Targeting Cancer Protein Profiles with Split-Enzyme Reporter Fragments to Achieve Chemical Resolution for Molecular Imaging

DTIC Science & Technology

2014-11-01

near-infrared fluorophore, Cy5.5, linked with up to three units of amino-ethoxy-ethoxy- acid (AEEA) at the N-terminal amine of the peptide. Table 1...RPMI or Dulbecco’s Modified Eagle’s Medium (DMEM; Gibco), respectively, and supplemented with 10% FBS and 1% penicillin–streptomycin. The cells were...peptide, compound 6, using the amino acid residues of the parent peptide (compound 5) in random order. Compound 2 targeted the tumor efficiently

Four possible types of dangerous viruses in aerospace traces of invasions in conditions of modern hybrid wars

NASA Astrophysics Data System (ADS)

Churyumov, K. I.; Steklov, A. F.; Vidmachenko, A. P.; Dashkiev, G. N.; Steklov, E. A.; Slipchenko, A. S.; Romaniuk, Ya. O.

2016-10-01

1. Reasons for the creation of modern services of terrestrial space monitoring. In recent years, an increasingly important role in an observation of traces of invasions fireball in an Earth's atmosphere, playing artificial earth satellites at low and medium orbits. But the time between such registrations - is about one and a half hours. And consequently, many types of traces of invasions of small fragments of nuclei of comets, asteroids and meteoroids - remain outside of the data. In the interest of safety of large and medium-sized cities need to create a special small basic observatories of terrestrial aerospace monitoring services. 2. Four types of dangerous viruses that may be present in traces of all kinds of dangerous invasions into the sky over our cities. In modern times the most dangerous commonly believed the cosmic viruses in the nuclei of comets and their fragments; orbital recurrent-mutant viruses, bacteria, fungi in an components of Space Debris (for example, in the fragments of space station "Mir"); as well as modern modified and synthetic viruses, that are easy and very effective is possible to apply in the invasion of simple, and suborbital unmanned aerial vehicles, especially with the function of self-destruction, in order to the invasion able to remain latent, secret, poorly registrable. 3. Our plans on criteria experimentation for active operations with a specialized astronomical aviation of special purpose. Essence of the method according to the ideas is very simple; but there are difficulties in its practical implementation. Organizational, registration of tracks of all kinds of dangerous invasions, is carried out from stationary, mobile and aircraft (quadrocopters, drones, unmanned aerial vehicles) astronomical observatories of terrestrial aerospace monitoring services. Registered by us at daytime and twilight traces can be seen from a few minutes, sometimes up to two hours [1, 2, 4, 6-10].

Methods for producing partially digested restriction DNA fragments and for producing a partially modified PCR product

DOEpatents

Wong, Kwong-Kwok

2000-01-01

The present invention is an improved method of making a partially modified PCR product from a DNA fragment with a polymerase chain reaction (PCR). In a standard PCR process, the DNA fragment is combined with starting deoxynucleoside triphosphates, a primer, a buffer and a DNA polymerase in a PCR mixture. The PCR mixture is then reacted in the PCR producing copies of the DNA fragment. The improvement of the present invention is adding an amount of a modifier at any step prior to completion of the PCR process thereby randomly and partially modifying the copies of the DNA fragment as a partially modified PCR product. The partially modified PCR product may then be digested with an enzyme that cuts the partially modified PCR product at unmodified sites thereby producing an array of DNA restriction fragments.

Effects of target fragmentation on evaluation of LET spectra from space radiations: implications for space radiation protection studies

NASA Technical Reports Server (NTRS)

Cucinotta, F. A.; Wilson, J. W.; Shinn, J. L.; Badavi, F. F.; Badhwar, G. D.

1996-01-01

We present calculations of linear energy transfer (LET) spectra in low earth orbit from galactic cosmic rays and trapped protons using the HZETRN/BRYNTRN computer code. The emphasis of our calculations is on the analysis of the effects of secondary nuclei produced through target fragmentation in the spacecraft shield or detectors. Recent improvements in the HZETRN/BRYNTRN radiation transport computer code are described. Calculations show that at large values of LET (> 100 keV/micrometer) the LET spectra seen in free space and low earth orbit (LEO) are dominated by target fragments and not the primary nuclei. Although the evaluation of microdosimetric spectra is not considered here, calculations of LET spectra support that the large lineal energy (y) events are dominated by the target fragments. Finally, we discuss the situation for interplanetary exposures to galactic cosmic rays and show that current radiation transport codes predict that in the region of high LET values the LET spectra at significant shield depths (> 10 g/cm2 of Al) is greatly modified by target fragments. These results suggest that studies of track structure and biological response of space radiation should place emphasis on short tracks of medium charge fragments produced in the human body by high energy protons and neutrons.

[Adsorption of perfluorooctanesulfonate (PFOS) onto modified activated carbons].

PubMed

Tong, Xi-Zhen; Shi, Bao-You; Xie, Yue; Wang, Dong-Sheng

2012-09-01

Modified coal and coconut shell based powdered activated carbons (PACs) were prepared by FeCl3 and medium power microwave treatment, respectively. Batch experiments were carried out to evaluate the characteristics of adsorption equilibrium and kinetics of perfluorooctanesulfonate (PFOS) onto original and modified PACs. Based on pore structure and surface functional groups characterization, the adsorption behaviors of modified and original PACs were compared. The competitive adsorption of humic acid (HA) and PFOS on original and modified coconut shell PACs were also investigated. Results showed that both Fe3+ and medium power microwave treatments changed the pore structure and surface functional groups of coal and coconut shell PACs, but the changing effects were different. The adsorption of PFOS on two modified coconut shell-based PACs was significantly improved. While the adsorption of modified coal-based activated carbons declined. The adsorption kinetics of PFOS onto original and modified coconut shell-based activated carbons were the same, and the time of reaching adsorption equilibrium was about 6 hours. In the presence of HA, the adsorption of PFOS by modified PAC was reduced but still higher than that of the original.

Fredkin and Toffoli Gates Implemented in Oregonator Model of Belousov-Zhabotinsky Medium

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

A thin-layer Belousov-Zhabotinsky (BZ) medium is a powerful computing device capable for implementing logical circuits, memory, image processors, robot controllers, and neuromorphic architectures. We design the reversible logical gates — Fredkin gate and Toffoli gate — in a BZ medium network of excitable channels with subexcitable junctions. Local control of the BZ medium excitability is an important feature of the gates’ design. An excitable thin-layer BZ medium responds to a localized perturbation with omnidirectional target or spiral excitation waves. A subexcitable BZ medium responds to an asymmetric perturbation by producing traveling localized excitation wave-fragments similar to dissipative solitons. We employ interactions between excitation wave-fragments to perform the computation. We interpret the wave-fragments as values of Boolean variables. The presence of a wave-fragment at a given site of a circuit represents the logical truth, absence of the wave-fragment — logically false. Fredkin gate consists of ten excitable channels intersecting at 11 junctions, eight of which are subexcitable. Toffoli gate consists of six excitable channels intersecting at six junctions, four of which are subexcitable. The designs of the gates are verified using numerical integration of two-variable Oregonator equations.

Chiroptical properties of an alternatingly functionalized cellotriose bearing two porphyrin groups

USDA-ARS?s Scientific Manuscript database

Alternatingly functionalized cellulose molecules have potential applications in optoelectronics and molecular receptors. For example, cellulose-based solar cells have been proposed. As a prototype for such molecules, the trisaccharide fragment of cellulose was modified by attachment of porphyrin gro...

Angular distribution of scission neutrons studied with time-dependent Schrödinger equation

NASA Astrophysics Data System (ADS)

Wada, Takahiro; Asano, Tomomasa; Carjan, Nicolae

2018-03-01

We investigate the angular distribution of scission neutrons taking account of the effects of fission fragments. The time evolution of the wave function of the scission neutron is obtained by integrating the time-dependent Schrodinger equation numerically. The effects of the fission fragments are taken into account by means of the optical potentials. The angular distribution is strongly modified by the presence of the fragments. In the case of asymmetric fission, it is found that the heavy fragment has stronger effects. Dependence on the initial distribution and on the properties of fission fragments is discussed. We also discuss on the treatment of the boundary to avoid artificial reflections

Colonisation of soilless growing media for tomato by Trichoderma harzianum.

PubMed

De Schutter, B; Aerts, R; Rombouts, L

2001-01-01

An experiment was conducted to evaluate the distribution of T. harzianum in soilless media used in greenhouse growing systems for tomatoes. Growing media based on rockwool and based on coconut fibre were included. The fungus was applied to the roots of the plant by means of a conidial suspension. The upper plant parts were removed from the coconut fibre an the rockwool slab after 10 and 15 weeks respectively. Both the coconut fibre and the rockwool slab were divided into fragments with a width of 10 cm. The coconut fibre medium fragments were again divided in an upper and a lower part. For every fragment the CFU/g was determined by two different methods. In the first method a known volume of growing medium was brought into suspension using a blender and diluted. Appropriate dilutions were plated on a selective medium. In the second method a known volume of growing medium was spread directly upon a selective medium in petri dishes. All dishes were incubated at room temperature and colonies were counted. Results showed that in the case of the coconut fibre growing medium T. harzianum was isolated in every fragment of the substrate. Highest densities were measured at the site of inoculation. In the lower part of the fragments less CFU/g were counted than in the upper part. In the case of the rockwool growing medium, there were several fragments in which no T. harzianum was isolated. The dilution technique demonstrated to be most useful in cases of high density. The direct spreading-method is best applied when low densities are expected. These observations demonstrate that the growing medium based upon coconut fibre is more appropriate for colonisation by T. harzianum. However, densities are higher at the site of inoculation in both tested growing media.

Cftr gene targeting in mouse embryonic stem cells mediated by Small Fragment Homologous Replacement (SFHR).

PubMed

Sangiuolo, Federica; Scaldaferri, Maria Lucia; Filareto, Antonio; Spitalieri, Paola; Guerra, Lorenzo; Favia, Maria; Caroppo, Rosa; Mango, Ruggiero; Bruscia, Emanuela; Gruenert, Dieter C; Casavola, Valeria; De Felici, Massimo; Novelli, Giuseppe

2008-01-01

Different gene targeting approaches have been developed to modify endogenous genomic DNA in both human and mouse cells. Briefly, the process involves the targeting of a specific mutation in situ leading to the gene correction and the restoration of a normal gene function. Most of these protocols with therapeutic potential are oligonucleotide based, and rely on endogenous enzymatic pathways. One gene targeting approach, "Small Fragment Homologous Replacement (SFHR)", has been found to be effective in modifying genomic DNA. This approach uses small DNA fragments (SDF) to target specific genomic loci and induce sequence and subsequent phenotypic alterations. This study shows that SFHR can stably introduce a 3-bp deletion (deltaF508, the most frequent cystic fibrosis (CF) mutation) into the Cftr (CF Transmembrane Conductance Regulator) locus in the mouse embryonic stem (ES) cell genome. After transfection of deltaF508-SDF into murine ES cells, SFHR-mediated modification was evaluated at the molecular levels on DNA and mRNA obtained from transfected ES cells. About 12% of transcript corresponding to deleted allele was detected, while 60% of the electroporated cells completely lost any measurable CFTR-dependent chloride efflux. The data indicate that the SFHR technique can be used to effectively target and modify genomic sequences in ES cells. Once the SFHR-modified ES cells differentiate into different cell lineages they can be useful for elucidating tissue-specific gene function and for the development of transplantation-based cellular and therapeutic protocols.

Multisegment nanowire sensors for the detection of DNA molecules.

PubMed

Wang, Xu; Ozkan, Cengiz S

2008-02-01

We describe a novel application for detecting specific single strand DNA sequences using multisegment nanowires via a straightforward surface functionalization method. Nanowires comprising CdTe-Au-CdTe segments are fabricated using electrochemical deposition, and electrical characterization indicates a p-type behavior for the multisegment nanostructures, in a back-to-back Schottky diode configuration. Such nanostructures modified with thiol-terminated probe DNA fragments could function as high fidelity sensors for biomolecules at very low concentration. The gold segment is utilized for functionalization and binding of single strand DNA (ssDNA) fragments while the CdTe segments at both ends serve to modulate the equilibrium Fermi level of the heterojunction device upon hybridization of the complementary DNA fragments (cDNA) to the ssDNA over the Au segment. Employing such multisegment nanowires could lead to the fabrication more sophisticated and high multispecificity biosensors via selective functionalization of individual segments for biowarfare sensing and medical diagnostics applications.

Polymer-based adsorption medium prepared using a fragment imprinting technique for homologues of chlorinated bisphenol A produced in the environment.

PubMed

Kubo, Takuya; Hosoya, Ken; Watabe, Yoshiyuki; Ikegami, Tohru; Tanaka, Nobuo; Sano, Tomoharu; Kaya, Kunimitsu

2004-03-12

A polymer-based adsorption medium having molecular recognition ability for homologues of chlorinated bisphenol A produced in environment was prepared using a fragment imprinting technique. 2,6-Dimethyl phenol was utilized as a pseudo-template molecule and the adsorption media prepared was evaluated by high performance liquid chromatography (HPLC) and solid-phase extraction (SPE). As results, the adsorption medium showed preferable chromatographic retention and specific adsorption ability for the chlorinated bisphenol As having chlorine substituents at 3,5-positions through fragment imprinting effect.

Recurrent Tricuspid Insufficiency

PubMed Central

Kara, Ibrahim; Koksal, Cengiz; Cakalagaoglu, Canturk; Sahin, Muslum; Yanartas, Mehmet; Ay, Yasin; Demir, Serdar

2013-01-01

This study compares the medium-term results of De Vega, modified De Vega, and ring annuloplasty techniques for the correction of tricuspid insufficiency and investigates the risk factors for recurrent grades 3 and 4 tricuspid insufficiency after repair. In our clinic, 93 patients with functional tricuspid insufficiency underwent surgical tricuspid repair from May 2007 through October 2010. The study was retrospective, and all the data pertaining to the patients were retrieved from hospital records. Functional capacity, recurrent tricuspid insufficiency, and risk factors aggravating the insufficiency were analyzed for each patient. In the medium term (25.4 ± 10.3 mo), the rates of grades 3 and 4 tricuspid insufficiency in the De Vega, modified De Vega, and ring annuloplasty groups were 31%, 23.1%, and 6.1%, respectively. Logistic regression analysis revealed that chronic obstructive pulmonary disease, left ventricular dysfunction (ejection fraction, < 0.50), pulmonary artery pressure ≥60 mmHg, and the De Vega annuloplasty technique were risk factors for medium-term recurrent grades 3 and 4 tricuspid insufficiency. Medium-term survival was 90.6% for the De Vega group, 96.3% for the modified De Vega group, and 97.1% for the ring annuloplasty group. Ring annuloplasty provided the best relief from recurrent tricuspid insufficiency when compared with DeVega annuloplasty. Modified De Vega annuloplasty might be a suitable alternative to ring annuloplasty when rings are not available. PMID:23466680

Recurrent tricuspid insufficiency: is the surgical repair technique a risk factor?

PubMed

Kara, Ibrahim; Koksal, Cengiz; Cakalagaoglu, Canturk; Sahin, Muslum; Yanartas, Mehmet; Ay, Yasin; Demir, Serdar

2013-01-01

This study compares the medium-term results of De Vega, modified De Vega, and ring annuloplasty techniques for the correction of tricuspid insufficiency and investigates the risk factors for recurrent grades 3 and 4 tricuspid insufficiency after repair. In our clinic, 93 patients with functional tricuspid insufficiency underwent surgical tricuspid repair from May 2007 through October 2010. The study was retrospective, and all the data pertaining to the patients were retrieved from hospital records. Functional capacity, recurrent tricuspid insufficiency, and risk factors aggravating the insufficiency were analyzed for each patient. In the medium term (25.4 ± 10.3 mo), the rates of grades 3 and 4 tricuspid insufficiency in the De Vega, modified De Vega, and ring annuloplasty groups were 31%, 23.1%, and 6.1%, respectively. Logistic regression analysis revealed that chronic obstructive pulmonary disease, left ventricular dysfunction (ejection fraction, < 0.50), pulmonary artery pressure ≥60 mmHg, and the De Vega annuloplasty technique were risk factors for medium-term recurrent grades 3 and 4 tricuspid insufficiency. Medium-term survival was 90.6% for the De Vega group, 96.3% for the modified De Vega group, and 97.1% for the ring annuloplasty group. Ring annuloplasty provided the best relief from recurrent tricuspid insufficiency when compared with DeVega annuloplasty. Modified De Vega annuloplasty might be a suitable alternative to ring annuloplasty when rings are not available.

Multiplicity and entropy scaling of medium-energy protons emitted in relativistic heavy-ion collisions

NASA Astrophysics Data System (ADS)

Abdelsalam, A.; Kamel, S.; Hafiz, M. E.

2015-10-01

The behavior and the properties of medium-energy protons with kinetic energies in the range 26 - 400 MeV is derived from measurements of the particle yields and spectra in the final state of relativistic heavy-ion collisions (16O-AgBr interactions at 60 A and 200 A GeV and 32S-AgBr interactions at 3.7 A and 200 A GeV) and their interpretation in terms of the higher order moments. The multiplicity distributions have been fitted well with the Gaussian distribution function. The data are also compared with the predictions of the modified FRITIOF model, showing that the FRITIOF model does not reproduce the trend and the magnitude of the data. Measurements of the ratio of the variance to the mean show that the production of target fragments at high energies cannot be considered as a statistically independent process. However, the deviation of each multiplicity distribution from a Poisson law provides evidence for correlations. The KNO scaling behavior of two types of scaling (Koba-Nielsen-Olesen (KNO) scaling and Hegyi scaling) functions in terms of the multiplicity distribution is investigated. A simplified universal function has been used in each scaling to display the experimental data. An examination of the relationship between the entropy, the average multiplicity, and the KNO function is performed. Entropy production and subsequent scaling in nucleus-nucleus collisions are carried out by analyzing the experimental data over a wide energy range (Dubna and SPS). Interestingly, the data points corresponding to various energies overlap and fall on a single curve, indicating the presence of a kind of entropy scaling.

Protein crystallization aboard the Space Shuttle and the Mir space station

NASA Technical Reports Server (NTRS)

Delbaere, Louis T. J.; Vandonselaar, Margaret; Prasad, Lata; Quail, J. W.; Birnbaum, George I.; Delucas, Lawrence J.; Moore, Karen; Bugg, Charles E.

1993-01-01

Two different protein crystallizations, namely ,the free Fab fragment of the Je142 monoclonal antibody and the complex of Fab fragment/HPr with antigen, were performed aboard the Discovery Space Shuttle flights and the Mir space station, respectively. Medium sized crystals of the Je142 Fab fragment were obtained. The Je142 Fab fragment/Hpr complex produced two medium-sized crystals after two months aboard the Mir space station. Microgravity was found to eliminate the tendency of these crystals to form clusters.

Effect of the cancer specific shorter form of human 6-phosphofructo-1-kinase on the metabolism of the yeast Saccharomyces cerevisiae.

PubMed

Andrejc, Darjan; Možir, Alenka; Legiša, Matic

2017-05-08

At first glance, there appears to be a high degree of similarity between the metabolism of yeast (the Crabtree effect) and human cancer cells (the Warburg effect). At the root of both effects is accelerated metabolic flow through glycolysis which leads to overflows of ethanol and lactic acid, respectively. It has been proposed that enhanced glycolytic flow in cancer cells is triggered by the altered kinetic characteristics of the key glycolytic regulatory enzyme 6-phosphofructo-1-kinase (Pfk). Through a posttranslational modification, highly active shorter Pfk-M fragments, which are resistant to feedback inhibition, are formed after the proteolytic cleavage of the C-terminus of the native human Pfk-M. Alternatively, enhanced glycolysis is triggered by optimal growth conditions in the yeast Saccharomyces cerevisiae. To assess the deregulation of glycolysis in yeast cells, the sfPFKM gene encoding highly active human shorter Pfk-M fragments was introduced into pfk-null S. cerevisiae. No growth of the transformants with the sfPFKM gene was observed on glucose and fructose. Glucose even induced rapid deactivation of Pfk1 activities in such transformants. However, Pfk1 activities of the sfPFKM transformants were detected in maltose medium, but the growth in maltose was possible only after the addition of 10 mM of ethanol to the medium. Ethanol seemed to alleviate the severely unbalanced NADH/NADPH ratio in the sfPFKM cells. However, the transformants carrying modified Pfk-M enzymes grew faster than the transformants with the human native human Pfk-M enzyme in a narrow ecological niche with a low maltose concentration medium that was further improved by additional modifications. Interestingly, periodic extracellular accumulation of phenylacetaldehyde was detected during the growth of the strain with modified Pfk-M but not with the strain encoding the human native enzyme. Highly active cancer-specific shorter Pfk-M fragments appear to trigger several controlling mechanisms in the primary metabolism of yeast S. cerevisiae cells. These results suggest more complex metabolic regulation is present in S. cerevisiae as free living unicellular eukaryotic organisms in comparison to metazoan human cells. However, increased productivity under broader growth conditions may be achieved if more gene engineering is performed to reduce or omit several controlling mechanisms.

Engineering of Fc Fragments with Optimized Physicochemical Properties Implying Improvement of Clinical Potentials for Fc-Based Therapeutics.

PubMed

Yang, Chunpeng; Gao, Xinyu; Gong, Rui

2017-01-01

Therapeutic monoclonal antibodies and Fc-fusion proteins are successfully used in treatment of various diseases mainly including cancer, immune disease, and viral infection, which belong to the Fc-based therapeutics. In recent years, engineered Fc-derived antibody domains have also shown potential for Fc-based therapeutics. To increase the druggability of Fc-based therapeutic candidates, many efforts have been made in optimizing physicochemical properties and functions mediated by Fc fragment. The desired result is that we can simultaneously obtain Fc variants with increased physicochemical properties in vitro and capacity of mediating appropriate functions in vivo . However, changes of physicochemical properties of Fc may result in alternation of Fc-mediated functions and vice versa , which leads to undesired outcomes for further development of Fc-based therapeutics. Therefore, whether modified Fc fragments are suitable for achievement of expected clinical results or not needs to be seriously considered. Now, this question comes to be noticed and should be figured out to make better translation from the results of laboratory into clinical applications. In this review, we summarize different strategies on engineering physicochemical properties of Fc, and preliminarily elucidate the relationships between modified Fc in vitro and the subsequent therapeutic influence in vivo .

