity through reassortment; however, this mechanism is considered to play little role in the generation of mosaic gene constellations between Wa-like and DS-1-like strains in genes other than the neutralization antigens. A pilot study was undertaken to analyze these two epidemiologically important strains at the genomic level in order to (i) identify intergenogroup reassortment and (ii) to make available additional reference genome sequences of G1P[8] and G2P[4] for future genomics analyses. The full or nearly complete coding region of all 11 genes for 3 G1P[8] (LB2719, LB2758, and LB2771) and 3 G2P[4] (LB2744, LB2764, and LB2772) strains isolated from children hospitalized with severe diarrhea in Long Beach, California, where these strains were circulating at comparable rates during 2005-2006 are described in this study. Based on the full-genome classification system, all G1P[8] strains had a conserved genomic constellation: G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-E1-H1 and were mostly identical to the few Wa-like strains whose genome sequences have already been determined. Similarly, the genome sequences of the 3 G2P[4] strains were highly conserved: G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-E2-H2 and displayed an overall lesser genetic divergence with reference DS-1-like strains. While intergenogroup reassortment was not seen between the G1P[8] and G2P[4] strains studied here, evidence for intragenogroup reassortment events was identified. Similar studies in the post-rotavirus genomic era will help uncover whether intergenogroup reassortment affecting the backbone genes could play a significant role in any potential vaccine breakthrough events by evading immunity of vaccinated children. Copyright © 2011 Wiley-Liss, Inc.

Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources

PubMed Central

Lee, Ming-Chun; Bringel, Françoise; Lajus, Aurélie; Zhou, Yang; Gourion, Benjamin; Barbe, Valérie; Chang, Jean; Cruveiller, Stéphane; Dossat, Carole; Gillett, Will; Gruffaz, Christelle; Haugen, Eric; Hourcade, Edith; Levy, Ruth; Mangenot, Sophie; Muller, Emilie; Nadalig, Thierry; Pagni, Marco; Penny, Christian; Peyraud, Rémi; Robinson, David G.; Roche, David; Rouy, Zoé; Saenampechek, Channakhone; Salvignol, Grégory; Vallenet, David; Wu, Zaining; Marx, Christopher J.; Vorholt, Julia A.; Olson, Maynard V.; Kaul, Rajinder; Weissenbach, Jean; Médigue, Claudine; Lidstrom, Mary E.

2009-01-01

Background Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. Methodology/Principal Findings The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name “island integration determinant” (iid). Conclusion/Significance These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles. PMID:19440302

Strain-stiffening response in organogels assembled using steroidal biomolecules

NASA Astrophysics Data System (ADS)

Tung, Shih-Huang; Raghavan, Srinivasa R.

2007-03-01

The phenomenon of strain-stiffening or strain-hardening refers to an increase in the elastic modulus (stiffness) of a material with increasing strain amplitude. While this response is exhibited by many biological materials, including gels of biopolymers such as actin, it is rarely seen in other types of soft matter. Here, we report strain-stiffening in a new class of self- assembled organogels being studied in our laboratory. These gels are formed in nonpolar organic liquids by combining a lipid (lecithin) or two-tailed surfactant (AOT) with a type of naturally occurring steroidal amphiphile called a bile salt. Based on rheological and scattering data, we deduce that the gel structure comprises a network of semiflexible filaments. Interestingly, gels induced by small organic molecules other than bile salts do not show strain-stiffening. We suggest that the bile salt molecules confer an intrinsic stiffness to the filaments in the gel, which is important for strain-stiffening.

High-Resolution Maps of Mouse Reference Populations

PubMed Central

Simecek, Petr; Forejt, Jiri; Williams, Robert W.; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E.; Bennett, Beth; Deschepper, Christian F.; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A.

2017-01-01

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. PMID:28839117

High-Resolution Maps of Mouse Reference Populations.

PubMed

Simecek, Petr; Forejt, Jiri; Williams, Robert W; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E; Bennett, Beth; Deschepper, Christian F; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A

2017-10-05

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. Copyright © 2017 Simecek et al.

Isolation and characterization of heterotrophic bacteria able to grow aerobically with quaternary ammonium alcohols as sole source of carbon and nitrogen.

PubMed

Kaech, Andres; Vallotton, Nathalie; Egli, Thomas

2005-04-01

The quaternary ammonium alcohols (QAAs) 2,3-dihydroxypropyl-trimethyl-ammonium (TM), dimethyl-diethanol-ammonium (DM) and methyl-triethanol-ammonium (MM) are hydrolysis products of their parent esterquat surfactants, which are widely used as softeners in fabric care. We isolated several bacteria growing with QAAs as the sole source of carbon and nitrogen. The strains were compared with a previously isolated TM-degrading bacterium, which was identified as a representative of the species Pseudomonas putida (Syst. Appl. Microbiol. 24 (2001) 252). Two bacteria were isolated with DM, referred to as strains DM 1 and DM 2, respectively. Based on 16S-rDNA analysis, they provided 97% (DM 1) and 98% (DM 2) identities to the closest related strain Zoogloea ramigera Itzigsohn 1868AL. Both strains were long, slim, motile rods but only DM 1 showed the floc forming activity, which is typical for representatives of the genus Zoogloea. Using MM we isolated a Gram-negative, non-motile rod referred to as strain MM 1. The 16S-rDNA sequence of the isolated bacterium revealed 94% identities (best match) to Rhodobacter sphaeroides only. The strains MM 1 and DM 1 exclusively grew with the QAA which was used for their isolation. DM 2 was also utilizing TM as sole source of carbon and nitrogen. However, all of the isolated bacteria were growing with the natural and structurally related compound choline.

Single-step scanner-based digital image correlation (SB-DIC) method for large deformation mapping in rubber

NASA Astrophysics Data System (ADS)

Goh, C. P.; Ismail, H.; Yen, K. S.; Ratnam, M. M.

2017-01-01

The incremental digital image correlation (DIC) method has been applied in the past to determine strain in large deformation materials like rubber. This method is, however, prone to cumulative errors since the total displacement is determined by combining the displacements in numerous stages of the deformation. In this work, a method of mapping large strains in rubber using DIC in a single-step without the need for a series of deformation images is proposed. The reference subsets were deformed using deformation factors obtained from the fitted mean stress-axial stretch ratio curve obtained experimentally and the theoretical Poisson function. The deformed reference subsets were then correlated with the deformed image after loading. The recently developed scanner-based digital image correlation (SB-DIC) method was applied on dumbbell rubber specimens to obtain the in-plane displacement fields up to 350% axial strain. Comparison of the mean axial strains determined from the single-step SB-DIC method with those from the incremental SB-DIC method showed an average difference of 4.7%. Two rectangular rubber specimens containing circular and square holes were deformed and analysed using the proposed method. The resultant strain maps from the single-step SB-DIC method were compared with the results of finite element modeling (FEM). The comparison shows that the proposed single-step SB-DIC method can be used to map the strain distribution accurately in large deformation materials like rubber at much shorter time compared to the incremental DIC method.

Application of genotypic and phenotypic analyses to commercial probiotic strain identity and relatedness.

PubMed

Yeung, P S M; Kitts, C L; Cano, R; Tong, P S; Sanders, M E

2004-01-01

The objective of this study was to generate strain-specific genomic patterns of a bank of 67 commercial and reference probiotic strains, with a focus on probiotic lactobacilli. Pulsed-field gel electrophoresis (PFGE) was used as the primary method for strain differentiation. This method was compared with carbohydrate fermentation analysis. To supplement visual comparison, PFGE patterns were analysed quantitatively by cluster analysis using unweighted pair group method with arithmetic averages. SmaI, NotI and XbaI were found to effectively generate clear and easy-to-interpret PFGE patterns of a range of probiotic strains. Some probiotic strains from different sources shared highly similar PFGE patterns. Results document the value of genotypic strain identification methods, combined with phenotypic methods, for determining probiotic strain identity and relatedness. No correlation was found between relatedness determined by carbohydrate fermentation profiles alone compared with PFGE analysis alone. Some commercial strains are probably derived from similar sources. This approach is valuable to the probiotic industry to develop commercial strain identification patterns, to provide quality control of strain manufacturing production runs, to track use of protected strains and to determine the relatedness among different research and commercial probiotic strains.

Design of hydrotherapy exercise pools.

PubMed

Edlich, R F; Abidin, M R; Becker, D G; Pavlovich, L J; Dang, M T

1988-01-01

Several hydrotherapy pools have been designed specifically for a variety of aquatic exercise. Aqua-Ark positions the exerciser in the center of the pool for deep-water exercise. Aqua-Trex is a shallow underwater treadmill system for water walking or jogging. Swim-Ex generates an adjustable laminar flow that permits swimming without turning. Musculoskeletal conditioning can be accomplished in the above-ground Arjo shallow-water exercise pool. A hydrotherapy pool also can be custom designed for musculoskeletal conditioning in its shallow part and cardiovascular conditioning in a deeper portion of the pool. Regardless of the type of exercise, there is general agreement that the specific exercise conducted in water requires significantly more energy expenditure than when the same exercise is performed on land.

Right ventricular diastolic performance in children with pulmonary arterial hypertension associated with congenital heart disease: correlation of echocardiographic parameters with invasive reference standards by high-fidelity micromanometer catheter.

PubMed

Okumura, Kenichi; Slorach, Cameron; Mroczek, Dariusz; Dragulescu, Andreea; Mertens, Luc; Redington, Andrew N; Friedberg, Mark K

2014-05-01

Right ventricular diastolic dysfunction influences outcomes in pulmonary arterial hypertension (PAH), but echocardiographic parameters have not been investigated in relation to invasive reference standards in pediatric PAH. We investigated echocardiographic parameters of right ventricular diastolic function in children with PAH in relation to simultaneously measured invasive reference measures. We prospectively recruited children undergoing a clinically indicated cardiac catheterization for evaluation of PAH and pulmonary vasoreactivity testing. Echocardiography was performed simultaneously with invasive reference measurements by high-fidelity micromanometer catheter. For analysis, patients were divided into shunt and nonshunt groups. Sixteen children were studied. In the group as a whole, significant correlations were found among τ and tricuspid deceleration time, E', E/E', TimeE-E', A wave velocity, and global early and late diastolic strain rate. dp/dt minimum correlated significantly with late diastolic tricuspid annular velocity (A'), tissue Doppler imaging-derived systolic:diastolic duration ratio, and global late diastolic strain rate. End-diastolic pressure correlated significantly with tissue Doppler imaging-derived systolic:diastolic duration ratio. On multivariate analysis, tricuspid deceleration time, TimeE-E', and global early diastolic strain rate were independent predictors of τ, whereas tissue Doppler imaging-derived systolic:diastolic duration ratio was an independent predictor of dp/dt minimum. In general, correlations between echocardiographic and invasive parameters were better in the shunt group than in the nonshunt group. Echocardiography correlates with invasive reference measures of right ventricular diastolic function in children with PAH, although it does not differentiate between early versus late diastolic abnormalities. Newer echocardiographic techniques may have added value to assess right ventricular diastolic dysfunction in this population. © 2014 American Heart Association, Inc.

Selection and evaluation of reference genes for RT-qPCR expression studies on Burkholderia tropica strain Ppe8, a sugarcane-associated diazotrophic bacterium grown with different carbon sources or sugarcane juice.

PubMed

da Silva, Paula Renata Alves; Vidal, Marcia Soares; de Paula Soares, Cleiton; Polese, Valéria; Simões-Araújo, Jean Luís; Baldani, José Ivo

2016-11-01

Among the members of the genus Burkholderia, Burkholderia tropica has the ability to fix nitrogen and promote sugarcane plant growth as well as act as a biological control agent. There is little information about how this bacterium metabolizes carbohydrates as well as those carbon sources found in the sugarcane juice that accumulates in stems during plant growth. Reverse transcription quantitative PCR (RT-qPCR) can be used to evaluate changes in gene expression during bacterial growth on different carbon sources. Here we tested the expression of six reference genes, lpxC, gyrB, recA, rpoA, rpoB, and rpoD, when cells were grown with glucose, fructose, sucrose, mannitol, aconitic acid, and sugarcane juice as carbon sources. The lpxC, gyrB, and recA were selected as the most stable reference genes based on geNorm and NormFinder software analyses. Validation of these three reference genes during strain Ppe8 growth on the same carbon sources showed that genes involved in glycogen biosynthesis (glgA, glgB, glgC) and trehalose biosynthesis (treY and treZ) were highly expressed when Ppe8 was grown in aconitic acid relative to other carbon sources, while otsA expression (trehalose biosynthesis) was reduced with all carbon sources. In addition, the expression level of the ORF_6066 (gluconolactonase) gene was reduced on sugarcane juice. The results confirmed the stability of the three selected reference genes (lpxC, gyrB, and recA) during the RT-qPCR and also their robustness by evaluating the relative expression of genes involved in glycogen and trehalose biosynthesis when strain Ppe8 was grown on different carbon sources and sugarcane juice.