Engineering of Fc Fragments with Optimized Physicochemical Properties Implying Improvement of Clinical Potentials for Fc-Based Therapeutics

PubMed Central

Yang, Chunpeng; Gao, Xinyu; Gong, Rui

2018-01-01

Therapeutic monoclonal antibodies and Fc-fusion proteins are successfully used in treatment of various diseases mainly including cancer, immune disease, and viral infection, which belong to the Fc-based therapeutics. In recent years, engineered Fc-derived antibody domains have also shown potential for Fc-based therapeutics. To increase the druggability of Fc-based therapeutic candidates, many efforts have been made in optimizing physicochemical properties and functions mediated by Fc fragment. The desired result is that we can simultaneously obtain Fc variants with increased physicochemical properties in vitro and capacity of mediating appropriate functions in vivo. However, changes of physicochemical properties of Fc may result in alternation of Fc-mediated functions and vice versa, which leads to undesired outcomes for further development of Fc-based therapeutics. Therefore, whether modified Fc fragments are suitable for achievement of expected clinical results or not needs to be seriously considered. Now, this question comes to be noticed and should be figured out to make better translation from the results of laboratory into clinical applications. In this review, we summarize different strategies on engineering physicochemical properties of Fc, and preliminarily elucidate the relationships between modified Fc in vitro and the subsequent therapeutic influence in vivo. PMID:29375551

Fission fragment excited laser system

DOEpatents

McArthur, David A.; Tollefsrud, Philip B.

1976-01-01

A laser system and method for exciting lasing action in a molecular gas lasing medium which includes cooling the lasing medium to a temperature below about 150 K and injecting fission fragments through the lasing medium so as to preferentially excite low lying vibrational levels of the medium and to cause population inversions therein. The cooled gas lasing medium should have a mass areal density of about 5 .times. 10.sup.-.sup.3 grams/square centimeter, relaxation times of greater than 50 microseconds, and a broad range of excitable vibrational levels which are excitable by molecular collisions.

Observation of medium induced modifications of jet fragmentation in PbPb collisions using isolated-photon-tagged jets

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

Sirunyan, Albert M; et al.

Measurements of fragmentation functions for jets associated with an isolated photon are presented for the first time in pp and PbPb collisions. The analysis uses data collected with the CMS detector at the CERN LHC at a nucleon-nucleon center-of-mass energy of 5.02 TeV. Fragmentation functions are obtained for jets with pmore » $$_\\mathrm{T}^\\text{jet} >$$ 30 GeV in events containing an isolated photon with p$$_\\mathrm{T}^\\gamma>$$ 60 GeV, using charged tracks with transverse momentum p$$_\\mathrm{T}^\\text{trk} >$$ 1 GeV in a cone around the jet axis. The association with an isolated photon constrains the initial p$$_\\mathrm{T}$$ and azimuthal angle of the parton whose shower produced the jet. For central PbPb collisions, modifications of the jet fragmentation functions are observed when compared to those measured in pp collisions, while no significant differences are found in the 50% most peripheral collisions. Jets in central PbPb events show an excess (depletion) of low (high) p$$_\\mathrm{T}$$ particles, with a transition around 3 GeV.« less

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

Kaothekar, Sachin, E-mail: sackaothekar@gmail.com

I have studied the effects of finite electron inertia, finite ion Larmor radius (FLR) corrections, and radiative heat-loss function on the thermal instability of an infinite homogeneous, viscous plasma incorporating the effect of thermal conductivity for star formation in interstellar medium (ISM). A general dispersion relation is derived using the normal mode analysis method with the help of relevant linearized perturbation equations of the problem. The wave propagation is discussed for longitudinal and transverse directions to the external magnetic field and the conditions of modified thermal instabilities and stabilities are discussed in different cases. We find that the thermal instabilitymore » criterion is get modified into radiative instability criterion by inclusion of radiative heat-loss functions with thermal conductivity. The viscosity of medium removes the effect of FLR corrections from the condition of radiative instability. Numerical calculation shows stabilizing effect of heat-loss function, viscosity and FLR corrections, and destabilizing effect of finite electron inertia on the thermal instability. Results carried out in this paper shows that stars are formed in interstellar medium mainly due to thermal instability.« less

Origin and Evolution of Prebiotic Organic Matter as Inferred from the Tagish Lake Meteorite

NASA Technical Reports Server (NTRS)

Herd, Christopher D.; Blinova, Alexandra; Simkus, Danielle N.; Huang, Yongsong; Tarozo, Rafael; Alexander, Conel M.; Gyngard, Frank; Nittler, Larry R.; Cody, George D.; Fogel, Marilyn L.;

Generation and Nuclear Translocation of Sumoylated Transmembrane Fragment of Cell Adhesion Molecule L1

PubMed Central

Lutz, David; Wolters-Eisfeld, Gerrit; Joshi, Gunjan; Djogo, Nevena; Jakovcevski, Igor; Schachner, Melitta; Kleene, Ralf

2012-01-01

The functions of the cell adhesion molecule L1 in the developing and adult nervous system are triggered by homophilic and heterophilic interactions that stimulate signal transductions that activate cellular responses. Here, we show that stimulation of signaling by function-triggering L1 antibodies or L1-Fc leads to serine protease-dependent cleavage of full-length L1 at the plasma membrane and generation of a sumoylated transmembrane 70-kDa fragment comprising the intracellular and transmembrane domains and part of the extracellular domain. The 70-kDa transmembrane fragment is transported from the plasma membrane to a late endosomal compartment, released from endosomal membranes into the cytoplasm, and transferred from there into the nucleus by a pathway that depends on importin and chromatin-modifying protein 1. Mutation of the sumoylation site at Lys1172 or of the nuclear localization signal at Lys1147 abolished L1-stimulated generation or nuclear import of the 70-kDa fragment, respectively. Nuclear import of the 70-kDa fragment may activate cellular responses in parallel or in association with phosphorylation-dependent signaling pathways. Alterations in the levels of the 70-kDa fragment during development and in the adult after spinal cord injury or in a mouse model of Alzheimer disease suggest that this fragment is functionally implicated in development, regeneration, neurodegeneration, tumorigenesis, and possibly synaptic plasticity in the mature nervous system. PMID:22431726

Stochastic transfer of polarized radiation in finite cloudy atmospheric media with reflective boundaries

NASA Astrophysics Data System (ADS)

Sallah, M.

2014-03-01

The problem of monoenergetic radiative transfer in a finite planar stochastic atmospheric medium with polarized (vector) Rayleigh scattering is proposed. The solution is presented for an arbitrary absorption and scattering cross sections. The extinction function of the medium is assumed to be a continuous random function of position, with fluctuations about the mean taken as Gaussian distributed. The joint probability distribution function of these Gaussian random variables is used to calculate the ensemble-averaged quantities, such as reflectivity and transmissivity, for an arbitrary correlation function. A modified Gaussian probability distribution function is also used to average the solution in order to exclude the probable negative values of the optical variable. Pomraning-Eddington approximation is used, at first, to obtain the deterministic analytical solution for both the total intensity and the difference function used to describe the polarized radiation. The problem is treated with specular reflecting boundaries and angular-dependent externally incident flux upon the medium from one side and with no flux from the other side. For the sake of comparison, two different forms of the weight function, which introduced to force the boundary conditions to be fulfilled, are used. Numerical results of the average reflectivity and average transmissivity are obtained for both Gaussian and modified Gaussian probability density functions at the different degrees of polarization.

Amphiphilic invertible polymers: Self-assembly into functional materials driven by environment polarity

NASA Astrophysics Data System (ADS)

Hevus, Ivan

Stimuli-responsive polymers adapt to environmental changes by adjusting their chain conformation in a fast and reversible way. Responsive polymeric materials have already found use in electronics, coatings industry, personal care, and bio-related areas. The current work aims at the development of novel responsive functional polymeric materials by manipulating environment-dependent self-assembly of a new class of responsive macromolecules strategically designed in this study,—amphiphilic invertible polymers (AIPs). Environment-dependent micellization and self-assembly of three different synthesized AIP types based on poly(ethylene glycol) as a hydrophilic fragment and varying hydrophobic constituents was demonstrated in polar and nonpolar solvents, as well as on the surfaces and interfaces. With increasing concentration, AIP micelles self-assemble into invertible micellar assemblies composed of hydrophilic and hydrophobic domains. Polarity-responsive properties of AIPs make invertible micellar assemblies functional in polar and nonpolar media including at interfaces. Thus, invertible micellar assemblies solubilize poorly soluble substances in their interior in polar and nonpolar solvents. In a polar aqueous medium, a novel stimuli-responsive mechanism of drug release based on response of AIP-based drug delivery system to polarity change upon contact with the target cell has been established using invertible micellar assemblies loaded with curcumin, a phytochemical drug. In a nonpolar medium, invertible micellar assemblies were applied simultaneously as nanoreactors and stabilizers for size-controlled synthesis of silver nanoparticles stable in both polar and nonpolar media. The developed amphiphilic nanosilver was subsequently used as seeds to promote anisotropic growth of CdSe semiconductor nanoparticles that have potential in different applications ranging from physics to medicine. Amphiphilic invertible polymers were shown to adsorb on the surface of silica nanoparticles strongly differing in polarity. AIP modified silica nanoparticles are able to adsolubilize molecules of poorly water-soluble 2-naphthol into the adsorbed polymer layer. The adsolubilization ability of adsorbed invertible macromolecules makes AIP-modified silica nanoparticles potentially useful in wastewater treatment or biomedical applications. Finally, the invertible micellar assemblies were used as functional additives to improve the appearance of electrospun silicon wires based on cyclohexasilane, a liquid silicon precursor. AIP-assisted fabrication of silicon wires from the liquid cyclohexasilane precursor has potential as a scalable method for developing electronic functional materials.

Keystone Species, Forest and Landscape: A Model to Select Protected Areas

NASA Astrophysics Data System (ADS)

Lins, Daniela Barbosa da Silva; Gardon, Fernando Ravanini; Meyer, João Frederico da Costa Azevedo; Santos, Rozely Ferreira dos

2017-06-01

The selection of forest fragments for conservation is usually based on spatial parameters as forest size and canopy integrity. This strategy assumes that chosen fragments present high conservation status, ensuring biodiversity and ecological functions. We argue that a well-preserved forest fragment that remains connected by the landscape structure, does not necessarily hold attributes that ensure the presence of keystone species. We also discuss that the presence of keystone species does not always mean that it has the best conditions for its occurrence and maintenance. We developed a model to select areas in forest landscapes to be prioritized for protection based on suitability curves that unify and compare spatial indicators of three categories: forest fragment quality, landscape quality, and environmental conditions for the occurrence of a keystone species. We use a case study to compare different suitability degrees for Euterpe edulis presence, considered an important functional element in Atlantic Forest (São Paulo, Brazil) landscapes and a forest resource for local people. The results show that the identification of medium or advanced stage fragments as singular indicator of forest quality does not guarantee the existence or maintenance of this keystone species. Even in some well-preserved forest fragments, connected to others and with palm presence, the reverse J-shaped distribution of the population size structure is not sustained and these forests continue to be threatened due to human disturbances.

Culture Phenotypes of Genomically and Geographically Diverse Mycobacterium avium subsp. paratuberculosis Isolates from Different Hosts▿

PubMed Central

Whittington, Richard J.; Marsh, Ian B.; Saunders, Vanessa; Grant, Irene R.; Juste, Ramon; Sevilla, Iker A.; Manning, Elizabeth J. B.; Whitlock, Robert H.

2011-01-01

Mycobacterium avium subsp. paratuberculosis causes paratuberculosis (Johne's disease) in ruminants in most countries. Historical data suggest substantial differences in culturability of M. avium subsp. paratuberculosis isolates from small ruminants and cattle; however, a systematic comparison of culture media and isolates from different countries and hosts has not been undertaken. Here, 35 field isolates from the United States, Spain, Northern Ireland, and Australia were propagated in Bactec 12B medium and Middlebrook 7H10 agar, genomically characterized, and subcultured to Lowenstein-Jensen (LJ), Herrold's egg yolk (HEY), modified Middlebrook 7H10, Middlebrook 7H11, and Watson-Reid (WR) agars, all with and without mycobactin J and some with sodium pyruvate. Fourteen genotypes of M. avium subsp. paratuberculosis were represented as determined by BstEII IS900 and IS1311 restriction fragment length polymorphism analysis. There was no correlation between genotype and overall culturability, although most S strains tended to grow poorly on HEY agar. Pyruvate was inhibitory to some isolates. All strains grew on modified Middlebrook 7H10 agar but more slowly and less prolifically on LJ agar. Mycobactin J was required for growth on all media except 7H11 agar, but growth was improved by the addition of mycobactin J to 7H11 agar. WR agar supported the growth of few isolates. The differences in growth of M. avium subsp. paratuberculosis that have historically been reported in diverse settings have been strongly influenced by the type of culture medium used. When an optimal culture medium, such as modified Middlebrook 7H10 agar, is used, very little difference between the growth phenotypes of diverse strains of M. avium subsp. paratuberculosis was observed. This optimal medium is recommended to remove bias in the isolation and cultivation of M. avium subsp. paratuberculosis. PMID:21430104

Finite Element Simulation and Experimental Verification of Internal Stress of Quenched AISI 4140 Cylinders

NASA Astrophysics Data System (ADS)

Liu, Yu; Qin, Shengwei; Hao, Qingguo; Chen, Nailu; Zuo, Xunwei; Rong, Yonghua

2017-03-01

The study of internal stress in quenched AISI 4140 medium carbon steel is of importance in engineering. In this work, the finite element simulation (FES) was employed to predict the distribution of internal stress in quenched AISI 4140 cylinders with two sizes of diameter based on exponent-modified (Ex-Modified) normalized function. The results indicate that the FES based on Ex-Modified normalized function proposed is better consistent with X-ray diffraction measurements of the stress distribution than FES based on normalized function proposed by Abrassart, Desalos and Leblond, respectively, which is attributed that Ex-Modified normalized function better describes transformation plasticity. Effect of temperature distribution on the phase formation, the origin of residual stress distribution and effect of transformation plasticity function on the residual stress distribution were further discussed.

Measurement of inclusive jet charged-particle fragmentation functions in Pb+Pb collisions at √ sNN = 2.76 TeV with the ATLAS detector

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2014-11-04

In this study, measurements of charged-particle fragmentation functions of jets produced in ultra-relativistic nuclear collisions can provide insight into the modification of parton showers in the hot, dense medium created in the collisions. ATLAS has measured jets in √s NN = 2.76 TeV Pb+Pb collisions at the LHC using a data set recorded in 2011 with an integrated luminosity of 0.14 nb –1. Jets were reconstructed using the anti-kt algorithm with distance parameter values R = 0.2, 0.3, and 0.4. Distributions of charged-particle transverse momentum and longitudinal momentum fraction are reported for seven bins in collision centrality for R=0.4 jetsmore » with p T jet. Commensurate minimum p T values are used for the other radii. The ratios of fragment distributions in each centrality bin to those measured in the most peripheral bin are presented. These ratios show a reduction of fragment yield in central collisions relative to peripheral collisions at intermediate z values, 0.04≲z≲0.2, and an enhancement in fragment yield for z≲0.04. A smaller, less significant enhancement is observed at large z and large p T in central collisions.« less

Material and method for promoting the growth of anaerobic bacteria

DOEpatents

Adler, H.I.

1984-10-09

A material and method is disclosed for promoting the growth of anaerobic bacteria which includes a nutrient media containing a hydrogen donor and sterile membrane fragments of bacteria having an electron transfer system which reduces oxygen to water. Dissolved oxygen in the medium is removed by adding the sterile membrane fragments to the nutrient medium and holding the medium at a temperature of about 10 to about 60 C until the dissolved oxygen is removed. No Drawings

Material and method for promoting the growth of anaerobic bacteria

DOEpatents

Adler, Howard I.

1984-01-01

A material and method for promoting the growth of anaerobic bacteria which includes a nutrient media containing a hydrogen donor and sterile membrane fragments of bacteria having an electron transfer system which reduces oxygen to water. Dissolved oxygen in the medium is removed by adding the sterile membrane fragments to the nutrient medium and holding the medium at a temperature of about 10.degree. to about 60.degree. C. until the dissolved oxygen is removed.

Ion-polycyclic aromatic hydrocarbon collisions: kinetic energy releases for specific fragmentation channels

NASA Astrophysics Data System (ADS)

Reitsma, G.; Zettergren, H.; Boschman, L.; Bodewits, E.; Hoekstra, R.; Schlathölter, T.

2013-12-01

We report on 30 keV He2 + collisions with naphthalene (C10H8) molecules, which leads to very extensive fragmentation. To unravel such complex fragmentation patterns, we designed and constructed an experimental setup, which allows for the determination of the full momentum vector by measuring charged collision products in coincidence in a recoil ion momentum spectrometer type of detection scheme. The determination of fragment kinetic energies is found to be considerably more accurate than for the case of mere coincidence time-of-flight spectrometers. In fission reactions involving two cationic fragments, typically kinetic energy releases of 2-3 eV are observed. The results are interpreted by means of density functional theory calculations of the reverse barriers. It is concluded that naphthalene fragmentation by collisions with keV ions clearly is much more violent than the corresponding photofragmentation with energetic photons. The ion-induced naphthalene fragmentation provides a feedstock of various small hydrocarbonic species of different charge states and kinetic energy, which could influence several molecule formation processes in the cold interstellar medium and facilitates growth of small hydrocarbon species on pre-existing polycyclic aromatic hydrocarbons.

In situ magnetic separation of antibody fragments from Escherichia coli in complex media

PubMed Central

2013-01-01

Background In situ magnetic separation (ISMS) has emerged as a powerful tool to overcome process constraints such as product degradation or inhibition of target production. In the present work, an integrated ISMS process was established for the production of his-tagged single chain fragment variable (scFv) D1.3 antibodies (“D1.3”) produced by E. coli in complex media. This study investigates the impact of ISMS on the overall product yield as well as its biocompatibility with the bioprocess when metal-chelate and triazine-functionalized magnetic beads were used. Results Both particle systems are well suited for separation of D1.3 during cultivation. While the triazine beads did not negatively impact the bioprocess, the application of metal-chelate particles caused leakage of divalent copper ions in the medium. After the ISMS step, elevated copper concentrations above 120 mg/L in the medium negatively influenced D1.3 production. Due to the stable nature of the model protein scFv D1.3 in the biosuspension, the application of ISMS could not increase the overall D1.3 yield as was shown by simulation and experiments. Conclusions We could demonstrate that triazine-functionalized beads are a suitable low-cost alternative to selectively adsorb D1.3 fragments, and measured maximum loads of 0.08 g D1.3 per g of beads. Although copper-loaded metal-chelate beads did adsorb his-tagged D1.3 well during cultivation, this particle system must be optimized by minimizing metal leakage from the beads in order to avoid negative inhibitory effects on growth of the microorganisms and target production. Hereby, other types of metal chelate complexes should be tested to demonstrate biocompatibility. Such optimized particle systems can be regarded as ISMS platform technology, especially for the production of antibodies and their fragments with low stability in the medium. The proposed model can be applied to design future ISMS experiments in order to maximize the overall product yield while the amount of particles being used is minimized as well as the number of required ISMS steps. PMID:23688064

Separation medium containing thermally exfoliated graphite oxide

NASA Technical Reports Server (NTRS)

Prud'homme, Robert K. (Inventor); Aksay, Ilhan A. (Inventor); Herrera-Alonso, Margarita (Inventor)

2012-01-01

A separation medium, such as a chromatography filling or packing, containing a modified graphite oxide material, which is a thermally exfoliated graphite oxide with a surface area of from about 300 m.sup.2/g to 2600 m.sup.2/g, wherein the thermally exfoliated graphite oxide has a surface that has been at least partially functionalized.

The effect of catastrophic collisional fragmentation and diffuse medium accretion on a computational interstellar dust system

NASA Technical Reports Server (NTRS)

Liffman, Kurt

1990-01-01

The effects of catastrophic collisional fragmentation and diffuse medium accretion on a the interstellar dust system are computed using a Monte Carlo computer model. The Monte Carlo code has as its basis an analytic solution of the bulk chemical evolution of a two-phase interstellar medium, described by Liffman and Clayton (1989). The model is subjected to numerous different interstellar processes as it transfers from one interstellar phase to another. Collisional fragmentation was found to be the dominant physical process that shapes the size spectrum of interstellar dust. It was found that, in the diffuse cloud phase, 90 percent of the refractory material is locked up in the dust grains, primarily due to accretion in the molecular medium. This result is consistent with the observed depletions of silicon. Depletions were found to be affected only slightly by diffuse cloud accretion.

Evaluation of ebselen supplementation on cryopreservation medium in human semen

PubMed Central

Khodayari Naeini, Zohreh; Hassani Bafrani, Hassan; Nikzad, Hossein

2014-01-01

Background: An effect of cryopreservation on human sperm is sublethal cryodamage, in which cell viability post-thaw is lost more rapidly at later times than in fresh cells. Objective: This study examined whether the addition of an antioxidant to cryopreservation medium could improve the post-thaw parameters and evaluation of sperm chromatin quality of cryopreserved human spermatozoa from men with normal semen parameters. Materials and Methods: Semen samples (n=35) were collected by masturbation and assessed following WHO standards. Individual samples were classified as two portions. One portion (n=10) was for elucidate the concentration of ebselen.Then the samples(n=25) were divided in to 5groups.The first aliquot remained fresh.The second aliquots was mixed with cryopreservation medium.The third aliquots were mixed with cryopreservation medium containing solvent of ebselen.The forth and fifth aliquots were mixed with cryopreservation medium containing 1.25 and 2.5 µm of ebselen.Samples were frozen and thawed samples were assessed for sperm parameters.Three-way ANOVA Multivariate measures were used to assess. According to this assesment the differences are observed in existent groups in post-thaw count, motility index, vitality staining, and morphology and DNA fragmentation. Results: After freezing the media containing of ebselen, DNA fragmentation is significantly different in comparison with control group. ebselen with 1.25 µm dose was significantly associated with post-thaw DNA fragmentation (p=0.047). Similarly ebselen with 2.5 µm dose was significantly associated with post-thaw DNA fragmentation (p=0.038). But other parameters were not altered. Conclusion: These results suggest that the addition of ebselen to cryopreservation medium doesnot improve post-thaw parameters and DNA fragmentation of sperm. PMID:24976819

Evaluation of ebselen supplementation on cryopreservation medium in human semen.

PubMed

Khodayari Naeini, Zohreh; Hassani Bafrani, Hassan; Nikzad, Hossein

2014-04-01

An effect of cryopreservation on human sperm is sublethal cryodamage, in which cell viability post-thaw is lost more rapidly at later times than in fresh cells. This study examined whether the addition of an antioxidant to cryopreservation medium could improve the post-thaw parameters and evaluation of sperm chromatin quality of cryopreserved human spermatozoa from men with normal semen parameters. Semen samples (n=35) were collected by masturbation and assessed following WHO standards. Individual samples were classified as two portions. One portion (n=10) was for elucidate the concentration of ebselen.Then the samples(n=25) were divided in to 5groups.The first aliquot remained fresh.The second aliquots was mixed with cryopreservation medium.The third aliquots were mixed with cryopreservation medium containing solvent of ebselen.The forth and fifth aliquots were mixed with cryopreservation medium containing 1.25 and 2.5 µm of ebselen.Samples were frozen and thawed samples were assessed for sperm parameters.Three-way ANOVA Multivariate measures were used to assess. According to this assesment the differences are observed in existent groups in post-thaw count, motility index, vitality staining, and morphology and DNA fragmentation. After freezing the media containing of ebselen, DNA fragmentation is significantly different in comparison with control group. ebselen with 1.25 µm dose was significantly associated with post-thaw DNA fragmentation (p=0.047). Similarly ebselen with 2.5 µm dose was significantly associated with post-thaw DNA fragmentation (p=0.038). But other parameters were not altered. These results suggest that the addition of ebselen to cryopreservation medium doesnot improve post-thaw parameters and DNA fragmentation of sperm.

Baryons and baryon resonances in nuclear matter

NASA Astrophysics Data System (ADS)

Lenske, Horst; Dhar, Madhumita; Gaitanos, Theodoros; Cao, Xu

2018-01-01

Theoretical approaches to the production of hyperons and baryon resonances in elementary hadronic reactions and heavy ion collisions are reviewed. The focus is on the production and interactions of baryons in the lowest SU(3) flavor octet and states from the next higher SU(3) flavor decuplet. Approaches using the SU(3) formalism for interactions of mesons and baryons and effective field theory for hyperons are discussed. An overview of application to free space and in-medium baryon-baryon interactions is given and the relation to a density functional theory is indicated. The intimate connection between baryon resonances and strangeness production is shown first for reactions on the nucleon. Pion-induced hypernuclear reactions are shown to proceed essentially through the excitation of intermediate nucleon resonances. Transport theory in conjunction with a statistical fragmentation model is an appropriate description of hypernuclear production in antiproton and heavy ion induced fragmentation reactions. The excitation of subnuclear degrees of freedom in peripheral heavy ion collisions at relativistic energies is reviewed. The status of in-medium resonance physics is discussed.

Sleep fragmentation alters brain energy metabolism without modifying hippocampal electrophysiological response to novelty exposure.

PubMed

Baud, Maxime O; Parafita, Julia; Nguyen, Audrey; Magistretti, Pierre J; Petit, Jean-Marie

2016-10-01

Sleep is viewed as a fundamental restorative function of the brain, but its specific role in neural energy budget remains poorly understood. Sleep deprivation dampens brain energy metabolism and impairs cognitive functions. Intriguingly, sleep fragmentation, despite normal total sleep duration, has a similar cognitive impact, and in this paper we ask the question of whether it may also impair brain energy metabolism. To this end, we used a recently developed mouse model of 2 weeks of sleep fragmentation and measured 2-deoxy-glucose uptake and glycogen, glucose and lactate concentration in different brain regions. In order to homogenize mice behaviour during metabolic measurements, we exposed them to a novel environment for 1 h. Using an intra-hippocampal electrode, we first showed that hippocampal electroencephalograph (EEG) response to exploration was unaltered by 1 or 14 days of sleep fragmentation. However, after 14 days, sleep fragmented mice exhibited a lower uptake of 2-deoxy-glucose in cortex and hippocampus and lower cortical lactate levels than control mice. Our results suggest that long-term sleep fragmentation impaired brain metabolism to a similar extent as total sleep deprivation without affecting the neuronal responsiveness of hippocampus to a novel environment. © 2016 European Sleep Research Society.

Enhanced kidney stone fragmentation by short delay tandem conventional and modified lithotriptor shock waves: a numerical analysis.

PubMed

Tham, Leung-Mun; Lee, Heow Pueh; Lu, Chun

2007-07-01

We evaluated the effectiveness of modified lithotriptor shock waves using computer models. Finite element models were used to simulate the propagation of lithotriptor shock waves in human renal calculi in vivo. Kidney stones were assumed to be spherical, homogeneous, isotropic and linearly elastic, and immersed in a continuum fluid. Single and tandem shock wave pulses modified to intensify the collapse of cavitation bubbles near the stone surface to increase fragmentation efficiency and suppress the expansion of intraluminal bubbles for decreased vascular injury were analyzed. The effectiveness of the modified shock waves was assessed by comparing the states of loading in the renal calculi induced by these shock waves to those produced by conventional shock waves. Our numerical simulations revealed that modified shock waves produced marginally lower stresses in spherical renal calculi than those produced by conventional shock waves. Tandem pulses of conventional or modified shock waves produced peak stresses in the front and back halves of the renal calculi. However, the single shock wave pulses generated significant peak stresses in only the back halves of the renal calculi. Our numerical simulations suggest that for direct stress wave induced fragmentation modified shock waves should be as effective as conventional shock waves for fragmenting kidney stones. Also, with a small interval of 20 microseconds between the pulses tandem pulse lithotripsy using modified or conventional shock waves could be considerably more effective than single pulse lithotripsy for fragmenting kidney stones.

Short-term storage of canine preantral ovarian follicles using a powdered coconut water (ACP)-based medium.

PubMed

Lima, G L; Costa, L L M; Cavalcanti, D M L P; Rodrigues, C M F; Freire, F A M; Fontenele-Neto, J D; Silva, A R

2010-07-01

The objective was to investigate the use of powdered coconut water (ACP)-based medium for short-term preservation of canine preantral follicles. Pairs of ovaries from mongrel bitches (n=9) were divided into fragments. One ovarian fragment, treated as a fresh control, was immediately fixed for histological analysis, whereas the other six ovarian fragments were stored either in phosphate-buffered saline (PBS; control group) or ACP medium in isothermal Styrofoam boxes containing biological ice packs. The boxes were sealed and opened only after 12, 24, or 36h. After opening each box, the ovarian fragments were submitted to histological analysis. In total, 12,302 preantral follicles were evaluated, with 64.5% primordial, 33.3% primary, and 2.3% secondary follicles. There were multiple oocytes in 1.3% of the follicles analyzed. At 24h, ACP was more efficient in preserving follicular morphology than PBS (P<0.05). Compared with the fresh control group, a significant reduction in the percentage of morphologically normal ovarian follicles was observed for PBS, starting at 24h; however, the decline started only at 36h for the ACP medium. During the experiment, the temperature inside the isothermal boxes increased from 3 to 9 degrees C (P<0.05), despite a constant room temperature. In conclusion, powdered coconut water (ACP) was an appropriate medium for short-term storage of canine preantral ovarian follicles.

Cytosolic expression of functional Fab fragments in Escherichia coli using a novel combination of dual SUMO expression cassette and EnBase® cultivation mode.

PubMed

Rezaie, F; Davami, F; Mansouri, K; Agha Amiri, S; Fazel, R; Mahdian, R; Davoudi, N; Enayati, S; Azizi, M; Khalaj, V

2017-05-08

The Escherichia coli expression system is highly effective in producing recombinant proteins. However, there are some limitations in this system, especially in obtaining correctly folded forms of some complex proteins such as Fab fragments. To improve the solubility and folding quality of Fab fragments, we have examined the effect of simultaneous application of a SUMO fusion tag, EnBase ® cultivation mode and a redox mutant strain in the E. coli expression system. A bicistronic gene construct was designed to express an antivascular endothelial growth factor (VEGF) Fab fragment as a model system. The construct contained a dual SUMO fusion gene fragment to encode SUMO-tagged heavy and light chains. While the expression of the construct in batch cultures of BL21 or SHuffle ® transformants produced insoluble and unfolded products, the induction of the transformants in EnBase ® medium resulted in soluble and correctly folded Fab fragment, reaching as high as 19% of the total protein in shuffle strain. The functional assays indicated that the biological activity of the target Fab is similar to the commercial anti-VEGF, Lucentis ® . This study demonstrated that the combination of SUMO fusion technology, EnBase ® cultivation system and recruiting a redox mutant of E. coli can efficiently enhance the solubility and productivity of recombinant Fab fragments. The presented strategy provides not only a novel method to produce soluble and active form of an anti-VEGF Fab but also may use in the efficient production of other antibody fragments. © 2017 The Society for Applied Microbiology.

Structural analysis and taste evaluation of γ-glutamyl peptides comprising sulfur-containing amino acids.

PubMed

Amino, Yusuke; Wakabayashi, Hidehiko; Akashi, Satoko; Ishiwatari, Yutaka

2018-03-01

The structures, flavor-modifying effects, and CaSR activities of γ-glutamyl peptides comprising sulfur-containing amino acids were investigated. The chemical structures, including the linkage mode of the N-terminal glutamic acid, of γ-L-glutamyl-S-(2-propenyl)-L-cysteine (γ-L-glutamyl-S-allyl-L-cysteine) and its sulfoxide isolated from garlic were established by comparing their NMR spectra with those of authentic peptides prepared using chemical methods. Mass spectrometric analysis also enabled determination of the linkage modes in the glutamyl dipeptides by their characteristic fragmentation. In sensory evaluation, these peptides exhibited flavor-modifying effects (continuity) in umami solutions less pronounced but similar to that of glutathione. Furthermore, the peptides exhibited intrinsic flavor due to the sulfur-containing structure, which may be partially responsible for their flavor-modifying effects. In CaSR assays, γ-L-glutamyl-S-methyl-L-cysteinylglycine was most active, which indicates that the presence of a medium-sized aliphatic substituent at the second amino acid residue in γ-glutamyl peptides enhances CaSR activity.

Mitochondrial DNA content in embryo culture medium is significantly associated with human embryo fragmentation.

PubMed

Stigliani, S; Anserini, P; Venturini, P L; Scaruffi, P

2013-10-01

Is the amount of cell-free DNA released by human embryos into culture medium correlated with embryo morphological features? The mitochondrial DNA (mtDNA) content of culture medium is significantly associated with the fragmentation rate on Days 2 and 3 of embryo development, whether the oocyte came from women ≤ 35 or >35 years old. Cellular fragmentation is often utilized as one of the morphological parameters for embryo quality assessment. The amount of cellular fragments is considered to be an important morphological parameter for embryo implantation potential. It has been hypothesized that fragments are apoptotic bodies or anuclear cytoplasmatic pieces of blastomeres, although no definitive conclusion has been drawn about their pathogenesis. Human fertilized oocytes were individually cultured from Day 1 to Days 2 and 3. A total of 800 samples (166 spent media from Day 2 and 634 from Day 3) were enrolled into the present study. Double-stranded DNA (dsDNA) was quantified in 800 spent embryo culture media by Pico Green dye fluorescence assay. After DNA purification, genomic DNA (gDNA) and mtDNA were profiled by specific quantitative PCR. Statistical analyses defined correlations among DNA contents, embryo morphology and maternal age. Different independent tests confirmed the presence of DNA into embryo culture medium and, for the first time, we demonstrate that both gDNA and mtDNA are detectable in the secretome. The amount of DNA is larger in embryos with bad quality cleavage compared with high-grade embryos, suggesting that the DNA profile of culture medium is an objective marker for embryo quality assessment. In particular, DNA profiles are significantly associated with fragmentation feature (total dsDNA: P = 0.0010; mtDNA; P = 0.0247) and advanced maternal age. It is necessary to establish whether DNA profiling of spent embryo culture medium is a robust onsite test that can improve the prediction of blastulation, implantation and/or pregnancy rate. The approach we are proposing may provide a novel, non-invasive, objective tool for embryo quality grading. The correlation between a high mtDNA concentration and the fragmentation rate of embryos is suggestive that fragments are mainly anuclear cytoplasmatic debris arising during cleavage. Therefore, blastomere shaping as an early event during in vitro development may play a homeostatic role and be related to embryo competence. This project was funded by Merck Serono (Grant for Fertility Innovation 2011). The sponsor had no role in study design, data collection, data analysis, data interpretation and writing of the paper. Authors declare no conflicts of interest. ClinicalTrials.gov Identifier: NCT01397136.

Global profiling of proteolytically modified proteins in human metastatic hepatocellular carcinoma cell lines reveals CAPN2 centered network.

PubMed

Shen, Chengpin; Yu, Yanyan; Li, Hong; Yan, Guoquan; Liu, Mingqi; Shen, Huali; Yang, Pengyuan

2012-06-01

Proteolysis affects every protein at some point in its life cycle. Many biomarkers of disease or cancer are stable proteolytic fragments in biological fluids. There is great interest and a challenge in proteolytically modified protein study to identify physiologic protease-substrate relationships and find potential biomarkers. In this study, two human hepatocellular carcinoma (HCC) cell lines with different metastasis potential, MHCC97L, and HCCLM6, were researched with a high-throughput and sensitive PROTOMAP platform. In total 391 proteins were found to be proteolytically processed and many of them were cleaved into persistent fragments instead of completely degraded. Fragments related to 161 proteins had different expressions in these two cell lines. Through analyzing these significantly changed fragments with bio-informatic tools, several bio-functions such as tumor cell migration and anti-apoptosis were enriched. A proteolysis network was also built up, of which the CAPN2 centered subnetwork, including SPTBN1, ATP5B, and VIM, was more active in highly metastatic HCC cell line. Interestingly, proteolytic modifications of CD44 and FN1 were found to affect their secretion. This work suggests that proteolysis plays an important role in human HCC metastasis. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

San Francisco 's Golden Gate: A bridge between historically distinct coyote (Canis latrans) populations?

USGS Publications Warehouse

Sacks, Benjamin N.; Ernest, Holly B.; Boydston, Erin E.

2006-01-01

Although coyotes (Canis latrans) are wellknown for their adaptability to human-modified landscapes (Riley et al. 2003), as with any medium to large-sized carnivore, they typically avoid highly urbanized areas (Crooks 2002), preferring instead to use habitat fragments linked by vegetated corridors (Tigas et al. 2002). However, recent observations of coyotes in San Francisco indicate their willingness to traverse even the most densely urbanized terrain (Rubenstein 2003). Herein we use DNA to show, in an extreme example, that an adult male coyote caught in the northern tip of the San Francisco peninsula traversed the 2-km Golden Gate Bridge, potentially linking historically distinct coyote populations.

Comprehensive interpretation of thermal dileptons measured at the CERN super proton synchrotron.

PubMed

van Hees, Hendrik; Rapp, Ralf

2006-09-08

Employing thermal dilepton rates based on a medium-modified electromagnetic correlation function we show that recent dimuon spectra of the NA60 Collaboration in central In-In collisions at the CERN-SPS can be understood in terms of radiation from a hot and dense hadronic medium. Earlier calculated in-medium rho-meson spectral functions provide an accurate description of the data up to dimuon invariant masses of about M approximately or equal to 0.9 GeV, with good sensitivity to the predicted rho-meson line shape, identifying baryon-induced modifications as the prevalent ones. A reliable evaluation of the contribution enables the study of further medium effects: at masses M>0.9 GeV, 4-pion type annihilation accounts for the experimentally observed excess (possibly augmented by effects of "chiral mixing"), while predictions for thermal emission from in-medium omega and phi mesons may be tested in the future.

Thrombospondin-induced adhesion of human keratinocytes.

PubMed Central

Varani, J; Nickoloff, B J; Riser, B L; Mitra, R S; O'Rourke, K; Dixit, V M

1988-01-01

Human epidermal keratinocytes obtained from normal skin attached and spread on thrombospondin (TSP)-coated plastic dishes but failed to attach and spread on untreated plastic culture dishes or dishes coated with fibronectin or laminin. These cells produced minimal amounts of immunoreactive TSP. Keratinocytes established in culture on MCDB 153 medium and maintained for one to three passages in an undifferentiated state by continued cultivation in this low Ca2+-containing medium attached and spread on plastic dishes as well as on TSP-coated dishes. These cells also secreted significant amounts of TSP into the culture medium. When the keratinocytes were incubated for one day in MCDB 153 medium supplemented with high Ca2+ or in MEM (which also contains high Ca2+), there was decreased secretion of TSP into the culture medium concomitant with a reduction in attachment and spreading on plastic culture dishes. Proteolytic fragments of TSP were examined for stimulation of keratinocyte attachment and spreading. A 140-kd fragment produced by removal of the 25-kd heparin-binding domain had similar activity to the intact molecule while the 25-kd fragment was without effect. Further proteolytic treatment of the 140-kd fragment gave rise to a fragment consisting of 120 kd and 18-D moieties held together in disulphide linkage. This fragment did not support attachment or spreading. This study reveals that normal epidermal keratinocytes grown under conditions that maintain the undifferentiated state are able to produce TSP and utilize it as an attachment factor. When keratinocytes are grown under conditions that promote differentiation, ability to produce and utilize TSP is diminished. Since TSP is present at the dermal-epidermal junction and because TSP promotes keratinocyte attachment and spreading, this molecule may play an important role in maintaining normal growth of the basal cell layer and may also participate in reepithelialization during wound repair. Images PMID:2452837

Establishment of a rat hepatoma-derived cell line proliferating in D-phenylalanine medium and expressing D-amino-acid oxidase.

PubMed

Yoda, N; Konno, R; Nagashima, S

2001-01-01

A cell line (R-Y121B.DF) has been established from a cell line (R-Y121B) derived from a rat hepatoma line (H4-II-E). The R-Y121B.DF cells have been continuously cultured in a serum-free modified Eagle's minimum essential medium in which L-phenylalanine was replaced by D-phenylalanine. They had D-amino-acid oxidase (DAO) activity which is essential for the growth in the medium containing D-amino acids. The enzyme activity of the R-Y121B.DF cells was approximately one-fourth of that of the rat liver. Northern hybridization using a DAO cDNA probe detected a hybridizing signal in the R-Y121B.DF cells and the rat liver but not in the parental R-Y121B and H4-II-E cells. Reverse transcription-polymerase chain reaction using DAO-specific primers amplified a DNA fragment of the expected size in the R-Y121B.DF cells but not in the R-Y121B and H4-II-E cells. This fragment was confirmed to be DAO cDNA by nucleotide sequencing. Western blotting showed that DAO protein was present in the R-Y121B.DF cells and the rat liver but not in the R-Y121B and H4-II-E cells. Southern hybridization showed that the DAO gene structure was not different among the R-Y121B.DF cells, R-Y121B cells, H4-II-E cells, and the rat liver. These results indicate that the R-Y121B.DF is a unique cell line which proliferates in the medium containing D-phenylalanine and explicitly expresses DAO. This line is useful for the study of DAO in vitro.

A Simple Model System to Demonstrate Antibody Structure and Functions.

ERIC Educational Resources Information Center

O'Kennedy, Richard

1991-01-01

A model that can be used to show the arrangement of light and heavy chains, disulfide linkages, domains, and subclass variations in antibodies is given. It can be constructed and modified to illustrate Fab, F(ab')2, and Fc fragments, single domain and bifunctional antibodies, and labeling of antibodies. (Author)

Binary full adder, made of fusion gates, in a subexcitable Belousov-Zhabotinsky system

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

2015-09-01

In an excitable thin-layer Belousov-Zhabotinsky (BZ) medium a localized perturbation leads to the formation of omnidirectional target or spiral waves of excitation. A subexcitable BZ medium responds to asymmetric local perturbation by producing traveling localized excitation wave-fragments, distant relatives of dissipative solitons. The size and life span of an excitation wave-fragment depend on the illumination level of the medium. Under the right conditions the wave-fragments conserve their shape and velocity vectors for extended time periods. I interpret the wave-fragments as values of Boolean variables. When two or more wave-fragments collide they annihilate or merge into a new wave-fragment. States of the logic variables, represented by the wave-fragments, are changed in the result of the collision between the wave-fragments. Thus, a logical gate is implemented. Several theoretical designs and experimental laboratory implementations of Boolean logic gates have been proposed in the past but little has been done cascading the gates into binary arithmetical circuits. I propose a unique design of a binary one-bit full adder based on a fusion gate. A fusion gate is a two-input three-output logical device which calculates the conjunction of the input variables and the conjunction of one input variable with the negation of another input variable. The gate is made of three channels: two channels cross each other at an angle, a third channel starts at the junction. The channels contain a BZ medium. When two excitation wave-fragments, traveling towards each other along input channels, collide at the junction they merge into a single wave-front traveling along the third channel. If there is just one wave-front in the input channel, the front continues its propagation undisturbed. I make a one-bit full adder by cascading two fusion gates. I show how to cascade the adder blocks into a many-bit full adder. I evaluate the feasibility of my designs by simulating the evolution of excitation in the gates and adders using the numerical integration of Oregonator equations.

Addition of sphingosine-1-phosphate to human oocyte culture medium decreases embryo fragmentation.

PubMed

Hannoun, Antoine; Ghaziri, Ghina; Abu Musa, Antoine; Zreik, Tony G; Hajameh, Fatiha; Awwad, Johnny

2010-03-01

Apoptosis is implicated in the fragmentation of preimplantation mammalian embryos, yet the extent of this association remains controversial. The aim of this study was to assess the ability of sphingosine-1-phosphate (S1P), a known anti-apoptotic substance, to reduce the fragmentation rate of human preimplantation embryos when added to their culture microenvironment. Mature human oocytes were inseminated using intracytoplasmic sperm injection, incubated for 3 days and evaluated for embryo quality and fragmentation by the same embryologist. Oocytes in the study group were manipulated and cultured in culture medium supplemented with S1P to a 20 micromol/l concentration. A total of 46 patients donated 177 mature oocytes for the study group and 546 oocytes for the control group. The fertilization rate was significantly lower in the S1P-supplemented group (52.4% versus 67.3%; P=0.002) and the proportion of grade I embryos with less than 15% fragmentation was significantly higher in the same group (79.5% versus 53.9%; P<0.0001). Sphingosine-1-phosphate added to the culture medium of human preimplantation embryos is associated with a significantly lower fragmentation rate and hence better quality embryos. The clinical significance of these findings on reproductive outcome remains highly speculative awaiting further studies to translate this improvement in embryo quality into better pregnancy rates. Copyright 2009 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Examination of the relevance of hydrodynamics for data measured at the BNL relativistic heavy ion collider

NASA Astrophysics Data System (ADS)

Trainor, Thomas A.

2010-08-01

Hydrodynamic (hydro) models applied to heavy ion data from the relativistic heavy ion collider (RHIC) suggest that a dense QCD medium nearly opaque to partons—a strongly coupled quark-gluon plasma—is formed in more-central Au-Au collisions and may have a small viscosity ('perfect liquid'). Claimed evidence for radial and elliptic flows and possible coalescence of 'constituent quarks' seems to support the conclusion. But other measurements provide contradictory evidence. Unbiased angular correlations indicate that most back-to-back jets from initial-state scattered partons with energies as low as 3 GeV survive as 'minijet' hadron correlations even in central Au-Au collisions, suggesting near transparency. Two-component analysis of single-particle spectra reveals a spectrum hard component (parton fragment distribution) which can be mistaken for 'radial flow' in some forms of analysis. Based on recent results, reinterpretation of 'elliptic flow' as a QCD quadrupole scattering process including fragmentation may be possible. In this paper we review conventional analysis methods in the context of two paradigms: a hydrodynamics/hard-probes paradigm and a quadrupole/minijets paradigm. Re-examination of fiducial data suggests that hydrodynamics may not be relevant to RHIC collisions. Collision evolution may be dominated by QCD scattering and fragmentation, albeit strongly modified in more-central A-A collisions.