Shear modulus of porcine coronary artery in reference to a new strain measure.

PubMed

Zhang, Wei; Lu, Xiao; Kassab, Ghassan S

2007-11-01

To simplify the stress-strain relationship of blood vessels, we define a logarithmic-exponential (log-exp) strain measure to absorb the nonlinearity. As a result, the constitutive relation between the second Piola-Kirchhoff stress and the log-exp strain can be written as a generalized Hooke's law. In this work, the shear modulus of porcine coronary arteries is determined from the experimental data in inflation-stretch-torsion tests. It is found that the shear modulus with respect to the log-exp strain can be viewed as a material constant in the full range of elasticity, and the incremental shear modulus for Cauchy shear stress and small shear strain at various loading levels can be predicted by the proposed Hooke's law. This result further validates the linear constitutive relation for blood vessels when shear deformation is involved.

International reference preparations of typhoid vaccine

PubMed Central

Melikova, E. N.; Lesnjak, S. V.

1967-01-01

International collaborative laboratory studies on the International Reference Preparations of Typhoid Vaccine have so far failed to provide data on which international units for these vaccines can be based. Further assays carried out using the active mouse protection test, with immunization by the subcutaneous, intraperitoneal or intravenous route, confirmed the findings by some workers that the International Reference Preparation of Typhoid Vaccine (Acetone-Inactivated) (vaccine K) was more effective than the International Reference Preparation of Typhoid Vaccine (Heat-Phenol-Inactivated) (vaccine L), and indicated that intraperitoneal immunization was the most promising method. Vaccine K, together with the material extracted by the acetone in the preparation of the vaccine, had a significantly lower effectiveness (at the 5% probability level) only when intraperitoneal immunization was used. The reasons for the differences found between the various vaccines and routes of immunization are discussed at length. It is suggested that challenge with a strain of Salmonella moscow instead of the strain of Salm. typhi used until now gives a true infection and forms the basis of a reliable method for the potency assay of typhoid vaccines. PMID:5301738

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

PubMed Central

Schneeberger, Korbinian; Ossowski, Stephan; Ott, Felix; Klein, Juliane D.; Wang, Xi; Lanz, Christa; Smith, Lisa M.; Cao, Jun; Fitz, Joffrey; Warthmann, Norman; Henz, Stefan R.; Huson, Daniel H.; Weigel, Detlef

2011-01-01

We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html. PMID:21646520

[Analysis of regions determining resistence to fluoroquinolones in genes gyrA and parC in clinical isolates of Mycoplasma hominis].

PubMed

Gushchin, A E; Ladygina, V G; Govorun, V M; Taraskina, A M; Savicheva, A M

2000-01-01

Fifteen strains of M. hominis isolated from patients with urogenital inflammations were analyzed. Variations in the quinolone resistance-determining regions (QRDR) have been found in fluoroquinolone-resistant M. hominis clinical isolates in comparison with the reference PG21 strain. In one isolate, parC had Asn substitute at position 91.

Type VI Secretion is a Major Virulence Determinant in Burkholderia Mallei

DTIC Science & Technology

2007-06-01

Strain or plasmid Relevant characteristicsb Reference E. coli TOP10 General cloning and blue/white screening Invitrogen Origami (DE3) D3 lysogen, KmR, SmR...was transformed into E. coli Origami (DE3) and the strain was grown in a 125 ml dispos- able Erlenmeyer flask containing 50 ml of LB with Cb, Tc and Km

Quantitative method for gait pattern detection based on fiber Bragg grating sensors

NASA Astrophysics Data System (ADS)

Ding, Lei; Tong, Xinglin; Yu, Lie

2017-03-01

This paper presents a method that uses fiber Bragg grating (FBG) sensors to distinguish the temporal gait patterns in gait cycles. Unlike most conventional methods that focus on electronic sensors to collect those physical quantities (i.e., strains, forces, pressure, displacements, velocity, and accelerations), the proposed method utilizes the backreflected peak wavelength from FBG sensors to describe the motion characteristics in human walking. Specifically, the FBG sensors are sensitive to external strain with the result that their backreflected peak wavelength will be shifted according to the extent of the influence of external strain. Therefore, when subjects walk in different gait patterns, the strains on FBG sensors will be different such that the magnitude of the backreflected peak wavelength varies. To test the reliability of the FBG sensor platform for gait pattern detection, the gold standard method using force-sensitive resistors (FSRs) for defining gait patterns is introduced as a reference platform. The reliability of the FBG sensor platform is determined by comparing the detection results between the FBG sensors and FSRs platforms. The experimental results show that the FBG sensor platform is reliable in gait pattern detection and gains high reliability when compared with the reference platform.

Fourier-Transform Infrared Microspectroscopy, a Novel and Rapid Tool for Identification of Yeasts

PubMed Central

Wenning, Mareike; Seiler, Herbert; Scherer, Siegfried

2002-01-01

Fourier-transform infrared (FT-IR) microspectroscopy was used in this study to identify yeasts. Cells were grown to microcolonies of 70 to 250 μm in diameter and transferred from the agar plate by replica stamping to an IR-transparent ZnSe carrier. IR spectra of the replicas on the carrier were recorded using an IR microscope coupled to an IR spectrometer, and identification was performed by comparison to reference spectra. The method was tested by using small model libraries comprising reference spectra of 45 strains from 9 genera and 13 species, recorded with both FT-IR microspectroscopy and FT-IR macrospectroscopy. The results show that identification by FT-IR microspectroscopy is equivalent to that achieved by FT-IR macrospectroscopy but the time-consuming isolation of the organisms prior to identification is not necessary. Therefore, this method also provides a rapid tool to analyze mixed populations. Furthermore, identification of 21 Debaryomyces hansenii and 9 Saccharomyces cerevisiae strains resulted in 92% correct identification at the strain level for S. cerevisiae and 91% for D. hansenii, which demonstrates that the resolution power of FT-IR microspectroscopy may also be used for yeast typing at the strain level. PMID:12324312

Investigating the Molecular Mechanisms of Organophosphate and Pyrethroid Resistance in the Fall Armyworm Spodoptera frugiperda

PubMed Central

Carvalho, Renato A.; Omoto, Celso; Field, Linda M.; Williamson, Martin S.; Bass, Chris

2013-01-01

The fall armyworm Spodoptera frugiperda is an economically important pest of small grain crops that occurs in all maize growing regions of the Americas. The intensive use of chemical pesticides for its control has led to the selection of resistant populations, however, to date, the molecular mechanisms underlying resistance have not been characterised. In this study the mechanisms involved in the resistance of two S. frugiperda strains collected in Brazil to chlorpyrifos (OP strain) or lambda-cyhalothrin (PYR strain) were investigated using molecular and genomic approaches. To examine the possible role of target-site insensitivity the genes encoding the organophosphate (acetylcholinesterase, AChE) and pyrethroid (voltage-gated sodium channel, VGSC) target-site proteins were PCR amplified. Sequencing of the S. frugiperda ace-1 gene identified several nucleotide changes in the OP strain when compared to a susceptible reference strain (SUS). These result in three amino acid substitutions, A201S, G227A and F290V, that have all been shown previously to confer organophosphate resistance in several other insect species. Sequencing of the gene encoding the VGSC in the PYR strain, identified mutations that result in three amino acid substitutions, T929I, L932F and L1014F, all of which have been shown previously to confer knockdown/super knockdown-type resistance in several arthropod species. To investigate the possible role of metabolic detoxification in the resistant phenotype of the OP and PYR stains all EST sequences available for S. frugiperda were used to design a gene-expression microarray. This was then used to compare gene expression in the resistant strains with the susceptible reference strain. Members of several gene families, previously implicated in metabolic resistance in other insects were found to be overexpressed in the resistant strains including glutathione S-transferases, cytochrome P450s and carboxylesterases. Taken together these results provide evidence that both target-site and metabolic mechanisms underlie the resistance of S. frugiperda to pyrethroids and organophosphates. PMID:23614047

Investigating the molecular mechanisms of organophosphate and pyrethroid resistance in the fall armyworm Spodoptera frugiperda.

PubMed

Carvalho, Renato A; Omoto, Celso; Field, Linda M; Williamson, Martin S; Bass, Chris

2013-01-01

The fall armyworm Spodoptera frugiperda is an economically important pest of small grain crops that occurs in all maize growing regions of the Americas. The intensive use of chemical pesticides for its control has led to the selection of resistant populations, however, to date, the molecular mechanisms underlying resistance have not been characterised. In this study the mechanisms involved in the resistance of two S. frugiperda strains collected in Brazil to chlorpyrifos (OP strain) or lambda-cyhalothrin (PYR strain) were investigated using molecular and genomic approaches. To examine the possible role of target-site insensitivity the genes encoding the organophosphate (acetylcholinesterase, AChE) and pyrethroid (voltage-gated sodium channel, VGSC) target-site proteins were PCR amplified. Sequencing of the S. frugiperda ace-1 gene identified several nucleotide changes in the OP strain when compared to a susceptible reference strain (SUS). These result in three amino acid substitutions, A201S, G227A and F290V, that have all been shown previously to confer organophosphate resistance in several other insect species. Sequencing of the gene encoding the VGSC in the PYR strain, identified mutations that result in three amino acid substitutions, T929I, L932F and L1014F, all of which have been shown previously to confer knockdown/super knockdown-type resistance in several arthropod species. To investigate the possible role of metabolic detoxification in the resistant phenotype of the OP and PYR stains all EST sequences available for S. frugiperda were used to design a gene-expression microarray. This was then used to compare gene expression in the resistant strains with the susceptible reference strain. Members of several gene families, previously implicated in metabolic resistance in other insects were found to be overexpressed in the resistant strains including glutathione S-transferases, cytochrome P450s and carboxylesterases. Taken together these results provide evidence that both target-site and metabolic mechanisms underlie the resistance of S. frugiperda to pyrethroids and organophosphates.

Molecular identification of pathogenicity genes and ERIC types in Vibrio cholerae O1 epidemic strains from Mozambique.

PubMed Central

Folgosa, E.; Mastrandrea, S.; Cappuccinelli, P.; Uzzau, S.; Rappelli, P.; Brian, M. J.; Colombo, M. M.

2001-01-01

The phenotypic and genotypic profiles of the V. cholerae strains causing the Mozambican 1997-8 epidemic were characterized to provide a reference for comparison with other epidemic strains. A total of 75 strains of V. cholerae O1 isolated in different provinces, were analysed. Strains were characterized by PCR for detecting toxin genes (ctxA, zot and ace), virulence associated genes (tcpA. nanH, hlyA and torR) and ERIC sequences. All V. cholerae strains were serotype O1, Ogawa, biotype El Tor. MIC testing showed a high proportion of strains multi-resistant to drugs (100% to cotrimoxazole and 52% to tetracycline) and susceptibility to ciprofloxacin. The isolates contained two intact copies of the CTX genetic element and all other genes tested. PCR of restricted DNA revealed two ERIC types: the first in provincial isolates, also predominant in other African epidemic strains, and the second in Maputo isolates (the national capital). PMID:11561970

Variation in genotype and higher virulence of a strain of Sporothrix schenckii causing disseminated cutaneous sporotrichosis.

PubMed

Zhang, Zhenying; Liu, Xiaoming; Lv, Xuelian; Lin, Jingrong

2011-12-01

Sporotrichosis is usually a localized, lymphocutaneous disease, but its disseminated type was rarely reported. The main objective of this study was to identify specific DNA sequence variation and virulence of a strain of Sporothrix schenckii isolated from the lesion of disseminated cutaneous sporotrichosis. We confirmed this strain to be S. schenckii by(®) tubulin and chitin synthase gene sequence analysis in addition to the routine mycological and partial ITS and NTS sequencing. We found a 10-bp deletion in the ribosomal NTS region of this strain, in reference to the sequence of control strains isolated from fixed cutaneous sporotrichosis. After inoculated into immunosuppressed mice, this strain caused more extensive system involvement and showed stronger virulence than the control strain isolated from a fixed cutaneous sporotrichosis. Our study thus suggests that different clinical manifestation of sporotrichosis may be associated with variation in genotype and virulence of the strain, independent of effects due to the immune status of the host.

Gram-positive bacteria of marine origin: a numerical taxonomic study on Mediterranean isolates.