Modification and uptake of a cisplatin carbonato complex by Jurkat cells.

PubMed

Centerwall, Corey R; Tacka, Kirk A; Kerwood, Deborah J; Goodisman, Jerry; Toms, Bonnie B; Dubowy, Ronald L; Dabrowiak, James C

2006-07-01

The interactions of Jurkat cells with cisplatin, cis-[Pt(15NH3)2Cl2]1, are studied using 1H-15N heteronuclear single quantum coherence (HSQC) NMR and inductively coupled plasma mass spectrometry. We show that Jurkat cells in culture rapidly modify the monocarbonato complex cis-[Pt(15NH3)2(CO3)Cl]- (4), a cisplatin species that forms in culture media and probably also in blood. Analysis of the HSQC NMR peak intensity for 4 in the presence of different numbers of Jurkat cells reveals that each cell is capable of modifying 0.0028 pmol of 4 within approximately 0.6 h. The amounts of platinum taken up by the cell, weakly bound to the cell surface, remaining in the culture medium, and bound to genomic DNA were measured as functions of time of exposure to different concentrations of drug. The results show that most of the 4 that has been modified by the cells remains in the culture medium as a substance of molecular mass <3 kDa, which is HSQC NMR silent, and is not taken up by the cell. These results are consistent with a hitherto undocumented extracellular detoxification mechanism in which the cells rapidly modify 4, which is present in the culture medium, so it cannot bind to the cell. Because there is only a slow decrease in the amount of unmodified 4 remaining in the culture medium after 1 h, -1.1 +/- 0.4 microM h(-1), the cells subsequently lose their ability to modify 4. These observations have important implications for the mechanism of action of cisplatin.

A recombinant estrogen receptor fragment-based homogeneous fluorescent assay for rapid detection of estrogens.

PubMed

Wang, Dan; Xie, Jiangbi; Zhu, Xiaocui; Li, Jinqiu; Zhao, Dongqin; Zhao, Meiping

2014-05-15

In this work, we demonstrate a novel estrogenic receptor fragment-based homogeneous fluorescent assay which enables rapid and sensitive detection of 17β-estradiol (E2) and other highly potent estrogens. A modified human estrogenic receptor fragment (N-His × 6-hER270-595-C-Strep tag II) has been constructed that contains amino acids 270-595 of wild-type human estrogenic receptor α (hER270-595) and two specific tags (6 × His and Strep tag II) fused to the N and C terminus, respectively. The designed receptor protein fragment could be easily produced by prokaryotic expression with high yield and high purity. The obtained protein exhibits high binding affinity to E2 and the two tags greatly facilitate the application of the recombinant protein. Taking advantage of the unique spectroscopic properties of coumestrol (CS), a fluorescent phytoestrogen, a CS/hER270-595-based fluorescent assay has been developed which can sensitively respond to E2 within 1.0 min with a linear working range from 0.1 to 20 ng/mL and a limit of detection of 0.1 ng/mL. The assay was successfully applied for rapid detection of E2 in the culture medium of rat hippocampal neurons. The method also holds great potential for high-throughput monitoring the variation of estrogen levels in complex biological fluids, which is crucial for investigation of the molecular basis of various estrogen-involved processes. Copyright © 2013 Elsevier B.V. All rights reserved.

Breast Cancer Cell Colonization of the Human Bone Marrow Adipose Tissue Niche.

PubMed

Templeton, Zach S; Lie, Wen-Rong; Wang, Weiqi; Rosenberg-Hasson, Yael; Alluri, Rajiv V; Tamaresis, John S; Bachmann, Michael H; Lee, Kitty; Maloney, William J; Contag, Christopher H; King, Bonnie L

2015-12-01

Bone is a preferred site of breast cancer metastasis, suggesting the presence of tissue-specific features that attract and promote the outgrowth of breast cancer cells. We sought to identify parameters of human bone tissue associated with breast cancer cell osteotropism and colonization in the metastatic niche. Migration and colonization patterns of MDA-MB-231-fLuc-EGFP (luciferase-enhanced green fluorescence protein) and MCF-7-fLuc-EGFP breast cancer cells were studied in co-culture with cancellous bone tissue fragments isolated from 14 hip arthroplasties. Breast cancer cell migration into tissues and toward tissue-conditioned medium was measured in Transwell migration chambers using bioluminescence imaging and analyzed as a function of secreted factors measured by multiplex immunoassay. Patterns of breast cancer cell colonization were evaluated with fluorescence microscopy and immunohistochemistry. Enhanced MDA-MB-231-fLuc-EGFP breast cancer cell migration to bone-conditioned versus control medium was observed in 12/14 specimens (P = .0014) and correlated significantly with increasing levels of the adipokines/cytokines leptin (P = .006) and IL-1β (P = .001) in univariate and multivariate regression analyses. Fluorescence microscopy and immunohistochemistry of fragments underscored the extreme adiposity of adult human bone tissues and revealed extensive breast cancer cell colonization within the marrow adipose tissue compartment. Our results show that breast cancer cells migrate to human bone tissue-conditioned medium in association with increasing levels of leptin and IL-1β, and colonize the bone marrow adipose tissue compartment of cultured fragments. Bone marrow adipose tissue and its molecular signals may be important but understudied components of the breast cancer metastatic niche. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Modified PEHPS medium as an alternative for the in vitro culture of Giardia lamblia.

PubMed

Vargas-Villarreal, Javier; Mata-Cárdenas, Benito D; Hernández-García, Magda E; Garza-González, Jesús N; De La Garza-Salinas, Laura H; González-Salazar, Francisco

2014-01-01

Commercial culture media present interlot variations in biological activity. We have previously designed a homemade and economic culture medium, PEHPS medium, for the axenic cultivation of Entamoeba histolytica and Trichomonas vaginalis. Trophozoites of amoebae and trichomonads grow well in this medium. Furthermore, the medium is stable for several months when stored frozen or refrigerated. The objective of this work was to modify PEHPS medium to support the in vitro growth of Giardia lamblia. Inocula of 5 × 10(3) trophozoites/mL of G. lamblia were incubated at 36.5°C in modified PEHPS or TYI-S-33 medium. Then, the growths of the three Giardia strains in both media were compared. The logarithmic growth phase lasted 72 h; the mean yield of the strains ranged from 10.06 to 11.43 × 10(5) Giardia trophozoites/mL, and the range of duplication time in the three strains was from 5.67 to 6.06 in modified PEHPS medium. These growth characteristics were not significantly different from those obtained with TYI-S-33 medium. We conclude that modified PEHPS medium might be used for the axenic cultivation of G. lamblia.

Effect of culture medium, host strain and oxygen transfer on recombinant Fab antibody fragment yield and leakage to medium in shaken E. coli cultures.

PubMed

Ukkonen, Kaisa; Veijola, Johanna; Vasala, Antti; Neubauer, Peter

2013-07-29

Fab antibody fragments in E. coli are usually directed to the oxidizing periplasmic space for correct folding. From periplasm Fab fragments may further leak into extracellular medium. Information on the cultivation parameters affecting this leakage is scarce, and the unpredictable nature of Fab leakage is problematic regarding consistent product recovery. To elucidate the effects of cultivation conditions, we investigated Fab expression and accumulation into either periplasm or medium in E. coli K-12 and E. coli BL21 when grown in different types of media and under different aeration conditions. Small-scale Fab expression demonstrated significant differences in yield and ratio of periplasmic to extracellular Fab between different culture media and host strains. Expression in a medium with fed-batch-like glucose feeding provided highest total and extracellular yields in both strains. Unexpectedly, cultivation in baffled shake flasks at 150 rpm shaking speed resulted in higher yield and accumulation of Fabs into culture medium as compared to cultivation at 250 rpm. In the fed-batch medium, extracellular fraction in E. coli K-12 increased from 2-17% of total Fab at 250 rpm up to 75% at 150 rpm. This was partly due to increased lysis, but also leakage from intact cells increased at the lower shaking speed. Total Fab yield in E. coli BL21 in glycerol-based autoinduction medium was 5 to 9-fold higher at the lower shaking speed, and the extracellular fraction increased from ≤ 10% to 20-90%. The effect of aeration on Fab localization was reproduced in multiwell plate by variation of culture volume. Yield and leakage of Fab fragments are dependent on expression strain, culture medium, aeration rate, and the combination of these parameters. Maximum productivity in fed-batch-like conditions and in autoinduction medium is achieved under sufficiently oxygen-limited conditions, and lower aeration also promotes increased Fab accumulation into extracellular medium. These findings have practical implications for screening applications and small-scale Fab production, and highlight the importance of maintaining consistent aeration conditions during scale-up to avoid changes in product yield and localization. On the other hand, the dependency of Fab leakage on cultivation conditions provides a practical way to manipulate Fab localization.

Effect of culture medium, host strain and oxygen transfer on recombinant Fab antibody fragment yield and leakage to medium in shaken E. coli cultures

PubMed Central

2013-01-01

Background Fab antibody fragments in E. coli are usually directed to the oxidizing periplasmic space for correct folding. From periplasm Fab fragments may further leak into extracellular medium. Information on the cultivation parameters affecting this leakage is scarce, and the unpredictable nature of Fab leakage is problematic regarding consistent product recovery. To elucidate the effects of cultivation conditions, we investigated Fab expression and accumulation into either periplasm or medium in E. coli K-12 and E. coli BL21 when grown in different types of media and under different aeration conditions. Results Small-scale Fab expression demonstrated significant differences in yield and ratio of periplasmic to extracellular Fab between different culture media and host strains. Expression in a medium with fed-batch-like glucose feeding provided highest total and extracellular yields in both strains. Unexpectedly, cultivation in baffled shake flasks at 150 rpm shaking speed resulted in higher yield and accumulation of Fabs into culture medium as compared to cultivation at 250 rpm. In the fed-batch medium, extracellular fraction in E. coli K-12 increased from 2-17% of total Fab at 250 rpm up to 75% at 150 rpm. This was partly due to increased lysis, but also leakage from intact cells increased at the lower shaking speed. Total Fab yield in E. coli BL21 in glycerol-based autoinduction medium was 5 to 9-fold higher at the lower shaking speed, and the extracellular fraction increased from ≤ 10% to 20-90%. The effect of aeration on Fab localization was reproduced in multiwell plate by variation of culture volume. Conclusions Yield and leakage of Fab fragments are dependent on expression strain, culture medium, aeration rate, and the combination of these parameters. Maximum productivity in fed-batch-like conditions and in autoinduction medium is achieved under sufficiently oxygen-limited conditions, and lower aeration also promotes increased Fab accumulation into extracellular medium. These findings have practical implications for screening applications and small-scale Fab production, and highlight the importance of maintaining consistent aeration conditions during scale-up to avoid changes in product yield and localization. On the other hand, the dependency of Fab leakage on cultivation conditions provides a practical way to manipulate Fab localization. PMID:23895637

Mass Extinction and the Disappearance of Unknown Mammal Species: Scenario and Perspectives of a Biodiversity Hotspot’s Hotspot

PubMed Central

Mendes Pontes, Antonio Rossano; Beltrão, Antonio Carlos Mariz; Normande, Iran Campello; Malta, Alexandre de Jesus Rodrigues; da Silva Júnior, Antonio Paulo; Santos, André Maurício Melo

2016-01-01

We aimed to determine the conservation status of medium- and large-sized mammals and evaluate the impact of 500 years of forest fragmentation on this group of animals in the Pernambuco Endemism Center, in the biogeographical zone of the Atlantic forest north of the São Francisco River in northeastern Brazil. Line transect surveys were performed in 21 forest fragments, resulting in a checklist of the mammals of the entire Pernambuco Endemism Center area. We ran a generalized linear model (Factorial ANCOVA) to analyze to what extent the vegetation type, fragment area, isolation, sampling effort (as total kilometers walked), or higher-order interactions predicted (a) richness and (b) sighting rates. To determine if the distribution of the species within the forest fragments exhibited a nested pattern, we used the NODF metric. Subsequently, we performed a Binomial Logistic Regression to predict the probability of encountering each species according to fragment size. Out of 38 medium- and large-sized mammal species formerly occurring in the study area, only 53.8% (n = 21) were sighted. No fragment hosted the entire remaining mammal community, and only four species (19%) occurred in very small fragments (73.3% of the remaining forest fragments, with a mean size of 2.8 ha). The mammalian community was highly simplified, with all large mammals being regionally extinct. Neither the species richness nor sighting rate was controlled by the vegetation type, the area of the forest fragments, isolation or any higher-order interaction. Although a highly significant nested subset pattern was detected, it was not related to the ranking of the area of forest fragments or isolation. The probability of the occurrence of a mammal species in a given forest patch varied unpredictably, and the probability of detecting larger species was even observed to decrease with increasing patch size. In an ongoing process of mass extinction, half of the studied mammals have gone extinct. The remaining medium-sized mammal community is highly simplified and homogenized. The persistence of these species in a forest patch is determined by their ability to adapt to a novel simplified diet, the efficient use of the surrounding matrix without being engulfed by the sink effect, and escaping hunting. Our results suggest that the 21st century medium-sized mammalian fauna of this region will comprise only four species unless strict conservation measures are implemented immediately and every forest fragment is effectively protected. PMID:27191719

Mass Extinction and the Disappearance of Unknown Mammal Species: Scenario and Perspectives of a Biodiversity Hotspot's Hotspot.

PubMed

Mendes Pontes, Antonio Rossano; Beltrão, Antonio Carlos Mariz; Normande, Iran Campello; Malta, Alexandre de Jesus Rodrigues; Silva Júnior, Antonio Paulo da; Santos, André Maurício Melo

2016-01-01

We aimed to determine the conservation status of medium- and large-sized mammals and evaluate the impact of 500 years of forest fragmentation on this group of animals in the Pernambuco Endemism Center, in the biogeographical zone of the Atlantic forest north of the São Francisco River in northeastern Brazil. Line transect surveys were performed in 21 forest fragments, resulting in a checklist of the mammals of the entire Pernambuco Endemism Center area. We ran a generalized linear model (Factorial ANCOVA) to analyze to what extent the vegetation type, fragment area, isolation, sampling effort (as total kilometers walked), or higher-order interactions predicted (a) richness and (b) sighting rates. To determine if the distribution of the species within the forest fragments exhibited a nested pattern, we used the NODF metric. Subsequently, we performed a Binomial Logistic Regression to predict the probability of encountering each species according to fragment size. Out of 38 medium- and large-sized mammal species formerly occurring in the study area, only 53.8% (n = 21) were sighted. No fragment hosted the entire remaining mammal community, and only four species (19%) occurred in very small fragments (73.3% of the remaining forest fragments, with a mean size of 2.8 ha). The mammalian community was highly simplified, with all large mammals being regionally extinct. Neither the species richness nor sighting rate was controlled by the vegetation type, the area of the forest fragments, isolation or any higher-order interaction. Although a highly significant nested subset pattern was detected, it was not related to the ranking of the area of forest fragments or isolation. The probability of the occurrence of a mammal species in a given forest patch varied unpredictably, and the probability of detecting larger species was even observed to decrease with increasing patch size. In an ongoing process of mass extinction, half of the studied mammals have gone extinct. The remaining medium-sized mammal community is highly simplified and homogenized. The persistence of these species in a forest patch is determined by their ability to adapt to a novel simplified diet, the efficient use of the surrounding matrix without being engulfed by the sink effect, and escaping hunting. Our results suggest that the 21st century medium-sized mammalian fauna of this region will comprise only four species unless strict conservation measures are implemented immediately and every forest fragment is effectively protected.

Regulation of macrophage migration by products of the complement system.

PubMed Central

Bianco, C; Götze, O; Cohn, Z A

1979-01-01

Agents formerly shown to induce rapid macrophage spreading were examined for their ability to modify the migration of macrophages in the capillary tube assay. Products of the activation of the contact phase of blood coagulation as well as the purified component Bb, the large cleavage fragment of factor B of the alternative complement pathway produced a dose-dependent inhibition of migration. In addition, inflammatory macrophages elicited with either a lipopolysaccharide endotoxin or thioglycollate medium exhibited rapid spreading and inhibited migration, whereas resident cells did not. A close correlation existed, therefore, between enhanced spreading and inhibited migration under both in vitro induced and in vivo situations. Cleavage products of component C5 of the classical complement pathway enhanced macrophage migration and did not alter spreading. In mixtures of C5 cleavage products and Bb, the predominant peptide determined the outcome of the reaction. Factor B, a normal secretory product of macrophages, may represent a common substrate for several of the proteases that induce spreading, inhibit migration, and lead to the generation of the enzymatically active fragment Bb. PMID:284412

Increased dipicolinic acid production with an enhanced spoVF operon in Bacillus subtilis and medium optimization.

PubMed

Takahashi, Fumikazu; Sumitomo, Nobuyuki; Hagihara, Hiroshi; Ozaki, Katsuya

2015-01-01

Dipicolinic acid (DPA) is a multi-functional agent for cosmetics, antimicrobial products, detergents, and functional polymers. The aim of this study was to design a new method for producing DPA from renewable material. The Bacillus subtilis spoVF operon encodes enzymes for DPA synthase and the part of lysine biosynthetic pathway. However, DPA is only synthesized in the sporulation phase, so the productivity of DPA is low level. Here, we report that DPA synthase was expressed in vegetative cells, and DPA was produced in the culture medium by replacement of the spoVFA promoter with other highly expressed promoter in B. subtilis vegetative cells, such as spoVG promoter. DPA levels were increased in the culture medium of genetically modified strains. DPA productivity was significantly improved up to 29.14 g/L in 72 h culture by improving the medium composition using a two-step optimization technique with the Taguchi methodology.

Drug screens based on the newly found role of dystroglycan proteolysis and restoration of dystroglycan function thereof

DOEpatents

Bissell, Mina J.; Muschler, John L.

2010-02-23

The present invention provides methods and compositions for the diagnosis and treatment of cells lacking normal growth arresting characteristic. The present invention demonstrates that many tumor cells lack normal cell surface .alpha.-dystroglycan and thereby lack dystroglycan function. Dystroglycan can be lost from the cell surface by proteolytic shedding of a fragment of .alpha.-dystroglycan into the surrounding medium. Upon restoration of dystroglycan function and over-expression of the dystroglycan gene, the once tumorigenic cells revert to non-tumorigenic cells which polarize and arrest cell growth in the presence of basement membrane proteins, demonstrating that dystroglycan functions as a tumor marker and suppressor.

Optical properties of medium size noble and transition metal nanoparticles

NASA Astrophysics Data System (ADS)

Idrobo, Juan C.; Pantelides, Sokrates T.

2009-03-01

Using first-principles methods within time dependent density functional theory and the local density approximation (TDLDA) the absorption spectra of medium size (˜20-80 atoms) silver, gold and copper nanoparticles have been calculated. The nanoparticles are fcc fragments with different aspect ratios. We find that in the case of Ag nanoparticles is well reproduced by classical electrodynamics theory based in Mie's formalism, using the dielectric function of bulk Ag and taking into account the nanoparticle shape. For the case of Cu and Au, there is a similarity in the overall features of the quantum mechanical and classical spectra, but no detailed agreement. We will discuss the role that the d-electrons among all the different elements and the surface states play in controlling the optical properties of the nanoparticles. This work was supported by GOALI NSF grant (DMR-0513048), DOE, the Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, and Alcoa Inc.

Identification of ubiquitin/ubiquitin-like protein modification from tandem mass spectra with various PTMs

PubMed Central

2011-01-01

Background Various solutions have been introduced for the identification of post-translational modification (PTM) from tandem mass spectrometry (MS/MS) in proteomics field but the identification of peptide modifiers, such as Ubiquitin (Ub) and ubiquitin-like proteins (Ubls), is still a challenge. The fragmentation of peptide modifier produce complex shifted ion mass patterns in combination with other PTMs, which makes it difficult to identify and locate the PTMs on a protein sequence. Currently, most PTM identification methods do not consider the complex fragmentation of peptide modifier or deals it separately from the other PTMs. Results We developed an advanced PTM identification method that inspects possible ion patterns of the most known peptide modifiers as well as other known biological and chemical PTMs to make more comprehensive and accurate conclusion. The proposed method searches all detectable mass differences of measured peaks from their theoretical values and the mass differences within mass tolerance range are grouped as mass shift classes. The most possible locations of multiple PTMs including peptide modifiers can be determined by evaluating all possible scenarios generated by the combination of the qualified mass shift classes.The proposed method showed excellent performance in the test with simulated spectra having various PTMs including peptide modifiers and in the comparison with recently developed methods such as QuickMod and SUMmOn. In the analysis of HUPO Brain Proteome Project (BPP) datasets, the proposed method could find the ubiquitin modification sites that were not identified by other conventional methods. Conclusions This work presents a novel method for identifying bothpeptide modifiers that generate complex fragmentation patternsand PTMs that are not fragmented during fragmentation processfrom tandem mass spectra. PMID:22373085

Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria.

PubMed

Hansen, M A; Kirpekar, F; Ritterbusch, W; Vester, B

2002-02-01

Posttranscriptional modifications were mapped in helices 90-92 of 23S rRNA from the following phylogenetically diverse organisms: Haloarcula marismortui, Sulfolobus acidocaldarius, Bacillus subtilis, and Bacillus stearothermophilus. Helix 92 is a component of the ribosomal A-site, which contacts the aminoacyl-tRNA during protein synthesis, implying that posttranscriptional modifications in helices 90-92 may be important for ribosome function. RNA fragments were isolated from 23S rRNA by site-directed RNase H digestion. A novel method of mapping modifications by analysis of short, nucleotide-specific, RNase digestion fragments with Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) was utilized. The MALDI-MS data were complemented by two primer extension techniques using reverse transcriptase. One technique utilizes decreasing concentrations of deoxynucleotide triphosphates to map 2'-O-ribose methylations. In the other, the rRNA is chemically modified, followed by mild alkaline hydrolysis to map pseudouridines (psis). A total of 10 posttranscriptionally methylated nucleotides and 6 psis were detected in the five organisms. Eight of the methylated nucleotides and one psi have not been reported previously. The distribution of modified nucleotides and their locations on the surface of the ribosomal peptidyl transferase cleft suggests functional importance.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes.

PubMed

Cisneros, Laura M; Fagan, Matthew E; Willig, Michael R

2016-01-01

Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

PubMed Central

Fagan, Matthew E.; Willig, Michael R.

2016-01-01

Background Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. Methods We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. Results The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Discussion Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space. PMID:27761338

Kinetics of a Migration-Driven Aggregation-Fragmentation Process

NASA Astrophysics Data System (ADS)

Zhuang, You-Yi; Lin, Zhen-Quan; Ke, Jian-Hong

2003-08-01

We propose a reversible model of the migration-driven aggregation-fragmentation process with the symmetric migration rate kernels K(k;j)=K^'(k;j)=λ kj^v and the constant aggregation rates I1, I2 and fragmentation rates J1, J2. Based on the mean-field theory, we investigate the evolution behavior of the aggregate size distributions in several cases with different values of index υ. We find that the fragmentation reaction plays a more important role in the kinetic behaviors of the system than the aggregation and migration. When J1=0 and J2 =0, the aggregate size distributions ak(t) and bk(t) obey the conventional scaling law, while when J1>0 and J2>0, they obey the modified scaling law with an exponential scaling function. The total mass of either species remains conserved. The project supported by National Natural Science Foundation of China under Grant Nos. 10275048 and 10175008, and Natural Science Foundation of Zhejiang Province of China under Grant No. 102067

M1.3 - a small scaffold for DNA origami

NASA Astrophysics Data System (ADS)

Said, Hassan; Schüller, Verena J.; Eber, Fabian J.; Wege, Christina; Liedl, Tim; Richert, Clemens

2012-12-01

The DNA origami method produces programmable nanoscale objects that form when one long scaffold strand hybridizes to numerous oligonucleotide staple strands. One scaffold strand is dominating the field: M13mp18, a bacteriophage-derived vector 7249 nucleotides in length. The full-length M13 is typically folded by using over 200 staple oligonucleotides. Here we report the convenient preparation of a 704 nt fragment dubbed ``M1.3'' as a linear or cyclic scaffold and the assembly of small origami structures with just 15-24 staple strands. A typical M1.3 origami is large enough to be visualized by TEM, but small enough to show a cooperativity in its assembly and thermal denaturation that is reminiscent of oligonucleotide duplexes. Due to its medium size, M1.3 origami with globally modified staples is affordable. As a proof of principle, two origami structures with globally 5'-capped staples were prepared and were shown to give higher UV-melting points than the corresponding assembly with unmodified DNA. M1.3 has the size of a gene, not a genome, and may function as a model for gene-based nanostructures. Small origami with M1.3 as a scaffold may serve as a workbench for chemical, physical, and biological experiments.The DNA origami method produces programmable nanoscale objects that form when one long scaffold strand hybridizes to numerous oligonucleotide staple strands. One scaffold strand is dominating the field: M13mp18, a bacteriophage-derived vector 7249 nucleotides in length. The full-length M13 is typically folded by using over 200 staple oligonucleotides. Here we report the convenient preparation of a 704 nt fragment dubbed ``M1.3'' as a linear or cyclic scaffold and the assembly of small origami structures with just 15-24 staple strands. A typical M1.3 origami is large enough to be visualized by TEM, but small enough to show a cooperativity in its assembly and thermal denaturation that is reminiscent of oligonucleotide duplexes. Due to its medium size, M1.3 origami with globally modified staples is affordable. As a proof of principle, two origami structures with globally 5'-capped staples were prepared and were shown to give higher UV-melting points than the corresponding assembly with unmodified DNA. M1.3 has the size of a gene, not a genome, and may function as a model for gene-based nanostructures. Small origami with M1.3 as a scaffold may serve as a workbench for chemical, physical, and biological experiments. Electronic supplementary information (ESI) available: Materials, full sequence of M1.3, alternative restriction reactions, sequences and origami designs, ALEX data, estimated cost of producing M13, additional melting data for origami, and MALDI spectra of individual capped oligonucleotides. See DOI: 10.1039/c2nr32393a

Precise Sequential DNA Ligation on A Solid Substrate: Solid-Based Rapid Sequential Ligation of Multiple DNA Molecules

PubMed Central

Takita, Eiji; Kohda, Katsunori; Tomatsu, Hajime; Hanano, Shigeru; Moriya, Kanami; Hosouchi, Tsutomu; Sakurai, Nozomu; Suzuki, Hideyuki; Shinmyo, Atsuhiko; Shibata, Daisuke

2013-01-01

Ligation, the joining of DNA fragments, is a fundamental procedure in molecular cloning and is indispensable to the production of genetically modified organisms that can be used for basic research, the applied biosciences, or both. Given that many genes cooperate in various pathways, incorporating multiple gene cassettes in tandem in a transgenic DNA construct for the purpose of genetic modification is often necessary when generating organisms that produce multiple foreign gene products. Here, we describe a novel method, designated PRESSO (precise sequential DNA ligation on a solid substrate), for the tandem ligation of multiple DNA fragments. We amplified donor DNA fragments with non-palindromic ends, and ligated the fragment to acceptor DNA fragments on solid beads. After the final donor DNA fragments, which included vector sequences, were joined to the construct that contained the array of fragments, the ligation product (the construct) was thereby released from the beads via digestion with a rare-cut meganuclease; the freed linear construct was circularized via an intra-molecular ligation. PRESSO allowed us to rapidly and efficiently join multiple genes in an optimized order and orientation. This method can overcome many technical challenges in functional genomics during the post-sequencing generation. PMID:23897972

Strategy to obtain axenic cultures from field-collected samples of the cyanobacterium Phormidium animalis.

PubMed

Vázquez-Martínez, Guadalupe; Rodriguez, Mario H; Hernández-Hernández, Fidel; Ibarra, Jorge E

2004-04-01

An efficient strategy, based on a combination of procedures, was developed to obtain axenic cultures from field-collected samples of the cyanobacterium Phormidium animalis. Samples were initially cultured in solid ASN-10 medium, and a crude separation of major contaminants from P. animalis filaments was achieved by washing in a series of centrifugations and resuspensions in liquid medium. Then, manageable filament fragments were obtained by probe sonication. Fragmentation was followed by forceful washing, using vacuum-driven filtration through an 8-microm pore size membrane and an excess of water. Washed fragments were cultured and treated with a sequential exposure to four different antibiotics. Finally, axenic cultures were obtained from serial dilutions of treated fragments. Monitoring under microscope examination and by inoculation in Luria-Bertani (LB) agar plates indicated either axenicity or the degree of contamination throughout the strategy.

Critical reappraisal of embryo quality as a predictive parameter for pregnancy outcome: a pilot study.

PubMed

Campo, R; Binda, M M; Van Kerkhoven, G; Frederickx, V; Serneels, A; Roziers, P; Lopes, A S; Gordts, S; Puttemans, P; Gordts, S

2010-01-01

Pilot study to analyse the efficacy and embryo morphology using a new human embryo culture medium (GM501) versus the conventional used medium (ISM1). Over a four-month period, all patients at the Leuven Institute of Fertility and Embryology (LIFE) were -randomly allocated to have their embryos cultured in either the standard sequential culture medium ISM1 (control) or in a new universal medium (GM501) (study group). Primary outcome parameters were clinical pregnancy and live birth rate. The secondary outcome parameter was the correlation of embryo fragmentation rate with pregnancy outcome. We did not observe any differences between the ISM1 control group and GM501 study group with regard to fertilization, pregnancy, implantation rates, ongoing pregnancy, and babies born. The number of embryos with a minimal fragmentation rate (less than 30%) was significantly higher in the GM501 study group. Although a significant higher embryo fragmentation rate was seen in In vitro culture of embryos in GM501, pregnancy outcome results were comparable to those of embryos cultured in ISM1. According to our results the value of embryo morphological criteria as a parameter for pregnancy outcome should be examined and discussed again.

Lipases as biocatalysts for the synthesis of structured lipids.

PubMed

Jala, Ram Chandra Reddy; Hu, Peng; Yang, Tiankui; Jiang, Yuanrong; Zheng, Yan; Xu, Xuebing

2012-01-01

Structured lipids (SL) are broadly referred to as modified or synthetic oils and fats or lipids with functional or pharmaceutical applications. Some structured lipids, such as triglycerides that contain both long-chain (mainly essential) fatty acids and medium- or short-chain fatty acids and also artificial products that mimic the structure of natural materials, namely human milk fat substitutes and cocoa butter equivalents, have been discussed. Further, other modified or synthetic lipids, such as structured phospholipids and synthetic phenolic lipids are also included in this chapter. For all the products described in this chapter, enzymatic production in industry has been already conducted in one way or another. Cocoa butter equivalents, healthy oil containing medium-chain fatty acids, phosphatidyl serine, and phenol lipids from enzyme technology have been reported for commercial operation. As the demand for better quality functional lipids is increasing, the production of structured lipids becomes an interesting area. Thus, in this chapter we have discussed latest developments as well as present industrial situation of all commercially important structured lipids.

Secreted Amyloid β-Proteins in a Cell Culture Model Include N-Terminally Extended Peptides That Impair Synaptic Plasticity

PubMed Central

2014-01-01

Evidence for a central role of amyloid β-protein (Aβ) in the genesis of Alzheimer’s disease (AD) has led to advanced human trials of Aβ-lowering agents. The “amyloid hypothesis” of AD postulates deleterious effects of small, soluble forms of Aβ on synaptic form and function. Because selectively targeting synaptotoxic forms of soluble Aβ could be therapeutically advantageous, it is important to understand the full range of soluble Aβ derivatives. We previously described a Chinese hamster ovary (CHO) cell line (7PA2 cells) that stably expresses mutant human amyloid precursor protein (APP). Here, we extend this work by purifying an sodium dodecyl sulfate (SDS)-stable, ∼8 kDa Aβ species from the 7PA2 medium. Mass spectrometry confirmed its identity as a noncovalently bonded Aβ40 homodimer that impaired hippocampal long-term potentiation (LTP) in vivo. We further report the detection of Aβ-containing fragments of APP in the 7PA2 medium that extend N-terminal from Asp1 of Aβ. These N-terminally extended Aβ-containing monomeric fragments are distinct from soluble Aβ oligomers formed from Aβ1-40/42 monomers and are bioactive synaptotoxins secreted by 7PA2 cells. Importantly, decreasing β-secretase processing of APP elevated these alternative synaptotoxic APP fragments. We conclude that certain synaptotoxic Aβ-containing species can arise from APP processing events N-terminal to the classical β-secretase cleavage site. PMID:24840308

Resonant electron capture by aspartame and aspartic acid molecules.

PubMed

Muftakhov, M V; Shchukin, P V

2016-12-30

The processes for dissociative electron capture are the key mechanisms for decomposition of biomolecules, proteins in particular, under interaction with low-energy electrons. Molecules of aspartic acid and aspartame, i.e. modified dipeptides, were studied herein to define the impact of the side functional groups on peptide chain decomposition in resonant electron-molecular reactions. The processes of formation and decomposition of negative ions of both aspartame and aspartic acid were studied by mass spectrometry of negative ions under resonant electron capture. The obtained mass spectra were interpreted under thermochemical analysis by quantum chemical calculations. Main channels of negative molecular ions fragmentation were found and characteristic fragment ions were identified. The СООН fragment of the side chain in aspartic acid is shown to play a key role like the carboxyl group in amino acids and aliphatic oligopeptides. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Adsorption of Cu(II), Hg(II), and Ni(II) ions by modified natural wool chelating fibers.

PubMed

Monier, M; Ayad, D M; Sarhan, A A

2010-04-15

The graft copolymerization of ethyl acrylate (EA) onto natural wool fibers initiated by potassium persulphate and Mohr's salt redox initiator system in limited aqueous medium was carried out in heterogeneous media. Ester groups of the grafted copolymers were partially converted into hydrazide function groups followed by hydrazone formation through reaction with isatin. Also the application of the modified fibers for metal ion uptake was studied using Cu(II), Hg(II) and Ni(II). The modified chelating fibers were characterized using FTIR spectroscopy, SEM and X-ray diffraction. 2009 Elsevier B.V. All rights reserved.

Pseudoscalar D and B mesons in the hot dense and nonstrange symmetric medium

NASA Astrophysics Data System (ADS)

Chhabra, Rahul; Kumar, Arvind

2017-01-01

We investigate the effect of temperature and density on the shift in the masses and decay constants of the pseudoscalar D and B mesons in the nonstrange symmetric medium. We use chiral SU(3) model to calculate the medium modified scalar and isoscalar fields σ, ζ, δ and χ. We use these modified fields to calculate the in-medium quark and gluon condensates by solving the coupled equations of motions in the chiral SU(3) model. We obtain the medium modified mass and decay constant through these medium modified condensates using the QCD sum rules. Further we use the 3P0 model by taking the internal structure of the mesons to calculate the in-medium decay width of the higher charmonium states χ(3556) , ψ(3686) and ψ(3770) to the D D pairs, through the in-medium mass of D meson and neglecting the mass modification of higher charmonium states. We also compare the present data with the previous results. These results of present investigation may be important to explain the possible outcomes of the experiments like CBM, Panda at GSI.

Carbon materials modified by plasma treatment as electrodes for supercapacitors

NASA Astrophysics Data System (ADS)

Lota, Grzegorz; Tyczkowski, Jacek; Kapica, Ryszard; Lota, Katarzyna; Frackowiak, Elzbieta

The carbon material was modified by RF plasma with various reactive gases: O 2, Ar and CO 2. Physicochemical properties of the final carbon products were characterized using different techniques such as gas adsorption method and XPS. Plasma modified materials enriched in oxygen functionalities were investigated as electrodes for supercapacitors in acidic medium. The electrochemical measurements have been carried out using cyclic voltammetry, galvanostatic charge/discharge and impedance spectroscopy. The electrochemical measurements have confirmed that capacity characteristics are closely connected with a type of plasma exposition. Modification processes have an influence on the kind and amount of surface functional groups in the carbon matrix. The moderate increase of capacity of carbon materials modified by plasma has been observed using symmetric two-electrode systems. Whereas investigations made in three-electrode system proved that the suitable selection of plasma modification parameters allows to obtain promising negative and positive electrode materials for supercapacitor application.

Evaluation of Cariogenic Bacteria

PubMed Central

Nishikawara, Fusao; Nomura, Yoshiaki; Imai, Susumu; Senda, Akira; Hanada, Nobuhiro

2007-01-01

Objectives The evaluation of Mutans streptococci (MS) is one of the index for caries risk. DentocultTM and CRTTM are commercial kits to detect and evaluate MS, conveniently. However, the evaluation of MS has also been carried out simply using an instruction manual. But the instruction manual is not easy to use for evaluation of MS. The aim of this study was to examine the utility of modified Mitis-Salivalius Bacitracin (MSB) agar medium compared with MSB agar medium and commercial kits, and to establish a convenient kit (mMSB-kit) using modified MSB agar. Methods The MS in stimulated saliva from 27 subjects were detected by MSB, modified MSB agar medium and commercial kits. Laboratory and clinically isolated strains of MS were similarly evaluated. The ratios of MS in detected bacteria were compared by ELISA. Results The scores using an mMSB-kit on the basis of modified MSB agar medium were tabulated. Saliva samples showed different levels of MS between culture methods and the commercial kit. Some samples which were full of MS were not detected by the commercial kit. The detection of MS by modified MSB agar medium and mMSB-kit were significantly higher when compared with MSB agar medium,CRTTM, (P< .01) and Dentocult SMTM (P<.05). Conclusion The sensitivity for detection of MS is higher for modified MSB agar medium when compared with MSB agar medium. The mMSB-kit can be used simply, and can be an important contributor for the evaluation of MS as a caries risk factor. PMID:19212495

High Fragmentation Steel Production Process

DTIC Science & Technology

1984-01-01

J/ FTA c« ;« MO G SO KM s s P WS W-U Hi ; T 14 434 CASK G S3 K 11 ma WM MM MM ACTS 1 TC*4 U S7« ill GC 135 V M NTA «M FT...relative feed range 2nd digit -relative force range FMd 1 Very Low Fore* t 2 Low 2 3 Medium Low 3 4 Medium 4 5 Medium 5 6 Medium High 6 7 Medium

Thickening compositions, and related materials and processes

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

O'Brien, Michael Joseph; Perry, Robert James; Enick, Robert Michael

A silicone polymer is provided, modified with at least one functional group from the class of anthraquinone amide groups; anthraquinone sulfonamide groups; thioxanthone amide groups; or thioxanthone sulfone amide groups. The polymer can be combined with a hydrocarbon solvent or with supercritical carbon dioxide (CO.sub.2), and is very effective for increasing the viscosity of either medium. A process for the recovery of oil from a subterranean, oil-bearing formation is also described, using supercritical carbon dioxide modified with the functionalized silicone polymer. A process for extracting natural gas or oil from a bedrock-shale formation is also described, again using the modifiedmore » silicone polymer.« less

Measurement of jet fragmentation in Pb+Pb and pp collisions at $$\\sqrt{s}$$$_ {NN}$$ = 2.76 TeV with the ATLAS detector at the LHC

DOE PAGES

Aaboud, M.; Aad, G.; Abbott, B.; ...

2017-06-08

The distributions of transverse momentum and longitudinal momentum fraction of charged particles in jets are measured in Pb+Pb and pp collisions with the ATLAS detector at the LHC. The distributions are measured as a function of jet transverse momentum and rapidity. The analysis utilises an integrated luminosity of 0.14 nb -1 of Pb+Pb data and 4.0 pb -1 of pp data collected in 2011 and 2013, respectively, at the same centre-of-mass energy of 2.76 TeV per colliding nucleon pair. The distributions measured in pp collisions are used as a reference for those measured in Pb+Pb collisions in order to evaluatemore » the impact on the internal structure of jets from the jet energy loss of fast partons propagating through the hot, dense medium created in heavy-ion collisions. Modest but significant centrality-dependent modifications of fragmentation functions in Pb+Pb collisions with respect to those in pp collisions are seen. Finally, no significant dependence of modifications on jet p T and rapidity selections is observed except for the fragments with the highest transverse momenta for which some reduction of yields is observed for more forward jets.« less

Critical reappraisal of embryo quality as a predictive parameter for pregnancy outcome: a pilot study

PubMed Central

Campo, R.; Binda, M.M.; Van Kerkhoven, G.; Frederickx, V.; Serneels, A.; Roziers, P.; Lopes, A.S.; Gordts, S.; Puttemans, P.; Gordts, S.

2010-01-01

Aim of the study: Pilot study to analyse the efficacy and embryo morphology using a new human embryo culture medium (GM501) versus the conventional used medium (ISM1). Methods: Over a four-month period, all patients at the Leuven Institute of Fertility and Embryology (LIFE) were randomly allocated to have their embryos cultured in either the standard sequential culture medium ISM1 (control) or in a new universal medium (GM501) (study group). Primary outcome parameters were clinical pregnancy and live birth rate. The secondary outcome parameter was the correlation of embryo fragmentation rate with pregnancy outcome. Results: We did not observe any differences between the ISM1 control group and GM501 study group with regard to fertilization, pregnancy, implantation rates, ongoing pregnancy, and babies born. The number of embryos with a minimal fragmentation rate (less than 30%) was significantly higher in the GM501 study group. Conclusion: Although a significant higher embryo fragmentation rate was seen in In vitro culture of embryos in GM501, pregnancy outcome results were comparable to those of embryos cultured in ISM1. According to our results the value of embryo morphological criteria as a parameter for pregnancy outcome should be examined and discussed again. PMID:25009716

Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria.

PubMed Central

Hansen, M A; Kirpekar, F; Ritterbusch, W; Vester, B

2002-01-01

Posttranscriptional modifications were mapped in helices 90-92 of 23S rRNA from the following phylogenetically diverse organisms: Haloarcula marismortui, Sulfolobus acidocaldarius, Bacillus subtilis, and Bacillus stearothermophilus. Helix 92 is a component of the ribosomal A-site, which contacts the aminoacyl-tRNA during protein synthesis, implying that posttranscriptional modifications in helices 90-92 may be important for ribosome function. RNA fragments were isolated from 23S rRNA by site-directed RNase H digestion. A novel method of mapping modifications by analysis of short, nucleotide-specific, RNase digestion fragments with Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) was utilized. The MALDI-MS data were complemented by two primer extension techniques using reverse transcriptase. One technique utilizes decreasing concentrations of deoxynucleotide triphosphates to map 2'-O-ribose methylations. In the other, the rRNA is chemically modified, followed by mild alkaline hydrolysis to map pseudouridines (psis). A total of 10 posttranscriptionally methylated nucleotides and 6 psis were detected in the five organisms. Eight of the methylated nucleotides and one psi have not been reported previously. The distribution of modified nucleotides and their locations on the surface of the ribosomal peptidyl transferase cleft suggests functional importance. PMID:11911366

Study of Analytic Statistical Model for Decay of Light and Medium Mass Nuclei in Nuclear Fragmentation

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Wilson, John W.

1996-01-01

The angular momentum independent statistical decay model is often applied using a Monte-Carlo simulation to describe the decay of prefragment nuclei in heavy ion reactions. This paper presents an analytical approach to the decay problem of nuclei with mass number less than 60, which is important for galactic cosmic ray (GCR) studies. This decay problem of nuclei with mass number less than 60 incorporates well-known levels of the lightest nuclei (A less than 11) to improve convergence and accuracy. A sensitivity study of the model level density function is used to determine the impact on mass and charge distributions in nuclear fragmentation. This angular momentum independent statistical decay model also describes the momentum and energy distribution of emitted particles (n, p, d, t, h, and a) from a prefragment nucleus.

Medium range order and structural relaxation in As–Se network glasses through FSDP analysis

DOE PAGES

Golovchak, R.; Lucas, P.; Oelgoetz, J.; ...

2015-01-13

We performed synchrotron X-ray diffraction and neutron scattering studies on As-Se glasses in two states: as-prepared (rejuvenated) and aged for similar to 27 years. The first sharp diffraction peak (FSDP) obtained from the structure factor data as a function of composition and temperature indicates that the cooperative processes that are responsible for structural relaxation do not affect FSDP. The results are correlated with the composition dependence of the complex heat capacity of the glasses and concentration of different structural fragments in the glass network. Furthermore, the comparison of structural information shows that density fluctuations, which were thought previously to havemore » a significant contribution to FSDP, have much smaller effect than the cation-cation correlations, presence of ordered structural fragments or cage molecules.« less

Comprehensive Study On The Metastable Negative Ion Fragmentation Of Individual Dna Components And Larger Oligonucleotides

NASA Astrophysics Data System (ADS)

Ingolfsson, O.; Flosadottir, H. D.; Omarsson, B.; Ilko, B.

2010-07-01

Here we present a systematic study on the unimolecular decay pathways of the deprotonated building blocks of DNA and RNA to address the following questions: 1. Are the negative ion fragmentation patterns observed in the metastable decay of individual DNA components still evident when these are combined to larger oligonucleotides? 2. What is the significance of the charge location in determining the fragmentation pathways in the metastable decay process? 3. Are those metastable decay channels relevant in dissociative electron attachment to DNA components? To address these questions we have studied the fragmentation patterns of the deprotonated ribose and ribose 5'-monophosphate, the fragmentation patterns of the individual bases, all nucleosides and all 2'-deoxynucleosides as well as the individual nucleotides and several combinations of hexameric oligonucleotides. Furthermore, to understand the significance of the charge location in determining the fragmentation path in the metastable decay process of these deprotonated ions we have also studied modified uridine and guanosine. These have been modified to block different deprotonation sites and thus to control the initial step in the in the fragmentation process i.e. the site of deprotonation. In addition to our experimental approach we have also simulated the metastable fragmentation of the deprotonated uridine and 2'-deoxyguanosine to clarify the mechanisms and fragmentation patterns observed. Where data is available, the results are compared to dissociative electron attachment to DNA components and discussed in context to the underlying mechanism. Experiments on modified nucleosides where selected deprotonation sites have been blocked are used to verify the predicted reaction paths and imulations on uridine and 2'-deoxyguanosine are compared to the experimental results and used to shed light on the mechanisms involved.