PubMed

Ortigosa, M; Garay, E; Pujalte, M J

1997-12-01

A numerical taxonomic study was performed on 65 Gram-positive wild strains of heterotrophic, aerobic, marine bacteria, and 9 reference strains. The isolates were obtained from oysters and seawater sampled monthly over one year, by direct plating on Marine Agar. The strains were characterized by 96 morphological, biochemical, physiological and nutritional tests. Clustering yielded 13 phena at 0.62 similarity level (Sl coefficient). Only one of the seven phena containing wild isolates could be identified (Bacillus marinus). A pronounced salt requirement was found in most isolates.

In Vitro Antibiotic Susceptibilities of Burkholderia mallei (Causative Agent of Glanders) Determined by Broth Microdilution and E-Test

PubMed Central

Heine, Henry S.; England, Marilyn J.; Waag, David M.; Byrne, W. Russell

2001-01-01

In vitro susceptibilities to 28 antibiotics were determined for 11 strains of Burkholderia mallei by the broth microdilution method. The B. mallei strains demonstrated susceptibility to aminoglycosides, macrolides, quinolones, doxycycline, piperacillin, ceftazidime, and imipenem. For comparison and evaluation, 17 antibiotic susceptibilities were also determined by the E-test. E-test values were always lower than the broth dilution values. Establishing and comparing antibiotic susceptibilities of specific B. mallei strains will provide reference information for assessing new antibiotic agents. PMID:11408233

Versatile Measurement Techniques to Validate Analytical Structural Mechanical Models

DTIC Science & Technology

2007-03-01

temperature is about 33 C. 109 34 For flight 4P temperature and strain data versus flight time is presented. Also a scatter plot of strain for gage 2...versus temperature is shown. As shown in the chart the maximum strain was about 91 microstrain during flight 4P . The maximum temperature is about 87...some more data will be taken on some tests of steel blocks for VASM. 153 33 References • SBIR Topic AF# SD01-CBM04 • LUNA Draft Marketing Manual • Luna

Genetic Diversity and Population Structure of Vibrio cholerae

PubMed Central

Beltrán, Pilar; Delgado, Gabriela; Navarro, Armando; Trujillo, Francisca; Selander, Robert K.; Cravioto, Alejandro

1999-01-01

Multilocus enzyme electrophoresis (MLEE) of 397 Vibrio cholerae isolates, including 143 serogroup reference strains and 244 strains from Mexico and Guatemala, identified 279 electrophoretic types (ETs) distributed in two major divisions (I and II). Linkage disequilibrium was demonstrated in both divisions and in subdivision Ic of division I but not in subdivision Ia, which includes 76% of the ETs. Despite this evidence of relatively frequent recombination, clonal lineages may persist for periods of time measured in at least decades. In addition to the pandemic clones of serogroups O1 and O139, which form a tight cluster of four ETs in subdivision Ia, MLEE analysis identified numerous apparent clonal lineages of non-O1 strains with intercontinental distributions. A clone of serogroup O37 that demonstrated epidemic potential in the 1960s is closely related to the pandemic O1/O139 clones, but the nontoxigenic O1 Inaba El Tor reference strain is not. A strain of serogroup O22, which has been identified as the most likely donor of exogenous rfb region DNA to the O1 progenitor of the O139 clone, is distantly related to the O1/O139 clones. The close evolutionary relationships of the O1, O139, and O37 epidemic clones indicates that new cholera clones are likely to arise by the modification of a lineage that is already epidemic or is closely related to such a clone. PMID:9986816

Genetic diversity and population structure of Vibrio cholerae.

PubMed

Beltrán, P; Delgado, G; Navarro, A; Trujillo, F; Selander, R K; Cravioto, A

1999-03-01

Multilocus enzyme electrophoresis (MLEE) of 397 Vibrio cholerae isolates, including 143 serogroup reference strains and 244 strains from Mexico and Guatemala, identified 279 electrophoretic types (ETs) distributed in two major divisions (I and II). Linkage disequilibrium was demonstrated in both divisions and in subdivision Ic of division I but not in subdivision Ia, which includes 76% of the ETs. Despite this evidence of relatively frequent recombination, clonal lineages may persist for periods of time measured in at least decades. In addition to the pandemic clones of serogroups O1 and O139, which form a tight cluster of four ETs in subdivision Ia, MLEE analysis identified numerous apparent clonal lineages of non-O1 strains with intercontinental distributions. A clone of serogroup O37 that demonstrated epidemic potential in the 1960s is closely related to the pandemic O1/O139 clones, but the nontoxigenic O1 Inaba El Tor reference strain is not. A strain of serogroup O22, which has been identified as the most likely donor of exogenous rfb region DNA to the O1 progenitor of the O139 clone, is distantly related to the O1/O139 clones. The close evolutionary relationships of the O1, O139, and O37 epidemic clones indicates that new cholera clones are likely to arise by the modification of a lineage that is already epidemic or is closely related to such a clone.

Phylogenomics of Colombian Helicobacter pylori isolates.

PubMed

Gutiérrez-Escobar, Andrés Julián; Trujillo, Esperanza; Acevedo, Orlando; Bravo, María Mercedes

2017-01-01

During the Spanish colonisation of South America, African slaves and Europeans arrived in the continent with their corresponding load of pathogens, including Helicobacter pylori . Colombian strains have been clustered with the hpEurope population and with the hspWestAfrica subpopulation in multilocus sequence typing (MLST) studies. However, ancestry studies have revealed the presence of population components specific to H. pylori in Colombia. The aim of this study was to perform a thorough phylogenomic analysis to describe the evolution of the Colombian urban H. pylori isolates. A total of 115 genomes of H. pylori were sequenced with Illumina technology from H. pylori isolates obtained in Colombia in a region of high risk for gastric cancer. The genomes were assembled, annotated and underwent phylogenomic analysis with 36 reference strains. Additionally, population differentiation analyses were performed for two bacterial genes. The phylogenetic tree revealed clustering of the Colombian strains with hspWestAfrica and hpEurope, along with three clades formed exclusively by Colombian strains, suggesting the presence of independent evolutionary lines for Colombia. Additionally, the nucleotide diversity of horB and vacA genes from Colombian isolates was lower than in the reference strains and showed a significant genetic differentiation supporting the hypothesis of independent clades with recent evolution. The presence of specific lineages suggest the existence of an hspColombia subtype that emerged from a small and relatively isolated ancestral population that accompanied crossbreeding of human population in Colombia.

Proteomic analysis of hyperadhesive Candida glabrata clinical isolates reveals a core wall proteome and differential incorporation of adhesins.

PubMed

Gómez-Molero, Emilia; de Boer, Albert D; Dekker, Henk L; Moreno-Martínez, Ana; Kraneveld, Eef A; Ichsan; Chauhan, Neeraj; Weig, Michael; de Soet, Johannes J; de Koster, Chris G; Bader, Oliver; de Groot, Piet W J

2015-12-01

Attachment to human host tissues or abiotic medical devices is a key step in the development of infections by Candida glabrata. The genome of this pathogenic yeast codes for a large number of adhesins, but proteomic work using reference strains has shown incorporation of only few adhesins in the cell wall. By making inventories of the wall proteomes of hyperadhesive clinical isolates and reference strain CBS138 using mass spectrometry, we describe the cell wall proteome of C. glabrata and tested the hypothesis that hyperadhesive isolates display differential incorporation of adhesins. Two clinical strains (PEU382 and PEU427) were selected, which both were hyperadhesive to polystyrene and showed high surface hydrophobicity. Cell wall proteome analysis under biofilm-forming conditions identified a core proteome of about 20 proteins present in all C. glabrata strains. In addition, 12 adhesin-like wall proteins were identified in the hyperadherent strains, including six novel adhesins (Awp8-13) of which only Awp12 was also present in CBS138. We conclude that the hyperadhesive capacity of these two clinical C. glabrata isolates is correlated with increased and differential incorporation of cell wall adhesins. Future studies should elucidate the role of the identified proteins in the establishment of C. glabrata infections. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Escherichia coli O78 isolated from septicemic lambs shows high pathogenicity in a zebrafish model.

PubMed

Kjelstrup, Cecilie K; Barber, Amelia E; Norton, J Paul; Mulvey, Matthew A; L'Abée-Lund, Trine M

2017-01-25

The pathogenicity of Escherichia coli O78 strain K46, originally isolated from an outbreak of septicemia in neonatal lambs, was investigated in zebrafish embryo and murine models of infection. Its biofilm potential, cellulose production, and the expression of type 1 pili and curli fimbriae were measured by in vitro assays. The strain was highly pathogenic in the zebrafish embryo model of infection, where it killed all embryos within 24 h post inoculation (hpi) at doses as low as 1000 colony forming units. Zebrafish embryos inoculated with similar doses of commensal E. coli strains showed no signs of disease, and cleared the bacteria within 24 h. E. coli K46 colonized the murine gut at the same level as the uropathogenic E. coli (UPEC) reference strain CFT073 in CBA/J mice after oral inoculation, but infected the murine bladder significantly less than CFT073 after transurethral inoculation. Type 1 pili were clearly expressed by E. coli K46, while curli fimbriae and cellulose production were weakly expressed. The ability to produce biofilm varied in different growth media, but overall E. coli K46 was a poorer biofilm producer compared to the reference strain E. coli UTI89. In conclusion, the zebrafish lethality model provides further evidence that E. coli K46 is highly pathogenic and might be useful in future studies to identify bacterial virulence factors.

Satisfaction with Life Scale (SWLS) in Caregivers of Clinically-Referred Youth: Psychometric Properties and Mediation Analysis

PubMed Central

Athay, M. Michele

2012-01-01

This paper presents the psychometric evaluation of the Satisfaction with Life Scale (SWLS; Diener, Emmons, Larson & Griffen, 1985) used with a large sample (N = 610) of caregivers for youth receiving mental health services. Methods from classical test theory, factor analysis and item response theory are utilized. Additionally, this paper investigates whether caregiver strain mediates the effect of youth symptom severity on caregiver life satisfaction (N = 356). Bootstrapped confidence intervals are used to determine the significance of the mediated effects. Results indicate that the SWLS is a psychometrically sound instrument to be used with caregivers of clinically-referred youth. Mediation analyses found that the effect of youth symptom severity on caregiver life satisfaction is mediated by caregiver strain but that the mediation effect differs based on the type of youth symptoms. Caregiver strain is a partial mediator when externalizing symptoms are measured and a full mediator when internalizing symptoms are measured. Implications for future research and clinical practice are discussed. PMID:22407554

An alternative hypothesis for high-T 40Ar/39Ar age spectrum discordance in polyphase extraterrestrial materials

NASA Astrophysics Data System (ADS)

Cassata, W. S.; Shuster, D. L.; Renne, P. R.; Weiss, B. P.

2009-12-01

A common feature observed in 40Ar/39Ar age spectra of extraterrestrial (ET) rocks is a conspicuous decrease in the ages of high temperature extractions relative to lower temperature steps and a correlated increase in Ca/K, often succeeded by a monotonic increase in ages. This feature is routinely attributed to recoil-implanted 39Ar from a potassium (K)-rich donor phase into a K-poor receptor phase (e.g., 1,2). While 39Ar recoil redistribution is undoubtedly manifested in many terrestrial and ET 40Ar/39Ar whole-rock age spectra, it cannot easily explain the magnitude of high release temperature 40Ar*/39ArK anomalies observed in Martian meteorites ALH 84001 and Nakhla, as well as other course-grained meteorites and lunar rocks. Depending on the aliquot and sample, 50 - 100% of the pyroxene release spectra in ALH 84001 and Nakhla appear strongly perturbed to lower ages. As the mean recoil distance of 39Ar ~0.1 µm, the recoil hypothesis demands that a high-K phase be ubiquitously distributed amongst sub-micron to micron sized pyroxene crystals to account for the observed pyroxene age spectra. However, in both Nakhla and ALH 84001, pyroxene is often completely isolated from high-K phases and individual grains commonly exceed 100 µm in diameter. 40Ar/39Ar analyses of pyroxene-bearing terrestrial basalts, wherein fine-grained pyroxene and plagioclase are intimately adjoined, show that recoil-implanted 39Ar into pyroxene produces much less precipitous anomalies in 40Ar*/39ArK, as predicted by the recoil lengthscale. An alternative hypothesis is that whole-rock age spectra of ET samples with anomalously low ages at high temperatures may reflect diffusive 40Ar distributions within considerably degassed pyroxene grains. Owing to apparent differences in activation energies between glass and/or plagioclase and pyroxene, 40Ar may diffuse more rapidly from pyroxene under certain high-temperature conditions (i.e., above the temperature at which the extrapolated Ar Arrhenius relationships intersect). Thus, very brief, high-temperature shock-heating events may preferentially degas pyroxene without significantly resetting glass and plagioclase 40Ar/39Ar age spectra. This effect would be enhanced by highly localized shock-heating focused along pyroxene (sub)grain boundaries, as has been inferred in other cases (e.g., 3). The shock and impact origin of this feature may explain its frequent appearance in ET samples, regardless of grain size, as well as the general absence of terrestrial analogs. We will present new 40Ar/39Ar data from Martian meteorites and physical models to distinguish between these competing hypotheses. References Cited: 1. Turner & Cadogan, 1974, Possible effects of 39Ar recoil in 40Ar-39Ar dating. Proc. 5th LPSC, 1601- 1615. 2. Huneke & Smith, 1976, The realities of recoil: 39Ar recoil out of small grains and anomalous age patterns in 40Ar-39Ar dating. Proc. 7th LPSC, 1987-2008. 3. Min et al., 2003, Single grain (U-Th)/He ages from phosphates in Acapulco meteorite and implications for thermal history. EPSL 209, 323-336.