High efficiency induction of callus and regeneration of sporophytes of Laminaria japonica (Phaeophyta)

NASA Astrophysics Data System (ADS)

Wang, Xi-Hua; Qin, Song; Li, Xin-Ping; Jiang, Peng; Zeng, Cheng-Kui; Qin, Mei

1998-03-01

Four media (PESI solid, MS liquid, MS solid and ASP-C-I solid medium) were used to induce callus from excised tissues of the kelp Laminaria japonica. Only PESI solid medium and MS solid medium produced calli. Modified MS solid medium supplemented with mannitol (3%,W/V), yeast extract (0.1%, W/V), VB2 (0.5 mg/ml), VB12 (0.5 mg/ml), kinetin (0.108 μg/ml) and NAA (1.860μg/ml) showed much better effect on callus induction than non-modified MS solid medium. After 24 days of induction 75.5% of tissues in PESI solid medium showed callus formation. For modified MS solid medium, after three months of induction 67.3% of tissues dedifferentiated into calli. No callus could be found after five months of induction in either MS liquid or ASP-C-I solid medium. When calli were squashed and cultured in N-P enriched autoclaved seawater, MS liquid medium and ASP12-NTA liquid medium (both modified with kelp extract), differentiation of cells and regeneration of sporophytes were only observed in ASP12-NTA medium supplemented with kelp extract. Gametophyte-like filaments formed first, then eggs were released. It was suggested that sporophyte formation could be a process of parthenogenesis. Sterilization techniques in tissue culture of L. japonica were also tested in this study.

Multiple successional pathways in human-modified tropical landscapes: new insights from forest succession, forest fragmentation and landscape ecology research.

PubMed

Arroyo-Rodríguez, Víctor; Melo, Felipe P L; Martínez-Ramos, Miguel; Bongers, Frans; Chazdon, Robin L; Meave, Jorge A; Norden, Natalia; Santos, Bráulio A; Leal, Inara R; Tabarelli, Marcelo

2017-02-01

Old-growth tropical forests are being extensively deforested and fragmented worldwide. Yet forest recovery through succession has led to an expansion of secondary forests in human-modified tropical landscapes (HMTLs). Secondary forests thus emerge as a potential repository for tropical biodiversity, and also as a source of essential ecosystem functions and services in HMTLs. Such critical roles are controversial, however, as they depend on successional, landscape and socio-economic dynamics, which can vary widely within and across landscapes and regions. Understanding the main drivers of successional pathways of disturbed tropical forests is critically needed for improving management, conservation, and restoration strategies. Here, we combine emerging knowledge from tropical forest succession, forest fragmentation and landscape ecology research to identify the main driving forces shaping successional pathways at different spatial scales. We also explore causal connections between land-use dynamics and the level of predictability of successional pathways, and examine potential implications of such connections to determine the importance of secondary forests for biodiversity conservation in HMTLs. We show that secondary succession (SS) in tropical landscapes is a multifactorial phenomenon affected by a myriad of forces operating at multiple spatio-temporal scales. SS is relatively fast and more predictable in recently modified landscapes and where well-preserved biodiversity-rich native forests are still present in the landscape. Yet the increasing variation in landscape spatial configuration and matrix heterogeneity in landscapes with intermediate levels of disturbance increases the uncertainty of successional pathways. In landscapes that have suffered extensive and intensive human disturbances, however, succession can be slow or arrested, with impoverished assemblages and reduced potential to deliver ecosystem functions and services. We conclude that: (i) succession must be examined using more comprehensive explanatory models, providing information about the forces affecting not only the presence but also the persistence of species and ecological groups, particularly of those taxa expected to be extirpated from HMTLs; (ii) SS research should integrate new aspects from forest fragmentation and landscape ecology research to address accurately the potential of secondary forests to serve as biodiversity repositories; and (iii) secondary forest stands, as a dynamic component of HMTLs, must be incorporated as key elements of conservation planning; i.e. secondary forest stands must be actively managed (e.g. using assisted forest restoration) according to conservation goals at broad spatial scales. © 2015 Cambridge Philosophical Society.

Aureole radiance field about a source in a scattering-absorbing medium.

PubMed

Zachor, A S

1978-06-15

A technique is described for computing the aureole radiance field about a point source in a medium that absorbs and scatters according to an arbitrary phase function. When applied to an isotropic source in a homogenous medium, the method uses a double-integral transform which is evaluated recursively to obtain the aureole radiances contributed by successive scattering orders, as in the Neumann solution of the radiative transfer equation. The normalized total radiance field distribution and the variation of flux with field of view and range are given for three wavelengths in the uv and one in the visible, for a sea-level model atmosphere assumed to scatter according to a composite of the Rayleigh and modified Henyey-Greenstein phase functions. These results have application to the detection and measurement of uncollimated uv and visible sources at short ranges in the lower atmosphere.

Process for modifying the metal ion sorption capacity of a medium

DOEpatents

Lundquist, Susan H.

2002-01-01

A process for modifying a medium is disclosed that includes treating a medium having a metal ion sorption capacity with a solution that includes: A) an agent capable of forming a complex with metal ions; and B) ions selected from the group consisting of sodium ions, potassium ions, magnesium ions, and combinations thereof, to create a medium having an increased capacity to sorb metal ions relative to the untreated medium.

Infrared dust bubble CS51 and its interaction with the surrounding interstellar medium

NASA Astrophysics Data System (ADS)

Das, Swagat R.; Tej, Anandmayee; Vig, Sarita; Liu, Hong-Li; Liu, Tie; Ishwara Chandra, C. H.; Ghosh, Swarna K.

2017-12-01

A multiwavelength investigation of the southern infrared dust bubble CS51 is presented in this paper. We probe the associated ionized, cold dust, molecular and stellar components. Radio continuum emission mapped at 610 and 1300 MHz, using the Giant Metrewave Radio Telescope, India, reveals the presence of three compact emission components (A, B, and C) apart from large-scale diffuse emission within the bubble interior. Radio spectral index map shows the co-existence of thermal and non-thermal emission components. Modified blackbody fits to the thermal dust emission using Herschel Photodetector Array Camera and Spectrometer and Spectral and Photometric Imaging Receiver data is performed to generate dust temperature and column density maps. We identify five dust clumps associated with CS51 with masses and radius in the range 810-4600 M⊙ and 1.0-1.9 pc, respectively. We further construct the column density probability distribution functions of the surrounding cold dust which display the impact of ionization feedback from high-mass stars. The estimated dynamical and fragmentation time-scales indicate the possibility of collect and collapse mechanism in play at the bubble border. Molecular line emission from the Millimeter Astronomy Legacy Team 90 GHz survey is used to understand the nature of two clumps which show signatures of expansion of CS51.

The influence of benign prostatic hyperplasia on sperm morphological features and sperm DNA integrity in dogs.

PubMed

Flores, R B; Angrimani, Dsr; Rui, B R; Brito, M M; Abreu, R A; Vannucchi, C I

2017-04-01

Benign prostatic hyperplasia (BPH) has a high incidence in older intact dogs. Due to the increased prostatic oxidative stress and hormonal imbalance of BPH, sperm damage can arise, such as sperm morphological alterations and DNA fragmentation. This study aimed to compare the reproductive potential of healthy dogs and those affected by benign prostatic hyperplasia. Ten dogs were assigned to two experimental groups: dogs without BPH (control; n = 5) and dogs diagnosed with BPH (n = 5), based on clinical signs and ultrasonographic findings. Three semen collections were performed from each dog within one month and analysed using computer-assisted sperm analysis (CASA) and functional tests. Control group showed higher percentage of sperm DNA integrity (95 ± 1.8%) compared to the BPH group (79.2 ± 6.4%). On the other hand, the percentage of minor sperm defects, amplitude of lateral sperm head displacement of the spermatozoa and medium sperm mitochondrial activity were higher in the BPH group. In conclusion, BPH decreases sperm DNA integrity, increases mitochondrial activity, as well as modifies sperm movement pattern. Therefore, a careful sperm analysis of aged dogs with BPH is required before a reproductive programme can be established for such patients. © 2016 Blackwell Verlag GmbH.

A comment on the validity of fragmentation parameters measured in nuclear emulsions. [cosmic ray nuclei

NASA Technical Reports Server (NTRS)

Waddington, C. J.

1978-01-01

Evidence is reexamined which has been cited as suggesting serious errors in the use of fragmentation parameters appropriate to an airlike medium deduced from measurements made in nuclear emulsions to evaluate corrections for certain effects in balloon-borne observations of cosmic-ray nuclei. Fragmentation parameters for hydrogenlike interactions are calculated and shown to be in overall good agreement with those obtained previously for air. Experimentally measured fragmentation parameters in emulsion are compared with values computed semiempirically, and reasonable agreement is indicated.

Effects of target plasma electron-electron collisions on correlated motion of fragmented protons.

PubMed

Barriga-Carrasco, Manuel D

2006-02-01

The objective of the present work is to examined the effects of plasma target electron-electron collisions on H2 + protons traversing it. Specifically, the target is deuterium in a plasma state with temperature Te=10 eV and density n=10(23) cm(-3), and proton velocities are vp=vth, vp=2vth, and vp=3vth, where vth is the electron thermal velocity of the target plasma. Proton interactions with plasma electrons are treated by means of the dielectric formalism. The interactions among close protons through plasma electronic medium are called vicinage forces. It is checked that these forces always screen the Coulomb explosions of the two fragmented protons from the same H2 + ion decreasing their relative distance. They also align the interproton vector along the motion direction, and increase the energy loss of the two protons at early dwell times while for longer times the energy loss tends to the value of two isolated protons. Nevertheless, vicinage forces and effects are modified by the target electron collisions. These collisions enhance the calculated self-stopping and vicinage forces over the collisionless results. Regarding proton correlated motion, when these collisions are included, the interproton vector along the motion direction overaligns at slower proton velocities (vp=vth) and misaligns for faster ones (vp=2vth, vp=3vth). They also contribute to a great extend to increase the energy loss of the fragmented H2 + ion. This later effect is more significant in reducing projectile velocity.

Grafting titanium nitride surfaces with sodium styrene sulfonate thin films

PubMed Central

Zorn, Gilad; Migonney, Véronique; Castner, David G.

2014-01-01

The importance of titanium nitride lies in its high hardness and its remarkable resistance to wear and corrosion, which has led to its use as a coating for the heads of hip prostheses, dental implants and dental surgery tools. However, the usefulness of titanium nitride coatings for biomedical applications could be significantly enhanced by modifying their surface with a bioactive polymer film. The main focus of the present work was to graft a bioactive poly(sodium styrene sulfonate) (pNaSS) thin film from titanium nitride surfaces via a two-step procedure: first modifying the surface with 3-methacryloxypropyltrimethoxysilane (MPS) and then grafting the pNaSS film from the MPS modified titanium through free radical polymerization. X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were used after each step to characterize success and completeness of each reaction. The surface region of the titanium nitride prior to MPS functionalization and NaSS grafting contained a mixture of titanium nitride, oxy-nitride, oxide species as well as adventitious surface contaminants. After MPS functionalization, Si was detected by XPS, and characteristic MPS fragments were detected by ToF-SIMS. After NaSS grafting, Na and S were detected by XPS and characteristic NaSS fragments were detected by ToF-SIMS. The XPS determined thicknesses of the MPS and NaSS overlayers were ∼1.5 and ∼1.7 nm, respectively. The pNaSS film density was estimated by the toluidine blue colorimetric assay to be 260 ± 70 ng/cm2. PMID:25280842

Surface deformation and shear flow in ligand mediated cell adhesion.

PubMed

Sircar, Sarthok; Roberts, Anthony J

2016-10-01

We present a unified, multiscale model to study the attachment/detachment dynamics of two deforming, charged, near spherical cells, coated with binding ligands and subject to a slow, homogeneous shear flow in a viscous, ionic fluid medium. The binding ligands on the surface of the cells experience both attractive and repulsive forces in an ionic medium and exhibit finite resistance to rotation via bond tilting. The microscale drag forces and couples describing the fluid flow inside the small separation gap between the cells, are calculated using a combination of methods in lubrication theory and previously published numerical results. For a selected range of material and fluid parameters, a hysteretic transition of the sticking probability curves (i.e., the function [Formula: see text]) between the adhesion phase (when [Formula: see text]) and the fragmentation phase (when [Formula: see text]) is attributed to a nonlinear relation between the total nanoscale binding forces and the separation gap between the cells. We show that adhesion is favoured in highly ionic fluids, increased deformability of the cells, elastic binders and a higher fluid shear rate (until a critical threshold value of shear rate is reached). Within a selected range of critical shear rates, the continuation of the limit points (i.e., the turning points where the slope of [Formula: see text] changes sign) predict a bistable region, indicating an abrupt switching between the adhesion and the fragmentation regimes. Although, bistability in the adhesion-fragmentation phase diagram of two deformable, charged cells immersed in an ionic aqueous environment has been identified by some in vitro experiments, but until now, has not been quantified theoretically.

Analytical solution for boundary heat fluxes from a radiating rectangular medium

NASA Technical Reports Server (NTRS)

Siegel, R.

1991-01-01

Reference is made to the work of Shah (1979) which demonstrated the possibility of partially integrating the radiative equations analytically to obtain an 'exact' solution. Shah's solution was given as a double integration of the modified Bessel function of order zero. Here, it is shown that the 'exact' solution for a rectangular region radiating to cold black walls can be conveniently derived, and expressed in simple form, by using an integral function, Sn, analogous to the exponential integral function appearing in plane-layer solutions.

[Hurricane impact on Thalassia testudinum (Hydrocharitaceae) beds in the Mexican Caribbean].

PubMed

Arellano-Méndez, Leonardo U; Liceaga-Correa, María de los Angeles; Herrera-Silveira, Jorge A; Hernández-Núñez, Héctor

2011-03-01

Hurricanes have increased in strength and frequency as a result of global climate change. This research was conducted to study the spatio-temporal distribution and changes of Thalassia testudinum, the dominant species in Bahia de la Ascension (Quintana Roo, Mexico), when affected by heavy weather conditions. To complete this objective, a 2001 Landsat ETM+ image and the information from 525 sampling stations on morpho-functional and coverage of T. testudinum were used, and the seeds generated for the classification of eight benthic habitats. To quantify the changes caused by two hurricanes, we used two images, one of 1988 (Gilberto) and another of 1995 (Roxanne); other three data sets (2003, 2005 and 2007) were also used to describe the study area without major weather effects. Six categorial maps were obtained and subjected to analysis by 8 Landscape Ecology indexes, that describe the spatial characteristics, structure, function, change of the elements (matrix-patch-corridor), effects on ecosystems, connectivity, edges, shape and patch habitat fragmentation. Models indicate that T. testudinum may be classified as a continuum (matrix), since the fragments were not observed intermittently, but as a progression from minimum to maximum areas in reference to their coverage (ecological corridors). The fragments do not have a regular shape, indicating that the impacts are recent and may be due to direct effects (high-intensity hurricanes) or indirect (sediment). Fragments of type "bare soils" have a discontinuous distribution, and are considered to be the sites that have remained stable over a long timescale. While more dense coverage areas ("beds", "medium prairie" and "prairie") have low fragmentation and high connection of fragments. Features have an irregular perimeter and radial growth of formal; suggesting that the impact of meteors has no effect on the resilience of T. testudinum in this ecosystem, indicating good environmental quality to grow in this bay.

General structure of fermion two-point function and its spectral representation in a hot magnetized medium

NASA Astrophysics Data System (ADS)

Das, Aritra; Bandyopadhyay, Aritra; Roy, Pradip K.; Mustafa, Munshi G.

2018-02-01

We have systematically constructed the general structure of the fermion self-energy and the effective quark propagator in the presence of a nontrivial background such as a hot magnetized medium. This is applicable to both QED and QCD. The hard thermal loop approximation has been used for the heat bath. We have also examined transformation properties of the effective fermion propagator under some of the discrete symmetries of the system. Using the effective fermion propagator we have analyzed the fermion dispersion spectra in a hot magnetized medium along with the spinor for each fermion mode obtained by solving the modified Dirac equation. The fermion spectra is found to reflect the discrete symmetries of the two-point functions. We note that for a chirally symmetric theory the degenerate left- and right-handed chiral modes in vacuum or in a heat bath get separated and become asymmetric in the presence of a magnetic field without disturbing the chiral invariance. The obtained general structure of the two-point functions is verified by computing the three-point function, which agrees with the existing results in one-loop order. Finally, we have computed explicitly the spectral representation of the two-point functions which would be very important to study the spectral properties of the hot magnetized medium corresponding to QED and QCD with background magnetic field.

Trimethylation enhancement using diazomethane (TrEnDi): rapid on-column quaternization of peptide amino groups via reaction with diazomethane significantly enhances sensitivity in mass spectrometry analyses via a fixed, permanent positive charge.

PubMed

Wasslen, Karl V; Tan, Le Hoa; Manthorpe, Jeffrey M; Smith, Jeffrey C

2014-04-01

Defining cellular processes relies heavily on elucidating the temporal dynamics of proteins. To this end, mass spectrometry (MS) is an extremely valuable tool; different MS-based quantitative proteomics strategies have emerged to map protein dynamics over the course of stimuli. Herein, we disclose our novel MS-based quantitative proteomics strategy with unique analytical characteristics. By passing ethereal diazomethane over peptides on strong cation exchange resin within a microfluidic device, peptides react to contain fixed, permanent positive charges. Modified peptides display improved ionization characteristics and dissociate via tandem mass spectrometry (MS(2)) to form strong a2 fragment ion peaks. Process optimization and determination of reactive functional groups enabled a priori prediction of MS(2) fragmentation patterns for modified peptides. The strategy was tested on digested bovine serum albumin (BSA) and successfully quantified a peptide that was not observable prior to modification. Our method ionizes peptides regardless of proton affinity, thus decreasing ion suppression and permitting predictable multiple reaction monitoring (MRM)-based quantitation with improved sensitivity.

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

Boskey, Adele L., E-mail: boskeya@hss.edu; Christensen, Brian, E-mail: bc@mb.au.dk; Taleb, Hayat, E-mail: Talebh@hss.edu

Highlights: Black-Right-Pointing-Pointer Thrombin-cleaved fragments of milk-osteopontin effect hydroxyapatite formation differently. Black-Right-Pointing-Pointer N- and C-terminal fragments promoted hydroxyapatite formation and growth. Black-Right-Pointing-Pointer A central fragment inhibited hydroxyapatite formation and growth. Black-Right-Pointing-Pointer Binding to collagen or hydroxyapatite seed crystals modified these effects. -- Abstract: The manuscript tests the hypothesis that posttranslational modification of the SIBLING family of proteins in general and osteopontin in particular modify the abilities of these proteins to regulate in vitro hydroxyapatite (HA) formation. Osteopontin has diverse effects on hydroxyapatite (HA) mineral crystallite formation and growth depending on the extent of phosphorylation. We hypothesized that different regions of full-lengthmore » OPN would also have distinct effects on the mineralization process. Thrombin fragmentation of milk OPN (mOPN) was used to test this hypothesis. Three fragments were tested in a de novo HA formation assay; an N-terminal fragment (aa 1-147), a central fragment (aa 148-204) denoted SKK-fragment and a C-terminal fragment (aa 205-262). Compared to intact mOPN the C- and N-terminal fragments behaved comparably, promoting HA formation and growth, but the central SKK-fragment acted as a mineralization inhibitor. In a seeded growth experiment all fragments inhibited mineral proliferation, but the SKK-fragment was the most effective inhibitor. These effects, seen in HA-formation and seeded growth assays in a gelatin gel system and in a pH-stat experiment were lost when the protein or fragments were dephosphorylated. Effects of the fully phosphorylated protein and fragments were also altered in the presence of fibrillar collagen. The diverse effects can be explained in terms of the intrinsically disordered nature of OPN and its fragments which enable them to interact with their multiple partners.« less

Electronically Recorded Music as a Communication Medium: A Structural Analysis with Selected Bibliography.

ERIC Educational Resources Information Center

Jorgensen, Earl; Mabry, Edward A.

During the past decade, the influence of electronically recorded music and the message it transmits have caused media scholars to reexamine and modify the theories upon which the basic process of communication is dependent. While the five primary functions (source, transmitter, channel, receiver, and destination) remain unchanged, an additional…

A xyloglucan from seeds of the native Brazilian species Hymenaea courbaril for micropropagation of Marubakaido and Jonagored apples.

PubMed

Lima-Nishimura, N; Quoirin, M; Naddaf, Y G; Wilhelm, H M; Ribas, L L F; Sierakowski, M-R

2003-01-01

Xyloglucan was extracted from seeds of Hymenaea courbaril and mixed with agar to prepare a solid culture medium used for micropropagation of the Marubakaido apple rootstock (Malus prunifolia Borkh) and cv. Jonagored (Malus domestica). The performance on gels created from a blend of 0.4%agar and 0.2% xyloglucan (w/v) was compared with that on media gelled with a standard concentration 0.6% (w/v) of agar. The growth of shoots and the multiplication rate were higher on the modified culture medium than on the agar-gelled medium. The occurrence of hyperhydric shoots was lower on the modified medium. In the absence of auxin, shoot rooting reached 70% (Marubakaido) and 66% (Jonagored) on the agar-xyloglucan medium and 6.7% and 10.4%, respectively, on the agar medium. When 0.25 microM indole-3-butyric acid (IBA) was added to both media, the modified medium gave better results in terms of rooting percentage and quality of roots than the agar-gelled medium.

Monte-Carlo Event Generators for Jet Modification in d(p)-A and A-A Collisions

NASA Astrophysics Data System (ADS)

Kordell, Michael C., III

This work outlines methods to use jet simulations to study both initial and final state nuclear effects in heavy-ion collisions. To study the initial state of heavy-ion collisions, the production of jets and high momentum hadrons from jets, produced in deuteron (d)-Au collisions at the relativistic heavy-ion collider (RHIC) and proton (p)- Pb collisions at the large hadron collider (LHC) are studied as a function of centrality, a measure of the impact parameter of the collision. A modified version of the event generator PYTHIA, widely used to simulate p-p collisions, is used in conjunction with a nuclear Monte-Carlo event generator which simulates the locations of the nucleons within a large nucleus. It is demonstrated how events with a hard jet may be simulated, in such a way that the parton distribution function of the projectile is frozen during its interaction with the extended nucleus. Using this approach, it is demonstrated that the puzzling enhancement seen in peripheral events at RHIC and the LHC, as well as the suppression seen in central events at the LHC are mainly due to mis-binning of central and semi-central events, containing a jet, as peripheral events. This occurs due to the suppression of soft particle production away from the jet, caused by the depletion of energy available in a nucleon of the deuteron (in d-Au at RHIC) or in the proton (in p-Pb at LHC), after the production of a hard jet. In conclusion, partonic correlations built out of simple energy conservation are responsible for such an effect, though these are sampled at the hard scale of jet production and, as such, represent smaller states. To study final state nuclear effects, the modification of hard jets in the Quark Gluon Plasma (QGP) is simulated using the MATTER event generator. Based on the higher twist formalism of energy loss, the MATTER event generator simulates the evolution of highly virtual partons through a medium. These partons sampled from an underlying PYTHIA kernel undergo splitting through a combination of vacuum and medium induced emission. The momentum exchange with the medium is simulated via the jet transport coefficient q̂, which is assumed to scale with the entropy density at a given location in the medium. The entropy density is obtained from a relativistic viscous fluid dynamics simulation (VISH2+1D) in 2+1 space time dimensions. Results for jet and hadron observables are presented using an independent fragmentation model.

Transient experiments with thermite melts for a core catcher concept based on water addition from below

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

Tromm, W.; Alsmeyer, H.

1995-09-01

A core catcher concept is proposed to be integrated into a new pressurized water reactor. The core catcher achieves coolability by spreading and fragmentation of the ex-vessel core melt based on a process of water inlet from the bottom through the melt. By highly effective heat removal that uses evaporating water in direct contact with the fragmented melt, the corium melt would solidify in a short time period, and long-term cooling could be maintained by continuous water evaporation from the flooded porous or fragmented corium bed. The key process for obtaining coolability is the coupling of the three effects: (a)more » water ingression from below and its evaporation, (b) break up and fragmentation of the corium layer, and (c) heat transfer and solidification of the let. These mechanisms are investigated in transient medium-scale experiments with thermite melts. The experimental setup represents a section of the proposed core catcher design. A thermite melt is located on the core catcher plate with a passive water supply from the bottom. After generation of the melt, the upper sacrificial layer is eroded until water penetrates into the melt for the bottom through plugs in the supporting plate. Fragmentation and fast solidification of the melt are observed, and long-term heat removal is guaranteed by the coolant water flooding the porous melt. Water inflow is sufficient to safely remove the decay heat in a comparable corium layer. The open porosity is created by the vapor streaming through the melt during the solidification process. Fracture of the solid by thermomechanical stresses is not observed. The experiments in their current stage show the principal feasibility of the proposed cooling concept and are used to prepare large-scale experiments to be performed in the modified BETA facility with sustained heating of the melt.« less

Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest

PubMed Central

Suárez-Montes, Pilar; Chávez-Pesqueira, Mariana

2016-01-01

Introduction Theory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate), indirect gene flow and contemporary pollen dynamics in the understory herb Aphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios. Methods Twelve populations of A. aurantiaca were sampled in large (4), medium (3), and small (5) forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28–30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population. Results Despite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (He = 0.61), weak genetic structure (Rst = 0.037), and slight inbreeding in small fragments. Effective population sizes (Ne) were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events were detected. Aphelandra aurantiaca shows a mixed mating system (tm = 0.81) and the outcrossing rate have not been affected by habitat fragmentation. A strong pollen pool structure was detected due to few effective pollen donors (Nep) and low distance pollen movement, pointing that most plants received pollen from close neighbors. Past demographic fluctuations may have affected the present population genetic structure as Bayesian coalescent analysis revealed the signature of past population expansion, possibly during warmer conditions after the last glacial maximum. Discussion Habitat fragmentation has not increased genetic differentiation or reduced genetic diversity of A. aurantiaca despite dozens of generations since the onset of fragmentation in the region of Los Tuxtlas. Instead, past population expansion is compatible with the lack of observed genetic structure. The predicted negative effects of rainforest fragmentation on genetic diversity and population structure of A. aurantiaca seem to have been buffered owing to its large effective populations and long-distance dispersal events. In particular, its mixed-mating system, mostly of outcrossing, suggests high efficiency of pollinators promoting connectivity and reducing inbreeding. However, some results point that the effects of fragmentation are underway, as two small fragments showed higher membership probabilities to their population of origin, suggesting genetic isolation. Our findings underscore the importance of fragment size to maintain genetic connectivity across the landscape. PMID:28028460

Adult primary angiitis of the central nervous system: isolated small-vessel vasculitis represents distinct disease pattern.

PubMed

de Boysson, Hubert; Boulouis, Grégoire; Aouba, Achille; Bienvenu, Boris; Guillevin, Loïc; Zuber, Mathieu; Touzé, Emmanuel; Naggara, Olivier; Pagnoux, Christian

2017-03-01

We aimed to identify whether presentations and outcomes in adult patients with isolated small-vessel primary angiitis of the CNS (PACNS) would differ from other patients with large/medium-vessel involvement. In the French PACNS cohort, we compared the characteristics, treatments and outcomes of patients with isolated small-vessel disease (normal CT, MR and/or conventional angiograms, brain biopsy positive for vasculitis) with other patients who had large/medium-vessel involvement (vessel abnormalities on CT, MR or conventional angiograms). A good functional outcome was defined as a modified Rankin scale ⩽2 at last follow-up, regardless of the occurrence of relapse. Among the 102 patients in the cohort, 26 (25%) had isolated small-vessel PACNS, whereas the 76 others demonstrated large/medium-vessel involvement. Patients with isolated small-vessel PACNS had more seizures (P < 0.0001), cognitive (P = 0.02) or consciousness impairment (P = 0.03) and more dyskinesias (P = 0.002) but less focal deficits (P = 0.0002) than other PACNS patients. They also had more abnormal cerebrospinal fluid analysis (P = 0.008) and gadolinium enhancements on MRI (P = 0.001) but less frequent acute ischaemic lesions (P < 0.0001) than patients with large/medium-vessel involvement. Treatments and modified Rankin scale at last follow-up did not differ between groups. Thirty-two (31%) patients relapsed; 14 (54%) with isolated small-vessel PACNS vs 18 (24%) with large/medium-vessel involvement (P = 0.004). Eight patients died, with no difference between the groups (P = 0.97). In our cohort, adult patients with isolated small-vessel PACNS presented some distinct disease features and relapsed more often than other PACNS patients who had large/medium-vessel involvement. Functional outcomes and mortality did not differ. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Eruption processes and deposit characteristics at the monogenetic Mt. Gambier Volcanic Complex, SE Australia: implications for alternating magmatic and phreatomagmatic activity

NASA Astrophysics Data System (ADS)

van Otterloo, Jozua; Cas, Raymond A. F.; Sheard, Malcolm J.

2013-08-01

The ˜5 ka Mt. Gambier Volcanic Complex in the Newer Volcanics Province, Australia is an extremely complex monogenetic, volcanic system that preserves at least 14 eruption points aligned along a fissure system. The complex stratigraphy can be subdivided into six main facies that record alternations between magmatic and phreatomagmatic eruption styles in a random manner. The facies are (1) coherent to vesicular fragmental alkali basalt (effusive/Hawaiian spatter and lava flows); (2) massive scoriaceous fine lapilli with coarse ash (Strombolian fallout); (3) bedded scoriaceous fine lapilli tuff (violent Strombolian fallout); (4) thin-medium bedded, undulating very fine lapilli in coarse ash (dry phreatomagmatic surge-modified fallout); (5) palagonite-altered, cross-bedded, medium lapilli to fine ash (wet phreatomagmatic base surges); and (6) massive, palagonite-altered, very poorly sorted tuff breccia and lapilli tuff (phreato-Vulcanian pyroclastic flows). Since most deposits are lithified, to quantify the grain size distributions (GSDs), image analysis was performed. The facies are distinct based on their GSDs and the fine ash to coarse+fine ash ratios. These provide insights into the fragmentation intensities and water-magma interaction efficiencies for each facies. The eruption chronology indicates a random spatial and temporal sequence of occurrence of eruption styles, except for a "magmatic horizon" of effusive activity occurring at both ends of the volcanic complex simultaneously. The eruption foci are located along NW-SE trending lineaments, indicating that the complex was fed by multiple dykes following the subsurface structures related to the Tartwaup Fault System. Possible factors causing vent migration along these dykes and changes in eruption styles include differences in magma ascent rates, viscosity, crystallinity, degassing and magma discharge rate, as well as hydrological parameters.

Tissue culture of three species of Laurencia complex

NASA Astrophysics Data System (ADS)

Shen, Songdong; Wu, Xunjian; Yan, Binlun; He, Lihong

2010-05-01

To establish a micropropagation system of three Laurencia complex species ( Laurencia okamurai, Laurencia tristicha, and Chondrophycus undulatus) by tissue culture techniques, we studied the regeneration characteristics and optimal culture conditions of axenic algal fragments cultured on solid medium and in liquid medium. Regeneration structures were observed and counted regularly under a reverse microscope to investigate the regeneration process, polarity and optimal illumination, and temperature and salinity levels. The results show that in most cultures of the three species, we obtained bud regeneration on solidified medium with 0.5% agar and in liquid medium. Rhizoid-like regeneration was filamentous and developed from the lower cut surface of fragments in L. okamurai, but was discoid and developed from the apical back side of bud regeneration in L. tristicha and C. undulatus. Regeneration polarity was localized to the apical part of algal fronds in all three species, and on fragments cut from the basal part of algae buds could develop from both the upper and the lower cut surfaces. Buds could develop from both the medullary and the cortical portions in L. okamurai and C. undulatus, while in L. tristicha, buds only emerged from the cortex. The optimal culture conditions for L. okamurai were 4 500 lx, 20°C and 35 (salinity); for C. undulatus, 4 500 lx, 20°C and 30; and for L. tristicha, 4 500 lx, 25°C and 30.

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

Aaboud, M.; Aad, G.; Abbott, B.

The distributions of transverse momentum and longitudinal momentum fraction of charged particles in jets are measured in Pb+Pb and pp collisions with the ATLAS detector at the LHC. The distributions are measured as a function of jet transverse momentum and rapidity. The analysis utilises an integrated luminosity of 0.14 nb -1 of Pb+Pb data and 4.0 pb -1 of pp data collected in 2011 and 2013, respectively, at the same centre-of-mass energy of 2.76 TeV per colliding nucleon pair. The distributions measured in pp collisions are used as a reference for those measured in Pb+Pb collisions in order to evaluatemore » the impact on the internal structure of jets from the jet energy loss of fast partons propagating through the hot, dense medium created in heavy-ion collisions. Modest but significant centrality-dependent modifications of fragmentation functions in Pb+Pb collisions with respect to those in pp collisions are seen. Finally, no significant dependence of modifications on jet p T and rapidity selections is observed except for the fragments with the highest transverse momenta for which some reduction of yields is observed for more forward jets.« less

Creation of forest edges has a global impact on forest vertebrates

PubMed Central

Peres, CA; Banks-Leite, C; Wearn, OR; Marsh, CJ; Butchart, SHM; Arroyo-Rodríguez, V; Barlow, J; Cerezo, A; Cisneros, L; D’Cruze, N; Faria, D; Hadley, A; Harris, S; Klingbeil, BT; Kormann, U; Lens, L; Medina-Rangel, GF; Morante-Filho, JC; Olivier, P; Peters, SL; Pidgeon, A; Ribeiro, DB; Scherber, C; Schneider-Maunory, L; Struebig, M; Urbina-Cardona, N; Watling, JI; Willig, MR; Wood, EM; Ewers, RM

2017-01-01

Summary Forest edges influence more than half the world’s forests and contribute to worldwide declines in biodiversity and ecosystem functions. However, predicting these declines is challenging in heterogeneous fragmented landscapes. We assembled an unmatched global dataset on species responses to fragmentation and developed a new statistical approach for quantifying edge impacts in heterogeneous landscapes to quantify edge-determined changes in abundance of 1673 vertebrate species. We show that 85% of species’ abundances are affected, either positively or negatively, by forest edges. Forest core species, which were more likely to be listed as threatened by the IUCN, only reached peak abundances at sites farther than 200-400 m from sharp high-contrast forest edges. Smaller-bodied amphibians, larger reptiles and medium-sized non-volant mammals experienced a larger reduction in suitable habitat than other forest core species. Our results highlight the pervasive ability of forest edges to restructure ecological communities on a global scale. PMID:29088701

Mechanistic study on the nuclear modifier gene MSS1 mutation suppressing neomycin sensitivity of the mitochondrial 15S rRNA C1477G mutation in Saccharomyces cerevisiae.

PubMed

Zhou, Qiyin; Wang, Wei; He, Xiangyu; Zhu, Xiaoyu; Shen, Yaoyao; Yu, Zhe; Wang, Xuexiang; Qi, Xuchen; Zhang, Xuan; Fan, Mingjie; Dai, Yu; Yang, Shuxu; Yan, Qingfeng

2014-01-01

The phenotypic manifestation of mitochondrial DNA (mtDNA) mutations can be modulated by nuclear genes and environmental factors. However, neither the interaction among these factors nor their underlying mechanisms are well understood. The yeast Saccharomyces cerevisiae mtDNA 15S rRNA C1477G mutation (PR) corresponds to the human 12S rRNA A1555G mutation. Here we report that a nuclear modifier gene mss1 mutation suppresses the neomycin-sensitivity phenotype of a yeast C1477G mutant in fermentable YPD medium. Functional assays show that the mitochondrial function of the yeast C1477G mutant was impaired severely in YPD medium with neomycin. Moreover, the mss1 mutation led to a significant increase in the steady-state level of HAP5 (heme activated protein), which greatly up-regulated the expression of glycolytic transcription factors RAP1, GCR1, and GCR2 and thus stimulated glycolysis. Furthermore, the high expression of the key glycolytic enzyme genes HXK2, PFK1 and PYK1 indicated that enhanced glycolysis not only compensated for the ATP reduction from oxidative phosphorylation (OXPHOS) in mitochondria, but also ensured the growth of the mss1(PR) mutant in YPD medium with neomycin. This study advances our understanding of the phenotypic manifestation of mtDNA mutations.

Consequences of extensive habitat fragmentation in landscape-level patterns of genetic diversity and structure in the Mediterranean esparto grasshopper

PubMed Central

Ortego, Joaquín; Aguirre, María P; Noguerales, Víctor; Cordero, Pedro J

2015-01-01

Anthropogenic habitat fragmentation has altered the distribution and population sizes in many organisms worldwide. For this reason, understanding the demographic and genetic consequences of this process is necessary to predict the fate of populations and establish management practices aimed to ensure their viability. In this study, we analyse whether the spatial configuration of remnant semi-natural habitat patches within a chronically fragmented landscape has shaped the patterns of genetic diversity and structure in the habitat-specialist esparto grasshopper (Ramburiella hispanica). In particular, we predict that agricultural lands constitute barriers to gene flow and hypothesize that fragmentation has restricted interpopulation dispersal and reduced local levels of genetic diversity. Our results confirmed the expectation that isolation and habitat fragmentation have reduced the genetic diversity of local populations. Landscape genetic analyses based on circuit theory showed that agricultural land offers ∽1000 times more resistance to gene flow than semi-natural habitats, indicating that patterns of dispersal are constrained by the spatial configuration of remnant patches of suitable habitat. Overall, this study shows that semi-natural habitat patches act as corridors for interpopulation gene flow and should be preserved due to the disproportionately large ecological function that they provide considering their insignificant area within these human-modified landscapes. PMID:26136826

The combination of a mineral trioxide aggregate and an adhesive restorative approach to treat a crown-root fracture coupled with lateral root perforation in a mandibular second molar: a case report.

PubMed

Wang, P; Wang, S; Ni, L

2009-01-01

The current paper describes a modified treatment procedure for a traumatized mandibular left second molar resulting in a crown-root fracture and root perforation with the fracture line below the gingival attachment and alveolar bone crest. After the mobile crown-root fragment was extracted, the root perforation was obturated with mineral trioxide aggregate (MTA), and the subgingival defect was directly repaired with polyacid-modified resin composites (Ionosite Baseline). A 24-month recall showed no evidence of periodontal inflammation and no adverse symptoms, and the treated tooth exhibited good healing and normal function.

Optimized surface topography of thermoplastics blends modified by graphene

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

Joshi, Girish M., E-mail: varadgm@gmail.com, E-mail: girish.joshi@vit.ac.in; Sharma, Ajay; Pandey, Mayank

2016-05-23

Polyacrilonitrile (PAN)/ Polyvinylfloride (PVDF) blends were modified by loading the graphene (0.5 to 1.5 wt %). The presence of graphene reveals the interesting surface properties. The decrease in surface roughness as function of graphene loading was confirmed by the topographic method of recording (two and three dimensional images) with atomic force microscope (AFM). The blends become smoother in nature due to occupied smaller surface area of graphene. This property may be useful for several applications in the marine, naval, nuclear domain and engineering applications as barrier medium.

Apollo 16 soils - Grain size analyses and petrography

NASA Technical Reports Server (NTRS)

Heiken, G. H.; Mckay, D. S.; Fruland, R. M.

1973-01-01

Soils from South Ray Crater, North Ray Crater, and the interray area of Station 10 have a similar provenance, containing breccia fragments of low to medium metamorphic grade and low light/dark lithic fragment ratios; these appear to be characteristic of the Cayley Formation. The primary difference between soils possibly derived from North Ray and South Ray craters is in the agglutinate content. A soil from Stone Mountain (Station 4) is characterized by breccia fragments of medium to high metamorphic grade and a high light/dark lithic fragment ratio; this soil may be derived from the Descartes Formation. Differences between the selenomorphic units, the Descartes and Cayley formations, may be lithologic as well as structural. The mean grain size varies from 84 to 280 microns, and all of the samples are poorly to very poorly sorted. There appears to be a relation between the sorting, grain size, and agglutinate content, with the finer-grained, better sorted soils containing more than 30% agglutinates. 'Shadowed' soils, collected close to large boulders, are similar in all respects to the 'reference' soils collected at least 5 m from the boulders.

If BZ medium did spanning trees these would be the same trees as Physarum built

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

2009-03-01

A sub-excitable Belousov-Zhabotinsky (BZ) medium exhibits self-localized wave-fragments which may travel for relatively long time preserving their shape. Using Oregonator model of the BZ medium we imitate foraging behavior of a true slime mold, Physarum polycephalum, on a nutrient-poor substrate. We show that given erosion post-processing operations the BZ medium can approximate a spanning tree of a planar set and thus is computationally equivalent to Physarum in the domain of proximity graph construction.

Quantitative analysis of modified proteins and their positional isomers by tandem mass spectrometry: human histone H4.

PubMed

Pesavento, James J; Mizzen, Craig A; Kelleher, Neil L

2006-07-01

Here we show that fragment ion abundances from dissociation of ions created from mixtures of multiply modified histone H4 (11 kDa) or of N-terminal synthetic peptides (2 kDa) correspond to their respective intact ion abundances measured by Fourier transform mass spectrometry. Isomeric mixtures of modified forms of the same protein are resolved and quantitated with a precision of

Over expression of anti-MUC1 single-domain antibody fragments in the yeast Pichia pastoris.

PubMed

Rahbarizadeh, Fatemeh; Rasaee, Mohammad J; Forouzandeh, Mehdi; Allameh, Abdol-Amir

2006-02-01

The methylotrophic yeast Pichia pastoris has become a highly popular expression host system for the recombinant production of a wide variety of proteins, such as antibody fragments. Camelids produce functional antibodies devoid of light chains and constant heavy-chain domain (CH1). The antigen binding fragments of such heavy chain antibodies are therefore comprised in one single domain, the so-called VH of the camelid heavy chain antibody (VHH). To test the feasibility of expressing VHHs in the yeast, which on account of their small size and antigen recognition properties would have a major impact on antibody engineering strategies, we constructed two VHH genes encoding the single-domain antibody fragments with specificity for a cancer associated mucin, MUC1. The recombinant strains of the yeast P. pastoris were developed which secrete single-domain antibody fragment to the culture supernatant as a biologically active protein. Supplementation of medium with sorbitol (in pre-induction phase) and casamino acid or EDTA (in induction phase) provided ideal condition of increasing the yield of VHH production compared to culture condition devoid of above recipe. The secreted protein was purified following a 80% ammonium sulfate precipitation step, followed by a affinity chromatography column. The specific activity in enzyme-linked immunosorbant assay (ELISA) of the purified yeast VHH was higher than that of a bacterial periplasmic counterpart. These results reaffirm that the yeast P. pastoris is a suitable host for high level and correctly folded production of VHH antibody fragments with potential in vivo diagnostic and therapeutic applications. This is the first report of expression of VHH in P. pastoris.

Direct Demonstration of the Concept of Unrestricted Effective-Medium Approximation

NASA Technical Reports Server (NTRS)

Mishchenko, Michael I.; Dlugach, Zhanna M.; Zakharova, Nadezhda T.

2014-01-01

The modified unrestricted effective-medium refractive index is defined as one that yields accurate values of a representative set of far-field scattering characteristics (including the scattering matrix) for an object made of randomly heterogeneous materials. We validate the concept of the modified unrestricted effective-medium refractive index by comparing numerically exact superposition T-matrix results for a spherical host randomly filled with a large number of identical small inclusions and Lorenz-Mie results for a homogeneous spherical counterpart. A remarkable quantitative agreement between the superposition T-matrix and Lorenz-Mie scattering matrices over the entire range of scattering angles demonstrates unequivocally that the modified unrestricted effective-medium refractive index is a sound (albeit still phenomenological) concept provided that the size parameter of the inclusions is sufficiently small and their number is sufficiently large. Furthermore, it appears that in cases when the concept of the modified unrestricted effective-medium refractive index works, its actual value is close to that predicted by the Maxwell-Garnett mixing rule.

A simple capillary gel electrophoresis approach for efficient and reproducible DNA separations. Analysis of genetically modified soy and maize.

PubMed

Sánchez, Laura; González, Ramón; Crego, Antonio L; Cifuentes, Alejandro

2007-03-01

It is generally assumed that in order to achieve suitable separations of DNA fragments, capillary gel electrophoresis (CGE)-coated capillaries should be used. In this work, a new method is presented that allows to obtain reproducible CGE separations of DNA fragments using bare fused-silica capillaries without any previous coating step. The proposed method only requires: (i) a capillary washing with 0.1 M hydrochloric acid between injections and (ii) a running buffer composed of Tris-phosphate-ethylenediamine tetraacetic acid (EDTA) and 4.5% of 2-hydroxyethyl cellulose (HEC) as sieving polymer. The use of this new CGE procedure gives highly resolved and reproducible separations of DNA fragments ranging from 50 to 750 bp. The separation of these DNA fragments is accomplished in less than 30 min with efficiencies up to 1.7 x 10(6) plates/m. Reproducibility values of migration times (given as %RSD) for the analyzed DNA fragments are better than 1.0% (n = 4) for the same day, 2.2% (n = 16) for four different days, and 2.3% (n = 16) for four different capillaries. The usefulness of this separation method is demonstrated by detecting genetically modified maize and genetically modified soy after DNA amplification by PCR. This new CGE procedure together with LIF as detector provides sensitive analysis of 0.9% of Bt11 maize, Mon810 maize, and Roundup Ready soy in flours with S/ N up to 542. These results demonstrate the usefulness of this procedure to fulfill the European regulation on detection of genetically modified organisms in foods.