Photobacterium damselae ssp. piscicida: detection by direct amplification of 16S rRNA gene sequences and genotypic variation as determined by amplified fragment length polymorphism (AFLP).

PubMed

Kvitt, H; Ucko, M; Colorni, A; Batargias, C; Zlotkin, A; Knibb, W

2002-04-05

A PCR protocol for the rapid diagnosis of fish 'pasteurellosis' based on 16S rRNA gene sequences was developed. The procedure combines low annealing temperature that detects low titers of Photobacterium damselae but also related species, and high annealing temperature for the specific identification of P. damselae directly from infected fish. The PCR protocol was validated on 19 piscine isolates of P. damselae ssp. piscicida from different geographic regions (Japan, Italy, Spain, Greece and Israel), on spontaneously infected sea bream Sparus aurata and sea bass Dicentrarchus labrax, and on closely related American Type Culture Collection (ATCC) reference strains. PCR using high annealing temperature (64 degrees C) discriminated between P. damselae and closely related reference strains, including P. histaminum. Sixteen isolates of P. damselae ssp. piscicida, 2 P. damselae ssp. piscicida reference strains and 1 P. damselae ssp. damselae reference strain were subjected to Amplified Fragment Length Polymorphism (AFLP) analysis, and a similarity matrix was produced. Accordingly, the Japanese isolates of P. damselae ssp. piscicida were distinguished from the Mediterranean/European isolates at a cut-off value of 83% similarity. A further subclustering at a cut-off value of 97% allowed discrimination between the Israeli P. damselae ssp. piscicida isolates and the other Mediterranean/European isolates. The combination of PCR direct amplification and AFLP provides a 2-step procedure, where P. damselae is rapidly identified at genus level on the basis of its 16S rRNA gene sequence and then grouped into distinct clusters on the basis of AFLP polymorphisms. The first step of direct amplification is highly sensitive and has immediate practical consequences, offering fish farmers a rapid diagnosis, while the AFLP is more specific and detects intraspecific variation which, in our study, also reflected geographic correspondence. Because of its superior discriminative properties, AFLP can be an important tool for epidemiological and taxonomic studies of this highly homogeneous genus.

Genomic and physiological characterization of a laboratory-isolated Acinetobacter schindleri ACE strain that quickly and efficiently catabolizes acetate.

PubMed

Sigala, Juan-Carlos; Suárez, Brisa Paola; Lara, Alvaro R; Borgne, Sylvie Le; Bustos, Patricia; Santamaría, Rosa Isela; González, Víctor; Martinez, Alfredo

2017-07-01

An Acinetobacter strain, designated ACE, was isolated in the laboratory. Phylogenetic tests and average nucleotide identity value comparisons suggested that ACE belongs to the species Acinetobacterschindleri. We report for the first time the complete genome sequence of an A. schindleri strain, which consists of a single circular chromosome of 3 001 209 bp with an overall DNA G+C content of 42.9 mol% and six plasmids that account for 266 844 bp of extrachromosomal material. The presence or absence of genes related to carbon catabolism and antibiotic resistance were in agreement with the phenotypic characterization of ACE. This strain grew faster and with a higher biomass yield on acetate than the reference strain Acinetobacter baylyi ADP1. However, ACE did not use aromatic compounds and was unable to grow on common carbon sources, such as glucose, xylose, glycerol or citrate. The gluconeogenic and the catechol pathways are complete in ACE, but compounds that are converted to protocatechuate did not sustain growth since some genes of this pathway are missing. Likewise, this strain could not grow on glucose because it lacks the genes of the Entner-Doudoroff pathway. Minimal inhibitory concentration data showed that ACE was susceptible to most of the antimicrobial agents recommended for the clinical treatment of Acinetobacter spp. Some genes related to a possible human-microbe interaction were found in the ACE genome. ACE is likely to have a low pathogenic risk, as is the case with other A. schindleri strains. These results provide a valuable reference for broadening the knowledge of the biology of Acinetobacter.

Is 2D speckle tracking echocardiography useful for detecting and monitoring myocardial dysfunction in adult m.3243A>G carriers? - a retrospective pilot study.

PubMed

Koene, S; Timmermans, J; Weijers, G; de Laat, P; de Korte, C L; Smeitink, J A M; Janssen, M C H; Kapusta, L

2017-03-01

Cardiomyopathy is a common complication of mitochondrial disorders, associated with increased mortality. Two dimensional speckle tracking echocardiography (2DSTE) can be used to quantify myocardial deformation. Here, we aimed to determine the usefulness of 2DSTE in detecting and monitoring subtle changes in myocardial dysfunction in carriers of the 3243A>G mutation in mitochondrial DNA. In this retrospective pilot study, 30 symptomatic and asymptomatic carriers of the mitochondrial 3243A>G mutation of whom two subsequent echocardiograms were available were included. We measured longitudinal, circumferential and radial strain using 2DSTE. Results were compared to published reference values. Speckle tracking was feasible in 90 % of the patients for longitudinal strain. Circumferential and radial strain showed low face validity (low number of images with sufficient quality; suboptimal tracking) and were therefore rejected for further analysis. Global longitudinal strain showed good face validity, and was abnormal in 56-70 % (depending on reference values used) of the carriers (n = 27). Reproducibility was good (mean difference of 0.83 for inter- and 0.40 for intra-rater reproducibility; ICC 0.78 and 0.89, respectively). The difference between the first and the second measurement exceeded the measurement variance in 39 % of the cases (n = 23; feasibility of follow-up 77 %). Even in data collected as part of clinical care, two-dimensional strain echocardiography seems a feasible method to detect and monitor subtle changes in longitudinal myocardial deformation in adult carriers of the mitochondrial 3243A>G mutation. Based on our data and the reported accuracy of global longitudinal strain in other studies, we suggest the use of global longitudinal strain in a prospective follow-up or intervention study.

Reynolds Stress Balance in Plane Wakes Subjected to Irrotational Strains

NASA Technical Reports Server (NTRS)

Rogers, Miichael M.; Merriam, Marshal (Technical Monitor)

1997-01-01

Direct numerical simulations of time-evolving turbulent plane wakes developing in the presence of various irrotational plane strains have been generated. A pseudospectral numerical method with up to 25 million modes is used to solve the equations in a reference frame moving with the irrotational strain. The initial condition for each simulation is taken from a previous turbulent self-similar plane wake direct numerical simulation at a velocity deficit Reynolds number, R(sub e), of about 2,000. All the terms in the equations governing the evolution of the Reynolds stresses have been calculated. The relative importance of the various terms is examined for the different strain geometries and the behavior of the individual terms is used to better assess whether the strained wakes are evolving self-similarly.

A natural outbreak of Aujeszky's disease in farm animals.

PubMed

Salwa, A

2004-01-01

An outbreak of Aujeszky's disease (AD) occurred in a herd of domestic animals that led to the death of seven cattle, three goats, three sheep, two cats and one dog, all of them with CNS signs. The animals were not in direct contact with swine. The ADV was detected in the tissue of affected animals by celi culture methods and PCR. Genome strains of ADV were characterized by restriction endonuclease analysis using BamH I. The results indicated that the strains of virus were identical and belonged to the type genome I of AD. Compared with vaccine and isolated strains obtained from the pig in the same region, considerable differences in DNA patterns were detected. Interestingly, the strains isolated from the dead animals were similar to Buk T-900 reference strains.

Strain Modal Analysis of Small and Light Pipes Using Distributed Fibre Bragg Grating Sensors

PubMed Central

Huang, Jun; Zhou, Zude; Zhang, Lin; Chen, Juntao; Ji, Chunqian; Pham, Duc Truong

2016-01-01

Vibration fatigue failure is a critical problem of hydraulic pipes under severe working conditions. Strain modal testing of small and light pipes is a good option for dynamic characteristic evaluation, structural health monitoring and damage identification. Unique features such as small size, light weight, and high multiplexing capability enable Fibre Bragg Grating (FBG) sensors to measure structural dynamic responses where sensor size and placement are critical. In this paper, experimental strain modal analysis of pipes using distributed FBG sensors ispresented. Strain modal analysis and parameter identification methods are introduced. Experimental strain modal testing and finite element analysis for a cantilever pipe have been carried out. The analysis results indicate that the natural frequencies and strain mode shapes of the tested pipe acquired by FBG sensors are in good agreement with the results obtained by a reference accelerometer and simulation outputs. The strain modal parameters of a hydraulic pipe were obtained by the proposed strain modal testing method. FBG sensors have been shown to be useful in the experimental strain modal analysis of small and light pipes in mechanical, aeronautic and aerospace applications. PMID:27681728

The Effect of Strain Rate on the Evolution of Plane Wakes Subjected to Irrotational Strains

NASA Technical Reports Server (NTRS)

Rogers, Michael M.; Merriam, Marshal (Technical Monitor)

1996-01-01

Direct numerical simulations of time-evolving turbulent plane wakes developing in the presence of irrotational plane strain applied at three different strain rates have been generated. The strain geometry is such that the flow is compressed in the streamwise direction and expanded in the cross-stream direction with the spanwise direction being unstrained. This geometry is the temporally evolving analogue of a spatially evolving wake in an adverse pressure gradient. A pseudospectral numerical method with up to 16 million modes is used to solve the equations in a reference frame moving with the irrotational strain. The initial condition for each simulation is taken from a previous turbulent self-similar plane wake direct numerical simulation at a velocity deficit Reynolds number, Re, of about 2,000. Although the evolutions of many statistics are nearly collapsed when plotted against total strain, there are some differences owing to the different strain rate histories. The impact of strain-rate on the wake spreading rate, the peak velocity deficit, the Reynolds stress profiles, and the flow structure is examined.

Calibration and assessment of full-field optical strain measurement procedures and instrumentation

NASA Astrophysics Data System (ADS)

Kujawinska, Malgorzata; Patterson, E. A.; Burguete, R.; Hack, E.; Mendels, D.; Siebert, T.; Whelan, Maurice

2006-09-01

There are no international standards or norms for the use of optical techniques for full-field strain measurement. In the paper the rationale and design of a reference material and a set of standarized materials for the calibration and evaluation of optical systems for full-field measurements of strain are outlined. A classification system for the steps in the measurement process is also proposed and allows the development of a unified approach to diagnostic testing of components in an optical system for strain measurement based on any optical technique. The results described arise from a European study known as SPOTS whose objectives were to begin to fill the gap caused by a lack of standards.

Reemergence of rabies in the southern Han river region, Korea.

PubMed

Oem, Jae-Ku; Kim, Seong-Hee; Kim, Yeon-Hee; Lee, Myoung-Heon; Lee, Kyoung-Ki

2014-07-01

Recently, 11 cases of animal rabies were reported in the southern region (Suwon and Hwaseong cities) of Gyeonggi Province, South Korea. The cases were temporally separated into two cases in dogs (Canis lupus familiaris) in spring 2012 and nine cases in domestic animals and wildlife in winter 2012-13. All carcasses were submitted for histopathologic examination and viral antigen identification. Sequences of the glycoprotein, nucleoprotein, and glycoprotein-large polymerase protein intergenic noncoding loci of the 11 strains were determined and compared with published reference sequences. All rabies strains were closely related to the Gangwon strains isolated in 2008-09, suggesting that the rabies virus strains isolated in Gyeonggi were introduced from Gangwon Province.

Utility of a stressed-SNP real-time PCR assay for the rapid identification of measles vaccine strain in patient samples.

PubMed

Tran, Thomas; Kostecki, Renata; Catton, Michael; Druce, Julian

2018-05-09

Rapid differentiation of wild-type measles virus from measles vaccine strains is crucial during a measles outbreak and in a measles elimination setting. A real-time RT-PCR for the rapid detection of measles vaccine strains was developed with high specificity and greater sensitivity than when compared to traditional measles genotyping methods. The "stressed" minor grove binder TaqMan probe design approach achieves specificity to vaccine strains only, without compromising sensitivity. This assay has proven to be extremely useful in outbreak settings, without requiring sequence genotyping, for over 4 years at the Regional Measles Reference Laboratory for the Western Pacific Region. Copyright © 2018 Tran et al.

Effect of Biaxial Isothermal Quasi-Continuous Deformation on Structure and Shape Memory Properties of Ti-Ni Alloys

NASA Astrophysics Data System (ADS)

Khmelevskaya, I.; Komarov, V.; Kawalla, R.; Prokoshkin, S.; Korpala, G.

2017-08-01

Severe plastic deformation (SPD) of Ti-50.0 at.% Ni alloy was carried out using the multi-axial deformation MaxStrain module of Gleeble system at 400, 370, 350 and 330 °C with accumulated true strains from e = 3.5 to 9.5. Kinetics of martensitic transformations was studied by DSC method, the structure features by x-ray diffraction and TEM. The recoverable strain was studied using a bending mode for strain inducing. A mixed nanocrystalline and nanosubgrained structure with average grain/subgrain size below 100 nm has been formed in a bulk sample as a result of SPD at as low as 330 °C. The resulting nanostructure provides an obvious advantage in the completely recoverable strain (9.3%) as compared to SPD at 350-400 °C (7-8%), and to reference treatment (2.5%). That correlates with Vickers hardness changes versus SPD strain.

Global Panel of HIV-1 Env Reference Strains for Standardized Assessments of Vaccine-Elicited Neutralizing Antibodies

PubMed Central

deCamp, Allan; Hraber, Peter; Bailer, Robert T.; Seaman, Michael S.; Ochsenbauer, Christina; Kappes, John; Gottardo, Raphael; Edlefsen, Paul; Self, Steve; Tang, Haili; Greene, Kelli; Gao, Hongmei; Daniell, Xiaoju; Sarzotti-Kelsoe, Marcella; Gorny, Miroslaw K.; Zolla-Pazner, Susan; LaBranche, Celia C.; Mascola, John R.; Korber, Bette T.

2014-01-01

ABSTRACT Standardized assessments of HIV-1 vaccine-elicited neutralizing antibody responses are complicated by the genetic and antigenic variability of the viral envelope glycoproteins (Envs). To address these issues, suitable reference strains are needed that are representative of the global epidemic. Several panels have been recommended previously, but no clear answers have been available on how many and which strains are best suited for this purpose. We used a statistical model selection method to identify a global panel of reference Env clones from among 219 Env-pseudotyped viruses assayed in TZM-bl cells with sera from 205 HIV-1-infected individuals. The Envs and sera were sampled globally from diverse geographic locations and represented all major genetic subtypes and circulating recombinant forms of the virus. Assays with a panel size of only nine viruses adequately represented the spectrum of HIV-1 serum neutralizing activity seen with the larger panel of 219 viruses. An optimal panel of nine viruses was selected and augmented with three additional viruses for greater genetic and antigenic coverage. The spectrum of HIV-1 serum neutralizing activity seen with the final 12-virus panel closely approximated the activity seen with subtype-matched viruses. Moreover, the final panel was highly sensitive for detection of many of the known broadly neutralizing antibodies. For broader assay applications, all 12 Env clones were converted to infectious molecular clones using a proviral backbone carrying a Renilla luciferase reporter gene (Env.IMC.LucR viruses). This global panel should facilitate highly standardized assessments of vaccine-elicited neutralizing antibodies across multiple HIV-1 vaccine platforms in different parts of the world. IMPORTANCE An effective HIV-1 vaccine will need to overcome the extraordinary genetic variability of the virus, where most variation occurs in the viral envelope glycoproteins that are the sole targets for neutralizing antibodies. Efforts to elicit broadly cross-reactive neutralizing antibodies that will protect against infection by most circulating strains of the virus are guided in part by in vitro assays that determine the ability of vaccine-elicited antibodies to neutralize genetically diverse HIV-1 variants. Until now, little information was available on how many and which strains of the virus are best suited for this purpose. We applied robust statistical methods to evaluate a large neutralization data set and identified a small panel of viruses that are a good representation of the global epidemic. The neutralization properties of this new panel of reference strains should facilitate the development of an effective HIV-1 vaccine. PMID:24352443

Global panel of HIV-1 Env reference strains for standardized assessments of vaccine-elicited neutralizing antibodies.

PubMed

deCamp, Allan; Hraber, Peter; Bailer, Robert T; Seaman, Michael S; Ochsenbauer, Christina; Kappes, John; Gottardo, Raphael; Edlefsen, Paul; Self, Steve; Tang, Haili; Greene, Kelli; Gao, Hongmei; Daniell, Xiaoju; Sarzotti-Kelsoe, Marcella; Gorny, Miroslaw K; Zolla-Pazner, Susan; LaBranche, Celia C; Mascola, John R; Korber, Bette T; Montefiori, David C

2014-03-01

Standardized assessments of HIV-1 vaccine-elicited neutralizing antibody responses are complicated by the genetic and antigenic variability of the viral envelope glycoproteins (Envs). To address these issues, suitable reference strains are needed that are representative of the global epidemic. Several panels have been recommended previously, but no clear answers have been available on how many and which strains are best suited for this purpose. We used a statistical model selection method to identify a global panel of reference Env clones from among 219 Env-pseudotyped viruses assayed in TZM-bl cells with sera from 205 HIV-1-infected individuals. The Envs and sera were sampled globally from diverse geographic locations and represented all major genetic subtypes and circulating recombinant forms of the virus. Assays with a panel size of only nine viruses adequately represented the spectrum of HIV-1 serum neutralizing activity seen with the larger panel of 219 viruses. An optimal panel of nine viruses was selected and augmented with three additional viruses for greater genetic and antigenic coverage. The spectrum of HIV-1 serum neutralizing activity seen with the final 12-virus panel closely approximated the activity seen with subtype-matched viruses. Moreover, the final panel was highly sensitive for detection of many of the known broadly neutralizing antibodies. For broader assay applications, all 12 Env clones were converted to infectious molecular clones using a proviral backbone carrying a Renilla luciferase reporter gene (Env.IMC.LucR viruses). This global panel should facilitate highly standardized assessments of vaccine-elicited neutralizing antibodies across multiple HIV-1 vaccine platforms in different parts of the world. An effective HIV-1 vaccine will need to overcome the extraordinary genetic variability of the virus, where most variation occurs in the viral envelope glycoproteins that are the sole targets for neutralizing antibodies. Efforts to elicit broadly cross-reactive neutralizing antibodies that will protect against infection by most circulating strains of the virus are guided in part by in vitro assays that determine the ability of vaccine-elicited antibodies to neutralize genetically diverse HIV-1 variants. Until now, little information was available on how many and which strains of the virus are best suited for this purpose. We applied robust statistical methods to evaluate a large neutralization data set and identified a small panel of viruses that are a good representation of the global epidemic. The neutralization properties of this new panel of reference strains should facilitate the development of an effective HIV-1 vaccine.

Virulence gene content in Escherichia coli isolates from poultry flocks with clinical signs of colibacillosis in Brazil.

PubMed

De Carli, Silvia; Ikuta, Nilo; Lehmann, Fernanda Kieling Moreira; da Silveira, Vinicius Proença; de Melo Predebon, Gabriela; Fonseca, André Salvador Kazantzi; Lunge, Vagner Ricardo

2015-11-01

Escherichia coli is a commensal bacterium of the bird's intestinal tract, but it can invade different tissues resulting in systemic symptoms (colibacillosis). This disease occurs only when the E. coli infecting strain presents virulence factors (encoded by specific genes) that enable the adhesion and proliferation in the host organism. Thus, it is important to differentiate pathogenic (APEC, avian pathogenic E. coli) and non-pathogenic or fecal (AFEC, avian fecal E. coli) isolates. Previous studies analyzed the occurrence of virulence factors in E. coli strains isolated from birds with colibacillosis, demonstrating a high frequency of the bacterial genes cvaC, iroN, iss, iutA, sitA, tsh, fyuA, irp-2, ompT and hlyF in pathogenic strains. The aim of the present study was to evaluate the occurrence and frequency of these virulence genes in E. coli isolated from poultry flocks in Brazil. A total of 138 isolates of E. coli was obtained from samples of different tissues and/or organs (spleen, liver, kidney, trachea, lungs, skin, ovary, oviduct, intestine, cloaca) and environmental swabs collected from chicken and turkey flocks suspected to have colibacillosis in farms from the main Brazilian producing regions. Total DNA was extracted and the 10 virulence genes were detected by traditional and/or real-time PCR. At least 11 samples of each gene were sequenced and compared to reference strains. All 10 virulence factors were detected in Brazilian E. coli isolates, with frequencies ranging from 39.9% (irp-2) to 68.8% (hlyF and sitA). Moreover, a high nucleotide similarity (over 99%) was observed between gene sequences of Brazilian isolates and reference strains. Seventy-nine isolates were defined as pathogenic (APEC) and 59 as fecal (AFEC) based on previously described criteria. In conclusion, the main virulence genes of the reference E. coli strains are also present in isolates associated with colibacillosis in Brazil. The analysis of this set of virulence factors can be used to differentiate between APEC and AFEC isolates in Brazil. © 2015 Poultry Science Association Inc.

Plasmids in Vibrio parahemolyticus strains isolated in Japan and Bangladesh with special reference to different distributions.

PubMed

Arai, T; Ando, T; Kusakabe, A; Ullah, M A

1983-01-01

We surveyed plasmids in naturally occurring Vibrio parahemolyticus strains isolated in Japan and Bangladesh. Among the strains isolated in Japan, about half of the strains isolated from stools of patients of domestic diarrhea outbreaks as well as of travelers returning from East Asia were found to have plasmids, but no strains from foods had plasmids. In contrast, among the strains isolated in Bangladesh, none of the four strains isolated from patients had plasmids, but two out of eight strains isolated from water had plasmids, suggesting that plasmids are common in strains from the water in Bangladesh. All plasmids so far reported in V. parahemolyticus were detected in strains isolated from stools of patients. Incidences of plasmids in this organism were not so high in either area. In Japan, all plasmids were detected in strains from human intestines at 37 C, but in Bangladesh, where the temperature is around 30-40 C, the plasmids were detected in strains from the natural environment. These results suggested the possibility that these plasmids can come from different bacteria under rather high temperatures and that incidences of plasmids are influenced by the incidences of plasmids in bacteria present in the vicinity of V. parahemolyticus strains. None of these plasmids were found to have any relation to the biological characters tested.

[Multilocus sequence-typing for characterization of Moscow strains of Haemophilus influenzae type b].

PubMed

Platonov, A E; Mironov, K O; Iatsyshina, S B; Koroleva, I S; Platonova, O V; Gushchin, A E; Shipulin, G A

2003-01-01

Haemophilius influenzae, type b (Hib) bacteria, were genotyped by multilocus sequence typing (MLST) using 5 loci (adk, fucK, mdh, pgi, recA). 42 Moscow Hib strains (including 38 isolates form cerebrospinal fluid of children, who had purulent meningitis in 1999-2001, and 4 strains isolated from healthy carriers of Hib), as well as 2 strains from Yekaterinburg were studied. In MLST a strain is characterized, by alleles and their combinations (an allele profile) referred to also as sequence-type (ST). 9 Sts were identified within the Russian Hib bacteria: ST-1 was found in 25 strains (57%), ST-12 was found in 8 strains (18%), ST-11 was found in 4 strains (9%) and ST-15 was found in 2 strains (4.5%); all other STs strains (13, 14, 16, 17, 51) were found in isolated cases (2.3%). A comparison of allelic profiles and of nucleotide sequences showed that 93% of Russian isolates, i.e. strain with ST-1, 11, 12, 13, 15 and 17, belong to one and the same clonal complex. 2 isolates from Norway and Sweden from among 7 foreign Hib strains studied up to now can be described as belonging to the same clonal complex; 5 Hib strains were different from the Russian ones.

Unique Phylogenetic Lineage Found in the Fusarium-like Clade after Re-examining BCCM/IHEM Fungal Culture Collection Material

PubMed Central

De Cremer, Koen; Piérard, Denis; Hendrickx, Marijke

2016-01-01

Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium-like clade was adopted. The few species of the Fusarium-like clade were moved to new, re-installed or existing genera or provisionally retained as "Fusarium." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium-like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium-like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium-like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides. The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium-like clade and were also found morphologically distinct from other members of the Fusarium-like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium-like clade. PMID:27790062

Antiprotozoal and antimycobacterial activities of Persea americana seeds.

PubMed

Jiménez-Arellanes, Adelina; Luna-Herrera, Julieta; Ruiz-Nicolás, Ricardo; Cornejo-Garrido, Jorge; Tapia, Amparo; Yépez-Mulia, Lilián

2013-05-16

Persea americana seeds are widely used in traditional Mexican medicine to treat rheumatism, asthma, infectious processes as well as diarrhea and dysentery caused by intestinal parasites. The chloroformic and ethanolic extracts of P. americana seeds were prepared by maceration and their amoebicidal, giardicidal and trichomonicidal activity was evaluated. These extracts were also tested against Mycobacterium tuberculosis H37Rv, four mono-resistant and two multidrug resistant strains of M. tuberculosis as well as five non tuberculosis mycobacterium strains by MABA assay. The chloroformic and ethanolic extracts of P. americana seeds showed significant activity against E. histolytica, G. lamblia and T. vaginalis (IC50 <0.634 μg/ml). The chloroformic extract inhibited the growth of M. tuberculosis H37Rv, M. tuberculosis MDR SIN 4 isolate, three M. tuberculosis H37Rv mono-resistant reference strains and four non tuberculosis mycobacteria (M. fortuitum, M. avium, M. smegmatis and M. absessus) showing MIC values ≤50 μg/ml. Contrariwise, the ethanolic extract affected only the growth of two mono-resistant strains of M. tuberculosis H37Rv and M. smegmatis (MIC ≤50 μg/ml). The CHCl3 and EtOH seed extracts from P. americana showed amoebicidal and giardicidal activity. Importantly, the CHCl3 extract inhibited the growth of a MDR M. tuberculosis isolate and three out of four mono-resistant reference strains of M. tuberculosis H37Rv, showing a MIC = 50 μg/ml. This extract was also active against the NTM strains, M. fortuitum, M. avium, M. smegmatis and M. abscessus, with MIC values <50 μg/ml.

VraR Binding to the Promoter Region of agr Inhibits Its Function in Vancomycin-Intermediate Staphylococcus aureus (VISA) and Heterogeneous VISA.

PubMed

Dai, Yuanyuan; Chang, Wenjiao; Zhao, Changcheng; Peng, Jing; Xu, Liangfei; Lu, Huaiwei; Zhou, Shusheng; Ma, Xiaoling

2017-05-01

Acquisition of vancomycin resistance in Staphylococcus aureus is often accompanied by a reduction in virulence, but the mechanisms underlying this change remain unclear. The present study was undertaken to investigate this process in a clinical heterogeneous vancomycin-intermediate S. aureus (hVISA) strain, 10827; an hVISA reference strain, Mu3; and a VISA reference strain, Mu50, along with their respective series of vancomycin-induced resistant strains. In these strains, increasing MICs of vancomycin were associated with increased expression of the vancomycin resistance-associated regulator gene ( vraR ) and decreased expression of virulence genes ( hla , hlb , and coa ) and virulence-regulated genes (RNAIII, agrA , and saeR ). These results suggested that VraR might have a direct or indirect effect on virulence in S. aureus In electrophoretic mobility shift assays, VraR did not bind to promoter sequences of hla , hlb , and coa genes, but it did bind to the agr promoter region. In DNase I footprinting assays, VraR protected a 15-nucleotide (nt) sequence in the intergenic region between the agr P2 and P3 promoters. These results indicated that when S. aureus is subject to induction by vancomycin, expression of vraR is upregulated, and VraR binding inhibits the function of the Agr quorum-sensing system, causing reductions in the virulence of VISA/hVISA strains. Our results suggested that VraR in S. aureus is involved not only in the regulation of vancomycin resistance but also in the regulation of virulence. Copyright © 2017 American Society for Microbiology.

An Analysis of Strain Accumulation in the Western Part of Black Sea Region in Turkey

NASA Astrophysics Data System (ADS)

Deniz, I.; Avsar, N. B.; Deniz, R.; Mekik, C.; Kutoglu, S.

2014-12-01

Turkish National Horizontal Control Network (TNHCN) based on the European Datum 1950 (ED50) was used as the principal geodetic network until 2005 in Turkey. Since 2005, Turkish Large Scale Map and Map Information Production Regulation have required that that all the densification points have been produced within the same datum of Turkish National Fundamental GPS Network (TNFGN) put into practise in 2002 and based on International Terrestrial Reference Frame (ITRF). Hence, the common points were produced in both European Datum 1950 (ED50), and TNFGN.It is known that the geological and geophysical information about the network area can be obtained by the evaluation of the coordinate and scale variations in a geodetic network. For one such evaluation, the coordinate variations and velocities of network points, and also the strains are investigated. However, the principal problem in derivation of velocities arises from two different datums. In this context, the computation of velocities using the coordinate data of the ED50 and TNFGN is not accurate and reliable. Likewise, the analysis of strain from the coordinate differences is not reliable. However, due to the fact that the scale of a geodetic network is independent from datum, the strains can be derived from scale variations accurately and reliably.In this study, a test area limited 39.5°-42.0° northern latitudes and 31.0°-37.0° eastern longitudes was chosen. The benchmarks in this test area are composed of 30 geodetic control points derived with the aim of cadastral and engineering applications. We used data mining to investigate the common benchmarks in both reference systems for this area. Accordingly, the ED50 and TNFGN coordinates refer 1954 and 2005, respectively. Thus, it has been investigated the strain accumulation of 51 years in this region. It should be also noted that since 1954, the earthquakes have not registered greater than magnitude 6.0 in the test area. It is a considerable situation for this evaluation. The finite element analysis is used in order to derive the strain accumulation and rates in the test area (Figure 1). The results have been indicated that the minimum and maximum strains are 17μs and 3041μs, respectively.

In Vitro Studies of Pharmacodynamic Properties of Vancomycin against Staphylococcus aureus and Staphylococcus epidermidis

PubMed Central

Löwdin, E.; Odenholt, I.; Cars, O.

1998-01-01

The bactericidal activities of vancomycin against two reference strains and two clinical isolates of Staphylococcus aureus and Staphylococcus epidermidis were studied with five different concentrations ranging from 2× to 64× the MIC. The decrease in the numbers of CFU at 24 h was at least 3 log10 CFU/ml for all strains. No concentration-dependent killing was observed. The postantibiotic effect (PAE) was determined by obtaining viable counts for two of the reference strains, and the viable counts varied markedly: 1.2 h for S. aureus and 6.0 h for S. epidermidis. The determinations of the PAE, the postantibiotic sub-MIC effect (PA SME), and the sub-MIC effect (SME) for all strains were done with BioScreen C, a computerized incubator for bacteria. The PA SMEs were longer than the SMEs for all strains tested. A newly developed in vitro kinetic model was used to expose the bacteria to continuously decreasing concentrations of vancomycin. A filter prevented the loss of bacteria during the experiments. One reference strain each of S. aureus and S. epidermidis and two clinical isolates of S. aureus were exposed to an initial concentration of 10× the MIC of vancomycin with two different half-lives (t1/2s): 1 or 5 h. The post-MIC effect (PME) was calculated as the difference in time for the bacteria to grow 1 log10 CFU/ml from the numbers of CFU obtained at the time when the MIC was reached and the corresponding time for an unexposed control culture. The difference in PME between the strains was not as pronounced as that for the PAE. Furthermore, the PME was shorter when a t1/2 of 5 h (approximate terminal t1/2 in humans) was used. The PMEs at t1/2s of 1 and 5 h were 6.5 and 3.6 h, respectively, for S. aureus. The corresponding figures for S. epidermidis were 10.3 and less than 6 h. The shorter PMEs achieved with a t1/2 of 5 h and the lack of concentration-dependent killing indicate that the time above the MIC is the parameter most important for the efficacy of vancomycin. PMID:9756787

Echocardiographic assessments of longitudinal left ventricular function in healthy English Springer spaniels.

PubMed

Dickson, D; Shave, R; Rishniw, M; Patteson, M

2017-08-01

To establish reference intervals for echocardiographic measures of longitudinal left ventricular function in adult English Springer spaniel (ESS) dogs. This study involved 42 healthy adult ESS. Animals were prospectively recruited from a general practice population in the United Kingdom. Dogs were examined twice, at least 12 months apart, to exclude dogs with progressive cardiac disease. Mitral annular plane systolic excursion, tissue Doppler imaging mitral annular velocities and two-dimensional speckle-tracking echocardiographic left ventricular longitudinal strain and strain rate were measured. Intraoperator and intraobserver variability were examined and reference intervals were calculated. The potential effects of body weight, age and heart rate on these variables were examined. Intraoperator and intraobserver variability was <10% for all parameters except tissue Doppler imaging E' (the peak velocity of early diastolic mitral annular motion as determined by pulsed wave Doppler) and two-dimensional speckle-tracking echocardiographic variables, which were all <20%. Thirty-nine dogs were used to create reference intervals. Significant (but mostly weak) effects of age, heart rate and body weight on were detected. Reference intervals were similar to previously published values in different breeds. Breed specific reference intervals for measures of longitudinal left ventricular function in the ESS are presented. Copyright © 2017 Elsevier B.V. All rights reserved.

Volcanic Soils as Sources of Novel CO-Oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a Member of the Burkholderia cepacia Complex

PubMed Central

Weber, Carolyn F.; King, Gary M.

2017-01-01

Previous studies showed that members of the Burkholderiales were important in the succession of aerobic, molybdenum-dependent CO oxidizing-bacteria on volcanic soils. During these studies, four isolates were obtained from Kilauea Volcano (Hawai‘i, USA); one strain was isolated from Pico de Orizaba (Mexico) during a separate study. Based on 16S rRNA gene sequence similarities, the Pico de Orizaba isolate and the isolates from Kilauea Volcano were provisionally assigned to the genera Burkholderia and Paraburkholderia, respectively. Each of the isolates possessed a form I coxL gene that encoded the catalytic subunit of carbon monoxide dehydrogenase (CODH); none of the most closely related type strains possessed coxL or oxidized CO. Genome sequences for Paraburkholderia type strains facilitated an analysis of 16S rRNA gene sequence similarities and average nucleotide identities (ANI). ANI did not exceed 95% (the recommended cutoff for species differentiation) for any of the pairwise comparisons among 27 reference strains related to the new isolates. However, since the highest 16S rRNA gene sequence similarity among this set of reference strains was 98.93%, DNA-DNA hybridizations (DDH) were performed for two isolates whose 16S rRNA gene sequence similarities with their nearest phylogenetic neighbors were 98.96 and 99.11%. In both cases DDH values were <16%. Based on multiple variables, four of the isolates represent novel species within the Paraburkholderia: Paraburkholderia hiiakae sp. nov. (type strain I2T = DSM 28029T = LMG 27952T); Paraburkholderia paradisi sp. nov. (type strain WAT = DSM 28027T = LMG 27949T); Paraburkholderia peleae sp. nov. (type strain PP52-1T = DSM 28028T = LMG 27950T); and Paraburkholderia metrosideri sp. nov. (type strain DNBP6-1T = DSM 28030T = LMG 28140T). The remaining isolate represents the first CO-oxidizing member of the Burkholderia cepacia complex: Burkholderia alpina sp. nov. (type strain PO-04-17-38T = DSM 28031T = LMG 28138T). PMID:28270796

Volcanic Soils as Sources of Novel CO-Oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a Member of the Burkholderia cepacia Complex.

PubMed

Weber, Carolyn F; King, Gary M

2017-01-01

Previous studies showed that members of the Burkholderiales were important in the succession of aerobic, molybdenum-dependent CO oxidizing-bacteria on volcanic soils. During these studies, four isolates were obtained from Kilauea Volcano (Hawai'i, USA); one strain was isolated from Pico de Orizaba (Mexico) during a separate study. Based on 16S rRNA gene sequence similarities, the Pico de Orizaba isolate and the isolates from Kilauea Volcano were provisionally assigned to the genera Burkholderia and Paraburkholderia , respectively. Each of the isolates possessed a form I coxL gene that encoded the catalytic subunit of carbon monoxide dehydrogenase (CODH); none of the most closely related type strains possessed coxL or oxidized CO. Genome sequences for Paraburkholderia type strains facilitated an analysis of 16S rRNA gene sequence similarities and average nucleotide identities (ANI). ANI did not exceed 95% (the recommended cutoff for species differentiation) for any of the pairwise comparisons among 27 reference strains related to the new isolates. However, since the highest 16S rRNA gene sequence similarity among this set of reference strains was 98.93%, DNA-DNA hybridizations (DDH) were performed for two isolates whose 16S rRNA gene sequence similarities with their nearest phylogenetic neighbors were 98.96 and 99.11%. In both cases DDH values were <16%. Based on multiple variables, four of the isolates represent novel species within the Paraburkholderia : Paraburkholderia hiiakae sp. nov. (type strain I2 T = DSM 28029 T = LMG 27952 T ); Paraburkholderia paradisi sp. nov. (type strain WA T = DSM 28027 T = LMG 27949 T ); Paraburkholderia peleae sp. nov. (type strain PP52-1 T = DSM 28028 T = LMG 27950 T ); and Paraburkholderia metrosideri sp. nov. (type strain DNBP6-1 T = DSM 28030 T = LMG 28140 T ). The remaining isolate represents the first CO-oxidizing member of the Burkholderia cepacia complex: Burkholderia alpina sp. nov. (type strain PO-04-17-38 T = DSM 28031 T = LMG 28138 T ).

Normal references of right ventricular strain values by two-dimensional strain echocardiography according to the age and gender.

PubMed

Park, Jae-Hyeong; Choi, Jin-Oh; Park, Seung Woo; Cho, Goo-Yeong; Oh, Jin Kyung; Lee, Jae-Hwan; Seong, In-Whan

2018-02-01

Right ventricular (RV) strain values by 2-dimensional strain echocardiography (STE) can be used as objective markers of RV systolic function. However, there is little data about normal reference RV strain values according to age and gender. We measured normal RV strain values by STE. RV strain values were analyzed from the digitally stored echocardiographic images from NORMAL (Normal echOcardiogRaphic diMensions and functions in KoreAn popuLation) study for the measurement of normal echocardiographic values performed in 23 Korean university hospitals. We enrolled total 1003 healthy persons in the NORMAL study. Of them, we analyzed 2-dimensional RV strain values in 493 subjects (261 females, mean 47 ± 15 years old) only with echocardiographic images by GE machines. Their LV systolic and diastolic functions were normal. RV fractional area change was 48 ± 6% and tricuspid annular plane systolic excursion was 23 ± 3 mm. Total RV global longitudinal peak systolic strain (RVGLS total ) was -21.5 ± 3.2%. Females had higher absolute RVGLS total (-22.3 ± 3.3 vs -20.7 ± 2.9%, p < 0.001) than males. Younger (<50 years old) females had higher absolute RVGLS total (-22.9 ± 3.2 vs -20.5 ± 2.8%, p < 0.001) than age matched males. RVGLS total in females gradually increased according to age (p for trend = 0.002) and becomes almost similar in age ≥50 years. However, this trend was not seen in males (p for trend = 0.287), and younger males had similar RVGLS total value to that of older males (age ≥50 years, -20.5 ± 2.8 vs -20.9 ± 3.1%, p = 0.224). We calculated normal RVGLS values in normal population. Females have higher absolute strain values than males, especially in younger age groups (<50 years old).

Monitoring the Wall Mechanics During Stent Deployment in a Vessel

PubMed Central

Steinert, Brian D.; Zhao, Shijia; Gu, Linxia

2012-01-01

Clinical trials have reported different restenosis rates for various stent designs1. It is speculated that stent-induced strain concentrations on the arterial wall lead to tissue injury, which initiates restenosis2-7. This hypothesis needs further investigations including better quantifications of non-uniform strain distribution on the artery following stent implantation. A non-contact surface strain measurement method for the stented artery is presented in this work. ARAMIS stereo optical surface strain measurement system uses two optical high speed cameras to capture the motion of each reference point, and resolve three dimensional strains over the deforming surface8,9. As a mesh stent is deployed into a latex vessel with a random contrasting pattern sprayed or drawn on its outer surface, the surface strain is recorded at every instant of the deformation. The calculated strain distributions can then be used to understand the local lesion response, validate the computational models, and formulate hypotheses for further in vivo study. PMID:22588353

Inter- and Intra-subtype genotypic differences that differentiate Mycobacterium avium subspecies paratuberculosis strains

PubMed Central

2012-01-01

Background Mycobacterium avium subspecies paratuberculosis (Map) is the aetiological agent of Johne’s disease or paratuberculosis and is included within the Mycobacterium avium complex (MAC). Map strains are of two major types often referred to as ‘Sheep’ or ‘S-type’ and ‘Cattle’ or ‘C-type’. With the advent of more discriminatory typing techniques it has been possible to further classify the S-type strains into two groups referred to as Type I and Type III. This study was undertaken to genotype a large panel of S-type small ruminant isolates from different hosts and geographical origins and to compare them with a large panel of well documented C-type isolates to assess the genetic diversity of these strain types. Methods used included Mycobacterial Interspersed Repetitive Units - Variable-Number Tandem Repeat analysis (MIRU-VNTR), analysis of Large Sequence Polymorphisms by PCR (LSP analysis), Single Nucleotide Polymorphism (SNP) analysis of gyr genes, Pulsed-Field Gel Electrophoresis (PFGE) and Restriction Fragment Length Polymorphism analysis coupled with hybridization to IS900 (IS900-RFLP) analysis. Results The presence of LSPA4 and absence of LSPA20 was confirmed in all 24 Map S-type strains analysed. SNPs within the gyr genes divided the S-type strains into types I and III. Twenty four PFGE multiplex profiles and eleven different IS900-RFLP profiles were identified among the S-type isolates, some of them not previously published. Both PFGE and IS900-RFLP segregated the S-type strains into types I and III and the results concurred with those of the gyr SNP analysis. Nine MIRU-VNTR genotypes were identified in these isolates. MIRU-VNTR analysis differentiated Map strains from other members of Mycobacterium avium Complex, and Map S-type from C-type but not type I from III. Pigmented Map isolates were found of type I or III. Conclusion This is the largest panel of S-type strains investigated to date. The S-type strains could be further divided into two subtypes, I and III by some of the typing techniques (IS900-RFLP, PFGE and SNP analysis of the gyr genes). MIRU-VNTR did not divide the strains into the subtypes I and III but did detect genetic differences between isolates within each of the subtypes. Pigmentation is not exclusively associated with type I strains. PMID:23164429

Residual stress analysis for oxide thin film deposition on flexible substrate using finite element method

NASA Astrophysics Data System (ADS)

Chen, Hsi-Chao; Huang, Chen-Yu; Lin, Ssu-Fan; Chen, Sheng-Hui

2011-09-01

Residual or internal stresses directly affect a variety of phenomena including adhesion, generation of crystalline defects, perfection of epitaxial layers and formation of film surface growths such as hillocks and whiskers. Sputtering oxide films with high density promote high compressive stress, and it offers researchers a reference if the value of residual stress could be analyzed directly. Since, the study of residual stress of SiO2 and Nb2O5 thin film deposited by DC magnetron sputtered on hard substrate (BK7) and flexible substrate (PET and PC). A finite element method (FEM) with an equivalent-reference-temperature (ERT) technique had been proposed and used to model and evaluate the intrinsic strains of layered structures. The research has improved the equivalent reference temperature (ERT) technique of the simulation of intrinsic strain for oxygen film. The results have also generalized two models connecting to the lattice volume to predict the residual stress of hard substrate and flexible substrate with error of 3% and 6%, respectively.

Structural characterization and antimicrobial activities of transition metal complexes of a hydrazone ligand

NASA Astrophysics Data System (ADS)

Bakale, Raghavendra P.; Naik, Ganesh N.; Machakanur, Shrinath S.; Mangannavar, Chandrashekhar V.; Muchchandi, Iranna S.; Gudasi, Kalagouda B.

2018-02-01

A hydrazone ligand has been synthesized by the condensation of 2-nitrobenzaldehyde and hydralazine, and its Co(II), Ni(II), Cu(II) and Zn(II) complexes have been reported. Structural characterization of the ligand and its metal complexes has been performed by various spectroscopic [IR, NMR, UV-Vis, Mass], thermal and other physicochemical methods. The structure of the ligand and its Ni(II) complex has been characterized by single crystal X-ray diffraction studies. All the synthesized compounds have been screened for in vitro antimicrobial activity. The antibacterial activity is tested against Gram-positive strains Enterococcus faecalis, Streptococcus mutans and Staphylococcus aureus and Gram-negative strains Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae using ciprofloxacin as the reference standard. Antifungal activity is tested against Candida albicans, Aspergillus fumigatus and Aspergillus niger using ketoconazole as the reference standard. The minimum inhibitory concentration (MIC) was determined for test compounds as well as for reference standard. Ligand, Cu(II) and Zn(II) complexes have shown excellent activity against Candida albicans.

[Phenotypic and genotypic characterization of Vibrio cholerae O1].

PubMed

Giono-Cerezo, S; Rodríguez Angeles, M G; Gutiérrez-Cogco, L; Valdespino-Gómez, J L

1994-01-01

We made 52180 tests for isolation and identification of toxigenic V. cholerae O1 from rectal swabs and reference strains. We isolated 17.6% V. cholerae O1 strains in 1991, 43.5% in 1992 and 38.9% in 1993. The main serovar in 1991 was Inaba, whereas in 1993 a similar percentage was serovar Ogawa. The phenotype of V. cholerae strains was determined by hemolysis test, Voges-Proskauer test, polymyxin B resistance and phages 4 and 5 resistance. All of the mexican strains were El Tor. There were 2.9-0.75% hemolytic strains from 1991 to 1993, but they were negative when the test was made in tube with human erythrocytes. The resistotypes were performed in 24526 selected strains by Kirby-Bauer method and MIC tests. All of the strains were sensitive, except more than 100 strains isolated in Veracruz that were resistant to tetracycline and doxycycline. Detection of cholera toxin was made by ELISA and on culture of Vero and CHO cells. All the V. cholerae O1 strains were toxigenic. The genotype was determined by PCR and ribotyping. The PCR amplified one 564 pb fragment on V. cholerae O1. The ribotypes of mexican strains were 5 and 6a.

Differentiation of Salmonella enteritidis phage type 8 strains: evaluation of three additional phage typing systems, plasmid profiles, antibiotic susceptibility patterns, and biotyping.

PubMed Central

Stubbs, A D; Hickman-Brenner, F W; Cameron, D N; Farmer, J J

1994-01-01

Three additional phage typing systems for Salmonella enteritidis, plasmid analysis, biochemical tests, and antimicrobial susceptibility tests, were used in an attempt to subdivide 30 phage type 8 (phage typing system used by the WHO International Center for Enteric Phage Typing, London, England) isolates. These isolates represented 18 different egg-related outbreaks (21 strains) and 9 reference strains or strains that were not egg-associated. Only 7 of the 30 strains (28%) were subdivided by one or more of the methods used; this included 3 of the 21 strains from egg-related outbreaks. Twenty-seven strains contained a 55-kb plasmid that is associated with S. enteritidis. Of 65 additional phages tested, 2 from the phage typing system obtained from the Pasteur Institute, Paris, France, were useful in differentiating the three strains that lacked the 55-kb plasmid. Although the results obtained for the 21 strains from egg-related outbreaks showed that the strains had minor phenotypic differences, the overall results suggested that the strains may represent a single clone. Studies are planned to test additional phages and other typing methods to see whether strains of phage type 8 can be further differentiated. PMID:8126179

Molecular epidemiology of tetM genes in Neisseria gonorrhoeae

PubMed Central

Turner, A.; Gough, K. R.; Leeming, J. P.

1999-01-01

OBJECTIVE: To examine the epidemiology of the tetM gene in Neisseria gonorrhoeae strains with high level resistance to tetracycline (TRNG) using a polymerase chain reaction (PCR) assay. METHODS: A single tube PCR was developed which distinguishes between the American and Dutch variants of the tetM gene. Between 1988 and 1995, 518 strains of TRNG (tetracycline MIC > 8.mg/l) were referred to the Gonococcus Reference Unit by other laboratories or isolated from routine swabs taken at local clinics. The strains were analysed for plasmid content, auxotype, serovar, and the tetM gene type. Travel details of the patients were determined by a questionnaire. RESULTS: A PCR product was obtained from all TRNG examined. 387 TRNG strains produced a 778 bp PCR product (American type tetM) and 131 produced a 443 by PCR product (Dutch type tetM). Infections acquired in the United Kingdom contributed 57% of the TRNG strains included in this study; 82% of these carried the American type of tetM. The number of UK acquired TRNG received by the GRU increased each year except 1993--from four strains received in 1990 to 92 in 1995. After the United Kingdom, Caribbean and African countries contributed most strains, with 56 and 60 TRNG acquired in each area respectively. All strains originating in Africa, except one from South Africa, contained the American type tetM. Infections caught in Nigeria and Kenya contributed most strains (15 and 14 respectively). The TRNG originating from Caribbean countries comprised 36% Dutch tetM type. Infections caught in Jamaica accounted for 82% of the Caribbean strains. All 35 TRNG strains originating in the Far East contained the Dutch type tetM. 25 of the Far East strains were also penicillinase producing (PPNG). Infections originating in Indonesia accounted for 49% of the Far East strains but these belonged to 12 different auxotype/serovar combinations. A geographical variation in the type of penicillinase coding plasmids found in PPNG/TRNG was also detected. CONCLUSIONS: These data suggest that the Dutch type tetM may have originated in the Far East and the American type in the African continent. Subsequent spread has resulted in a heterogeneous distribution of TRNG types in other parts of the world. At completion of the survey the numbers of TRNG imported each year from the major overseas sources had reached a plateau while UK contracted TRNG continued to rise providing evidence for the establishment of endemic TRNG strains in the United Kingdom. 


 PMID:10448346

Conceptual Design of Four Surface Effect Ships for U.S. Coast Guard Applications.

DTIC Science & Technology

1985-05-01

00 KNTS H : El -13.000 -10.000 -3.000 0.000 0. 000 20.000 30.000 40.000 000 7 000 0. 600 DEGREES DRAFT: &.920 ś.53 6.210 6.230 7.03 S 9" 0.3 -5.472...0C. (R0D . 21.67 FT AUY a*L~ Ta0., .-. rFTACTN-.E (’Ar1 . 312. 2 FT A2V AULA LO. rE1ACEN:ER MOIL .P $ 971.02 FT ACV ttfl* 1RA....41C C; t~l? - 0.00 FT...RSy ARIA. DRAFT 067 VP Owl 2.00 FT AIV OaRIA M3047240 ARKS -VO- HEELS IN INTACT CONDITIO WIND SF000 - 22.00 RAIO pt EL -3.0W -10. 000 -5.000 0.000

Microvariability in Seyfert galaxies

USGS Publications Warehouse

Carini, M.T.; Noble, J.C.; Miller, H.R.

2003-01-01

We present the results of a search for microvariability in a sample of eight Seyfert galaxies. Microvariability (i.e., variations occurring on timescales of tens of minutes to hours) has been conclusively demonstrated to exist in the class of active galactic nuclei (AGNs) known as blazars. Its existence in other classes of AGNs is far less certain. We present the results of a study of eight Seyfert 1 galaxies, which were intensively monitored in order to determine whether such variations exist in these objects. Only one object, Ark 120, displayed any evidence of microvariations. The implications of these results with respect to current models of the mechanisms responsible for the observed emission in Seyfert galaxies are discussed. We compare our results with those obtained from other studies of microvariability in different classes of AGNs.

A Small-Unit Amphibious Operation Combat Model.

DTIC Science & Technology

1983-03-01

7THE FuNCTICNS HloSPD, IND PNG, "tHE ARGUMENT T C IS 71IE TIME SIhCE 11-E ’othvE 6EYNG 40ORESSE-D C CPCSSEO IHE 50CO PETER GFFSHCFE M4ARK~ C...SSpD𔃿FFD0(I m PXX()-A.ACCNG5SI.* G /SZPO PXY( ! )-(?.! !ANLC4-’,*( -Al ISSP; C ALL VAL(,ES N~C% IN PETERS CN 0 -- 109000 GRID 1CC CCT114UE REtC(5...EACH SUCH ELLIPSE NE IS=0 C lIiiAXaC . IF(NCVcL!*EQ.Cl GCIO 270 Do ZeC K;I;fGFSC I A’IGX( I) I 𔄁. IGY (K I NaNC(IX, IY) IF(?d.EQ.0D GC TC 26C 128

Occurance of Staphylococcus nepalensis strains in different sources including human clinical material.

PubMed

Nováková, Dana; Pantůcek, Roman; Petrás, Petr; Koukalová, Dagmar; Sedlácek, Ivo

2006-10-01

Five isolates of coagulase-negative staphylococci were obtained from human urine, the gastrointestinal tract of squirrel monkeys, pig skin and from the environment. All key biochemical characteristics of the tested strains corresponded with the description of Staphylococcus xylosus species. However, partial 16S rRNA gene sequences obtained from analysed strains corresponded with those of Staphylococcus nepalensis reference strains, except for two strains which differed in one residue. Ribotyping with EcoRI and HindIII restriction enzymes, whole cell protein profile analysis performed by SDS-PAGE and SmaI macrorestriction analysis were used for more precise characterization and identification of the analysed strains. Obtained results showed that EcoRI and HindIII ribotyping and whole cell protein fingerprinting are suitable and reliable methods for the differentiation of S. nepalensis strains from the other novobiocin resistant staphylococci, whereas macrorestriction analysis was found to be a good tool for strain typing. The isolation of S. nepalensis is sporadic, and according to our best knowledge this study is the first report of the occurrence of this species in human clinical material as well as in other sources.

Genetic characterization of strains of Saccharomycescerevisiae responsible for 'refermentation' in Botrytis-affected wines.

PubMed

Divol, B; Miot-Sertier, C; Lonvaud-Funel, A

2006-03-01

Saccharomyces cerevisiae is responsible for alcoholic fermentation of wines. However, some strains can also spoil sweet Botrytis-affected wines. Three 'refermentation' strains were isolated during maturation. Characterization of those strains in regards to their fingerprint, rDNA sequence and resistance to SO2, which constituted the main source of stress in Botrytis-affected wines, was carried out. Refermentation strains could be clearly discriminated by interdelta fingerprinting. However, they exhibited close relationships by karyotyping. A part of RDN1 locus sequence was examined by using PCR-RFLP and PCR-DGGE. The resistance of refermentation strains to SO2 was performed by using real time quantitative PCR focusing on SSU1 gene. Results suggested that refermentation strains were heterozygote in 26S rDNA and their ITS1-5.8S rDNA-ITS2 region sequence revealed relationships with 'flor' strains. As described in the literature for flor strain, two out of three refermentation strains constitutively developed a higher level of SSU1 expression than the reference strains, improving their putative tolerance to SO2. Therefore, refermentation strains of S. cerevisiae had developed many strategies to survive during maturing sweet wines. Singularities in rDNA sequence and SSU1 overexpression revealed a natural adaptation. Moreover, genomic relationship between flor and refermentation strains suggested that stress sources could induced selection of survivor strains.

Comparison of Three Different Methods for Pile Integrity Testing on a Cylindrical Homogeneous Polyamide Specimen

NASA Astrophysics Data System (ADS)

Lugovtsova, Y. D.; Soldatov, A. I.

2016-01-01

Three different methods for pile integrity testing are proposed to compare on a cylindrical homogeneous polyamide specimen. The methods are low strain pile integrity testing, multichannel pile integrity testing and testing with a shaker system. Since the low strain pile integrity testing is well-established and standardized method, the results from it are used as a reference for other two methods.

Condition assessment of reinforced concrete beams using dynamic data measured with distributed long-gage macro-strain sensors

NASA Astrophysics Data System (ADS)

Hong, W.; Wu, Z. S.; Yang, C. Q.; Wan, C. F.; Wu, G.; Zhang, Y. F.

2012-06-01

A new condition assessment strategy of reinforced concrete (RC) beams is proposed in this paper. This strategy is based on frequency analysis of the dynamic data measured with distributed long-gage macro-stain sensors. After extracting modal macro-strain, the reference-based damage index is theoretically deducted in which the variations of modal flexural rigidity and modal neutral axis height are considered. The reference-free damage index is also presented for comparison. Both finite element simulation and experiment investigations were carried out to verify the proposed method. The manufacturing procedure of long-gage fiber Bragg grating (FBG) sensor chosen in the experiment is firstly presented, followed by an experimental study on the essential sensing properties of the long-gage macro-strain sensors and the results verify the excellent sensing properties, in particular the measurement accuracy and dynamic measuring capacity. Modal analysis results of a concrete beam show that the damage appearing in the beam can be well identified by the damage index while the vibration testing results of a RC beam show that the proposed method can not only capture small crack initiation but its propagation. It can be concluded that distributed long-gage dynamic macro-strain sensing technique has great potential for the condition assessment of RC structures subjected to dynamic loading.

Species identification of mutans streptococci by groESL gene sequence.

PubMed

Hung, Wei-Chung; Tsai, Jui-Chang; Hsueh, Po-Ren; Chia, Jean-San; Teng, Lee-Jene

2005-09-01

The near full-length sequences of the groESL genes were determined and analysed among eight reference strains (serotypes a to h) representing five species of mutans group streptococci. The groES sequences from these reference strains revealed that there are two lengths (285 and 288 bp) in the five species. The intergenic spacer between groES and groEL appears to be a unique marker for species, with a variable size (ranging from 111 to 310 bp) and sequence. Phylogenetic analysis of groES and groEL separated the eight serotypes into two major clusters. Strains of serotypes b, c, e and f were highly related and had groES gene sequences of the same length, 288 bp, while strains of serotypes a, d, g and h were also closely related and their groES gene sequence lengths were 285 bp. The groESL sequences in clinical isolates of three serotypes of S. mutans were analysed for intraspecies polymorphism. The results showed that the groESL sequences could provide information for differentiation among species, but were unable to distinguish serotypes of the same species. Based on the determined sequences, a PCR assay was developed that could differentiate members of the mutans streptococci by amplicon size and provide an alternative way for distinguishing mutans streptococci from other viridans streptococci.

Improved Regression Analysis of Temperature-Dependent Strain-Gage Balance Calibration Data

NASA Technical Reports Server (NTRS)

Ulbrich, N.

2015-01-01

An improved approach is discussed that may be used to directly include first and second order temperature effects in the load prediction algorithm of a wind tunnel strain-gage balance. The improved approach was designed for the Iterative Method that fits strain-gage outputs as a function of calibration loads and uses a load iteration scheme during the wind tunnel test to predict loads from measured gage outputs. The improved approach assumes that the strain-gage balance is at a constant uniform temperature when it is calibrated and used. First, the method introduces a new independent variable for the regression analysis of the balance calibration data. The new variable is designed as the difference between the uniform temperature of the balance and a global reference temperature. This reference temperature should be the primary calibration temperature of the balance so that, if needed, a tare load iteration can be performed. Then, two temperature{dependent terms are included in the regression models of the gage outputs. They are the temperature difference itself and the square of the temperature difference. Simulated temperature{dependent data obtained from Triumph Aerospace's 2013 calibration of NASA's ARC-30K five component semi{span balance is used to illustrate the application of the improved approach.

The roles of sexual and asexual reproduction in the origin and dissemination of strains causing fungal infectious disease outbreaks.

PubMed

Ashu, Eta Ebasi; Xu, Jianping

2015-12-01

Sexual reproduction commonly refers to the reproductive process in which genomes from two sources are combined into a single cell through mating and then the zygote genomes are partitioned to progeny cells through meiosis. Reproduction in the absence of mating and meiosis is referred to as asexual or clonal reproduction. One major advantage of sexual reproduction is that it generates genetic variation among progeny which may allow for faster adaptation of the population to novel and/or stressful environments. However, adaptation to stressful or new environments can still occur through mutation, in the absence of sex. In this review, we analyzed the relative contributions of sexual and asexual reproduction in the origin and spread of strains causing fungal infectious diseases outbreaks. The necessity of sex and the ability of asexual fungi to initiate outbreaks are discussed. We propose a framework that relates the modes of reproduction to the origin and propagation of fungal disease outbreaks. Our analyses suggest that both sexual and asexual reproduction can play critical roles in the origin of outbreak strains and that the rapid spread of outbreak strains is often accomplished through asexual expansion. Copyright © 2015 Elsevier B.V. All rights reserved.

Improved sake metabolic profile during fermentation due to increased mitochondrial pyruvate dissimilation.

PubMed

Agrimi, Gennaro; Mena, Maria C; Izumi, Kazuki; Pisano, Isabella; Germinario, Lucrezia; Fukuzaki, Hisashi; Palmieri, Luigi; Blank, Lars M; Kitagaki, Hiroshi

2014-03-01

Although the decrease in pyruvate secretion by brewer's yeasts during fermentation has long been desired in the alcohol beverage industry, rather little is known about the regulation of pyruvate accumulation. In former studies, we developed a pyruvate under-secreting sake yeast by isolating a strain (TCR7) tolerant to ethyl α-transcyanocinnamate, an inhibitor of pyruvate transport into mitochondria. To obtain insights into pyruvate metabolism, in this study, we investigated the mitochondrial activity of TCR7 by oxigraphy and (13) C-metabolic flux analysis during aerobic growth. While mitochondrial pyruvate oxidation was higher, glycerol production was decreased in TCR7 compared with the reference. These results indicate that mitochondrial activity is elevated in the TCR7 strain with the consequence of decreased pyruvate accumulation. Surprisingly, mitochondrial activity is much higher in the sake yeast compared with CEN.PK 113-7D, the reference strain in metabolic engineering. When shifted from aerobic to anaerobic conditions, sake yeast retains a branched mitochondrial structure for a longer time than laboratory strains. The regulation of mitochondrial activity can become a completely novel approach to manipulate the metabolic profile during fermentation of brewer's yeasts. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.