Isospin dependence of fragment spectra in heavy/super-heavy colliding nuclei at intermediate energies

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

Chugh, Rajiv, E-mail: rajivchug@gmail.com; Kumar, Rohit, E-mail: rohitksharma.pu@gmail.com; Vinayak, Karan Singh, E-mail: drksvinayak@gmail.com

2016-05-06

Using isospin-dependent quantum molecular dynamics (IQMD) approach, we performed a theoretical investigation of the evolution of various kinds of fragments in heavy and superheavy-ion reactions in the intermediate/medium energy domain. We demonstrated direct impact of symmetry energy and Coulomb interactions on the evolution of fragments. Final fragment spectra (yields) obtained from the analysis of various heavy/super-heavy ion reactions at different reaction conditions show high sensitivity towards Coulomb interactions and less significant sensitivity to symmetry energy forms. No inconsistent pattern of fragment structure is obtained in case of super-heavy ion involved reactions for all the parameterizations of density dependence of symmetrymore » energy.« less

ITO Modification for Efficient Inverted Organic Solar Cells.

PubMed

Susarova, Diana K; Akkuratov, Alexander V; Kukharenko, Andrey I; Cholakh, Seif O; Kurmaev, Ernst Z; Troshin, Pavel A

2017-10-03

We demonstrate a facile approach to designing transparent electron-collecting electrodes by depositing thin layers of medium and low work function metals on top of transparent conductive metal oxides (TCOs) such as ITO and FTO. The modified electrodes were fairly stable for months under ambient conditions and maintained their electrical characteristics. XPS spectroscopy data strongly suggested integration of the deposited metal in the TCO structure resulting in additional doping of the conducting oxide at the interface. Kelvin probe microscopy measurements revealed a significant decrease in the ITO work function after modification. Organic solar cells based on three different conjugated polymers have demonstrated state of the art performances in inverted device geometry using Mg- or Yb-modified ITO as electron collecting electrode. The simplicity of the proposed approach and the excellent ambient stability of the modified ITO electrodes allows one to expect their wide utilization in research laboratories and electronic industry.

The non-photosynthetic, pathogenic green alga Helicosporidium sp. has retained a modified, functional plastid genome.

PubMed

Tartar, Aurélien; Boucias, Drion G

2004-04-01

A fragment of the Helicosporidium sp. (Chlorophyta: Trebouxiophyceae) plastid genome has been sequenced. The genome architecture was compared to that of both a non-photosynthetic relative (Prototheca wickerhamii) and a photosynthetic relative (Chlorella vulgaris). Comparative genomic analysis indicated that Helicosporidium and Prototheca are closely related genera. The analyses also revealed that the Helicosporidium sp. plastid genome has been rearranged. In particular, two ribosomal protein-encoding genes (rpl19 and rps23) appeared to have been transposed, or lost from the Helicosporidium sp. plastid genome. RT-PCR reactions demonstrated that the retained plastid genes were transcribed, suggesting that, despite rearrangement(s), the Helicosporidium sp. plastid genome has remained functional. The modified plastid genome architecture is a novel apomorphy that indicates that the Helicosporidia are highly derived green algae, more so than Prototheca spp. As such, they represent a promising model to study organellar genome reorganizations in parasitic protists.

Optimization of the Synthesis of Structured Phosphatidylcholine with Medium Chain Fatty Acid.

PubMed

Ochoa-Flores, Angélica A; Hernández-Becerra, Josafat A; Cavazos-Garduño, Adriana; Vernon-Carter, Eduardo J; García, Hugo S

2017-11-01

Structured phosphatidylcholine was successfully produced by acidolysis between phosphatidylcholine and free medium chain fatty acid, using phospholipase A 1 immobilized on Duolite A568. Response surface methodology was applied to optimize the reaction system using three process parameters: molar ratio of substrates (phosphatidylcholine to free medium chain fatty acid), enzyme loading, and reaction temperature. All parameters evaluated showed linear and quadratic significant effects on the production of modified phosphatidylcholine; molar ratio of substrates contributed positively, but temperature influenced negatively. Increased enzyme loading also led to increased production of modified phosphatidylcholine but only during the first 9 hours of the acidolysis reaction. Optimal conditions obtained from the model were a ratio of phosphatidylcholine to free medium chain fatty acid of 1:15, an enzyme loading of 12%, and a temperature of 45°C. Under these conditions a production of modified phosphatidylcholine of 52.98 % were obtained after 24 h of reaction. The prediction was confirmed from the verification experiments; the production of modified phosphatidylcholine was 53.02%, the total yield of phosphatidylcholine 64.28% and the molar incorporation of medium chain fatty acid was 42.31%. The acidolysis reaction was scaled-up in a batch reactor with a similar production of modified phosphatidylcholine, total yield of phosphatidylcholine and molar incorporation of medium chain fatty acid. Purification by column chromatography of the structured phosphatidylcholine yielded 62.53% of phosphatidylcholine enriched with 42.52% of medium chain fatty acid.

HZEFRG1 - SEMIEMPIRICAL NUCLEAR FRAGMENTATION MODEL

NASA Technical Reports Server (NTRS)

Townsend, L. W.

1994-01-01

The high charge and energy (HZE), Semiempirical Nuclear Fragmentation Model, HZEFRG1, was developed to provide a computationally efficient, user-friendly, physics-based program package for generating nuclear fragmentation databases. These databases can then be used in radiation transport applications such as space radiation shielding and dosimetry, cancer therapy with laboratory heavy ion beams, and simulation studies of detector design in nuclear physics experiments. The program provides individual element and isotope production cross sections for the breakup of high energy heavy ions by the combined nuclear and Coulomb fields of the interacting nuclei. The nuclear breakup contributions are estimated using an energy-dependent abrasion-ablation model of heavy ion fragmentation. The abrasion step involves removal of nucleons by direct knockout in the overlap region of the colliding nuclei. The abrasions are treated on a geometric basis and uniform spherical nuclear density distributions are assumed. Actual experimental nuclear radii obtained from tabulations of electron scattering data are incorporated. Nuclear transparency effects are included by using an energy-dependent, impact-parameter-dependent average transmission factor for the projectile and target nuclei, which accounts for the finite mean free path of nucleons in nuclear matter. The ablation step, as implemented by Bowman, Swiatecki, and Tsang (LBL report no. LBL-2908, July 1973), was treated as a single-nucleon emission for every 10 MeV of excitation energy. Fragmentation contributions from electromagnetic dissociation (EMD) processes, arising from the interacting Coulomb fields, are estimated by using the Weiszacker-Williams theory, extended to include electric dipole and electric quadrupole contributions to one-nucleon removal cross sections. HZEFRG1 consists of a main program, seven function subprograms, and thirteen subroutines. Each is fully commented and begins with a brief description of its functionality. The inputs, which are provided interactively by the user in response to on-screen questions, consist of the projectile kinetic energy in units of MeV/nucleon and the masses and charges of the projectile and target nuclei. With proper inputs, HZEFRG1 first calculates the EMD cross sections and then begins the calculations for nuclear fragmentation by searching through a specified number of isotopes for each charge number (Z) from Z=1 (hydrogen) to the charge of the incident fragmenting nucleus (Zp). After completing the nuclear fragmentation cross sections, HZEFRG1 sorts through the results and writes the sorted output to a file in descending order, based on the charge number of the fragmented nucleus. Details of the theory, extensive comparisons of its predictions with available experimental cross section data, and a complete description of the code implementing it are given in the program documentation. HZEFRG1 is written in ANSI FORTRAN 77 to be machine independent. It was originally developed on a DEC VAX series computer, and has been successfully implemented on a DECstation running RISC ULTRIX 4.3, a Sun4 series computer running SunOS 4.1, an HP 9000 series computer running HP-UX 8.0.1, a Cray Y-MP series computer running UNICOS, and IBM PC series computers running MS-DOS 3.3 and higher. HZEFRG1 requires 1Mb of RAM for execution. In addition, a FORTRAN 77 compiler is required to create an executable. A sample output run is included on the distribution medium for numerical comparison. The standard distribution medium for this program is a 3.5 inch 1.44Mb MS-DOS format diskette. Alternate distribution media and formats are available upon request. HZEFRG1 was completed in 1992.

Modular Simulation of HEI Fragments and Blast Pressure.

DTIC Science & Technology

1992-03-01

TEU04D MODULAR SIMULATION OF Accesion For HEI FRAGMENTS AND BLAST PRESSURE NTIS CRAMI DTIC TAB 1] THESIS U.a:’ ouIced Jusification Gordon Galloway C... sustained by a component due to disturbances cre- ated in the medium surrounding the component when no fragment im- pacts are possible. In general, a...component will sustain a maximum kill if located within a minimum range from the burst point [RB(MAX)], and will sustain no damage if it is located beyond a

The use of autologous adult, allogenic juvenile, and combined juvenile-adult cartilage fragments for the repair of chondral defects.

PubMed

Bonasia, Davide Edoardo; Martin, James A; Marmotti, Antonio; Kurriger, Gail L; Lehman, Abigail D; Rossi, Roberto; Amendola, Annunziato

2016-12-01

The goal of the study was to evaluate the repair of chondral lesions treated with combined autologous adult/allogenic juvenile cartilage fragments, compared with isolated adult and isolated juvenile cartilage fragments. Fifty-eight adult (>16 week old) and five juvenile (<6 week old) New Zealand White female rabbits were used. A large osteochondral defect was created in the center of the femoral trochlea of adult rabbits. The rabbits were divided in four groups: Group 1 = untreated defects (controls); Group 2 = adult cartilage fragments; Group 3 = juvenile cartilage fragments; and Group 4 = adult + juvenile cartilage fragments. Killings were performed at 3 and 6 months. The defects were evaluated with ICRS macroscopic score, modified O'Driscoll score, and Collagen type II immunostaining. At 3 months, Group 4 performed better than Group 1, in terms of modified O'Driscoll score (p = 0.001) and Collagen type II immunostaining (p = 0.015). At 6 months, Group 4 showed higher modified O'Driscoll score (p = 0.003) and Collagen type II immunostaining score (p < 0.001) than Group 1. Histologically, also Group 3 performed better than Group 1 (p = 0.03), and Group 4 performed better than Group 2 (p = 0.004). Mixing adult and juvenile cartilage fragments improved cartilage repair in a rabbit model. In the clinical setting, a new "one-stage" procedure combining the two cartilage sources can be hypothesized, with the advantages of improved chondral repair and large defect coverage, because of the use of an off-the-shelf juvenile allograft. Further studies on larger animals and clinical trials are required to confirm these results.

Organic Chemistry in Space

NASA Technical Reports Server (NTRS)

Charnley, Steven

2009-01-01

Astronomical observations, theoretical modeling, laboratory simulation and analysis of extraterrestrial material have enhanced our knowledge of the inventory of organic matter in the interstellar medium (ISM) and on small bodies such as comets and asteroids (Ehrenfreund & Charnley 2000). Comets, asteroids and their fragments, meteorites and interplanetary dust particles (IDPs), contributed significant amounts of extraterrestrial organic matter to the young Earth. This material degraded and reacted in a terrestrial prebiotic chemistry to form organic structures that may have served as building blocks for life on the early Earth. In this talk I will summarize our current understanding of the organic composition and chemistry of interstellar clouds. Molecules of astrobiological relevance include the building blocks of our genetic material: nucleic acids, composed of subunits such as N-heterocycles (purines and pyrimidines), sugars and amino acids. Signatures indicative of inheritance of pristine and modified interstellar material in comets and meteorites will also be discussed.

Dispersion and Attenuation Due to Scattering from Heterogeneities of the Frame Bulk Modulus of a Poroelastic Medium

DTIC Science & Technology

2010-02-19

attenuation is a function of the Hurst exponent which characterizes the fractal het- erogeneity. Muller and Gurevich15,16 used statistical smoothing of...modified Bessel function of the third kind, Γ denotes the gamma function, and ν is the Hurst coefficient which is assumed to be 0 < ν ≤ 1. The three...The Hurst coefficient, ν, is ν = 0.1 (long-dashed line), ν = 0.5 (short-dashed line), and ν = 0.9 (long-short dashed line). In (a) the sound speed

Improving the reliability of road materials based on micronized sulfur composites

NASA Astrophysics Data System (ADS)

Abdrakhmanova, K. K.

2015-01-01

The work contains the results of a nano-structural modification of sulfur that prevents polymorphic transformations from influencing the properties of sulfur composites where sulfur is present in a thermodynamic stable condition that precludes destruction when operated. It has been established that the properties of sulfur-based composite materials can be significantly improved by modifying sulfur and structuring sulfur binder by nano-dispersed fiber particles and ultra-dispersed state filler. The paper shows the possibility of modifying Tengiz sulfur by its fragmenting which ensures that the structured sulfur is structurally changed and stabilized through reinforcement by ultra-dispersed fiber particles allowing the phase contact area to be multiplied. Interaction between nano-dispersed fibers of chrysotile asbestos and sulfur ensures the implementation of the mechanical properties of chrysotile asbestos tubes in reinforced composite and its integrity provided that the surface of chrysotile asbestos tubes are highly moistened with molten sulfur and there is high adhesion between the tubes and the matrix that, in addition to sulfur, contains limestone microparticles. Ability to apply materials in severe operation conditions and possibility of exposure in both aggressive medium and mechanical loads makes produced sulfur composites required by the road construction industry.

The Contribution of the Activation Entropy to the Gas-Phase Stability of Modified Nucleic Acid Duplexes

NASA Astrophysics Data System (ADS)

Hari, Yvonne; Dugovič, Branislav; Istrate, Alena; Fignolé, Annabel; Leumann, Christian J.; Schürch, Stefan

2016-07-01

Tricyclo-DNA (tcDNA) is a sugar-modified analogue of DNA currently tested for the treatment of Duchenne muscular dystrophy in an antisense approach. Tandem mass spectrometry plays a key role in modern medical diagnostics and has become a widespread technique for the structure elucidation and quantification of antisense oligonucleotides. Herein, mechanistic aspects of the fragmentation of tcDNA are discussed, which lay the basis for reliable sequencing and quantification of the antisense oligonucleotide. Excellent selectivity of tcDNA for complementary RNA is demonstrated in direct competition experiments. Moreover, the kinetic stability and fragmentation pattern of matched and mismatched tcDNA heteroduplexes were investigated and compared with non-modified DNA and RNA duplexes. Although the separation of the constituting strands is the entropy-favored fragmentation pathway of all nucleic acid duplexes, it was found to be only a minor pathway of tcDNA duplexes. The modified hybrid duplexes preferentially undergo neutral base loss and backbone cleavage. This difference is due to the low activation entropy for the strand dissociation of modified duplexes that arises from the conformational constraint of the tc-sugar-moiety. The low activation entropy results in a relatively high free activation enthalpy for the dissociation comparable to the free activation enthalpy of the alternative reaction pathway, the release of a nucleobase. The gas-phase behavior of tcDNA duplexes illustrates the impact of the activation entropy on the fragmentation kinetics and suggests that tandem mass spectrometric experiments are not suited to determine the relative stability of different types of nucleic acid duplexes.

Release of ICTP and CTX telopeptides from demineralized dentin matrices: Effect of time, mass and surface area.

PubMed

Turco, Gianluca; Cadenaro, Milena; Maravić, Tatjana; Frassetto, Andrea; Marsich, Eleonora; Mazzoni, Annalisa; Di Lenarda, Roberto; Tay, Franklin R; Pashley, David H; Breschi, Lorenzo

2018-03-01

The present study evaluated the influence of time, mass and surface area of demineralized dentin collagen matrices on telopeptides release. The hypotheses tested were that the rates of ICTP and CTX release by matrix bound endogenous proteases are 1) not time-dependent, 2) unrelated to specimen mass, 3) unrelated to specimen surface area. Non-carious human molars (N=24) were collected and randomly assigned to three groups. Dentin slabs with three different thicknesses: 0.37mm, 0.75mm, and 1.50mm were completely demineralized and stored in artificial saliva for one week. Collagen degradation was evaluated by sampling storage media for ICTP and CTX telopeptidases. Activity of MMPs in the aging medium was evaluated using fluorometric activity assay kit. A statistically significant (p<0.05) decrease in the release of both ICTP and CTX fragments over time was observed irrespective of the specimen thickness. When data were normalized by the specimen mass, no significant differences were observed. Releases of ICTP and CTX were significantly related to the aging time as a function of surface area for the first 12h. Total MMP activity, mainly related to MMP-2 and -9, decreased with time (p<0.05). Because the release of collagen fragments was influenced by specimen storage time and surface area, it is likely that cleaved collagen fragments closer to the specimen surface diffuse into the incubation medium; those further away from the exposed surface are still entrapped within the demineralized dentin matrix. Bound MMPs can only degrade the substrate within the limited zone of their molecular mobility. Copyright © 2017 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Improvement of exopolysaccharide production by Porphyridium marinum.

PubMed

Soanen, Nastasia; Da Silva, Elise; Gardarin, Christine; Michaud, Philippe; Laroche, Céline

2016-08-01

With the aim to optimize the production of exopolysaccharide (EPS) by Porphyridium marinum, cultures in photobioreactors were conducted on a modified Provasoli medium (P) and compared to a new medium (Pm) with an elemental composition of N0.0205S0.0597P0.005. Cultivation on this medium allowed the increase of EPS concentration up to 2.5gL(-1), without modification of the EPS productivity (0.096gL(-1)) and EPS structure. In a second time, photosynthetic activity of the strain was monitored as a function of irradiance and temperature, allowing improvement of kinetic parameters of growth and EPS production. A semi-continuous culture, carried out with the Pm medium, an optimal irradiance and temperature of respectively 360μmolphotonsm(-2)s(-1) and 28°C led to an EPS process productivity of 0.031gh(-1) instead of 0.020gh(-1) in batch culture. Copyright © 2016 Elsevier Ltd. All rights reserved.

Relativistic direct Urca processes in cooling neutron stars

NASA Astrophysics Data System (ADS)

Leinson, L. B.; Pérez, A.

2001-10-01

We derive a relativistic expression for neutrino energy losses caused by the direct Urca processes in degenerate baryon matter of neutron stars. We use two different ways to calculate the emissivity caused by the reactions to our interest. First we perform a standard calculation by Fermi's ``golden'' rule. The second calculation, resulting in the same expression, is performed with the aid of polarization functions of the medium. Our result for neutrino energy losses strongly differs from previous nonrelativistic results. We also discuss nonconservation of the baryon vector current in reactions through weak charged currents in the medium, when the asymmetry between protons and neutrons is considered. The above effects, not discussed in the literature before, substantially modify the polarization functions responsible for the induced weak charged currents in baryon matter.

Cluster kinetics model of particle separation in vibrated granular media.

PubMed

McCoy, Benjamin J; Madras, Giridhar

2006-01-01

We model the Brazil-nut effect (BNE) by hypothesizing that granules form clusters that fragment and aggregate. This provides a heterogeneous medium in which the immersed intruder particle rises (BNE) or sinks (reverse BNE) according to relative convection currents and buoyant and drag forces. A simple relationship proposed for viscous drag in terms of the vibrational intensity and the particle to grain density ratio allows simulation of published experimental data for rise and sink times as functions of particle radius, initial depth of the particle, and particle-grain density ratio. The proposed model correctly describes the experimentally observed maximum in risetime.

Heavy and light flavor jet quenching at RHIC and LHC energies

NASA Astrophysics Data System (ADS)

Cao, Shanshan; Luo, Tan; Qin, Guang-You; Wang, Xin-Nian

2018-02-01

The Linear Boltzmann Transport (LBT) model coupled to hydrodynamical background is extended to include transport of both light partons and heavy quarks through the quark-gluon plasma (QGP) in high-energy heavy-ion collisions. The LBT model includes both elastic and inelastic medium-interaction of both primary jet shower partons and thermal recoil partons within perturbative QCD (pQCD). It is shown to simultaneously describe the experimental data on heavy and light flavor hadron suppression in high-energy heavy-ion collisions for different centralities at RHIC and LHC energies. More detailed investigations within the LBT model illustrate the importance of both initial parton spectra and the shapes of fragmentation functions on the difference between the nuclear modifications of light and heavy flavor hadrons. The dependence of the jet quenching parameter q ˆ on medium temperature and jet flavor is quantitatively extracted.

Heavy and light flavor jet quenching at RHIC and LHC energies

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

Cao, Shanshan; Luo, Tan; Qin, Guang-You

The Linear Boltzmann Transport (LBT) model coupled to hydrodynamical background is extended to include transport of both light partons and heavy quarks through the quark–gluon plasma (QGP) in high-energy heavy-ion collisions. The LBT model includes both elastic and inelastic medium-interaction of both primary jet shower partons and thermal recoil partons within perturbative QCD (pQCD). It is shown to simultaneously describe the experimental data on heavy and light flavor hadron suppression in high-energy heavy-ion collisions for different centralities at RHIC and LHC energies. More detailed investigations within the LBT model illustrate the importance of both initial parton spectra and the shapes of fragmentation functions on the difference between the nuclear modifications of light and heavy flavor hadrons. Finally, the dependence of the jet quenching parametermore » $$\\hat{q}$$ on medium temperature and jet flavor is quantitatively extracted.« less

Heavy and light flavor jet quenching at RHIC and LHC energies

DOE PAGES

Cao, Shanshan; Luo, Tan; Qin, Guang-You; ...

2017-12-14

The Linear Boltzmann Transport (LBT) model coupled to hydrodynamical background is extended to include transport of both light partons and heavy quarks through the quark–gluon plasma (QGP) in high-energy heavy-ion collisions. The LBT model includes both elastic and inelastic medium-interaction of both primary jet shower partons and thermal recoil partons within perturbative QCD (pQCD). It is shown to simultaneously describe the experimental data on heavy and light flavor hadron suppression in high-energy heavy-ion collisions for different centralities at RHIC and LHC energies. More detailed investigations within the LBT model illustrate the importance of both initial parton spectra and the shapes of fragmentation functions on the difference between the nuclear modifications of light and heavy flavor hadrons. Finally, the dependence of the jet quenching parametermore » $$\\hat{q}$$ on medium temperature and jet flavor is quantitatively extracted.« less

Robustness of plant-insect herbivore interaction networks to climate change in a fragmented temperate forest landscape.

PubMed

Bähner, K W; Zweig, K A; Leal, I R; Wirth, R

2017-10-01

Forest fragmentation and climate change are among the most severe and pervasive forms of human impact. Yet, their combined effects on plant-insect herbivore interaction networks, essential components of forest ecosystems with respect to biodiversity and functioning, are still poorly investigated, particularly in temperate forests. We addressed this issue by analysing plant-insect herbivore networks (PIHNs) from understories of three managed beech forest habitats: small forest fragments (2.2-145 ha), forest edges and forest interior areas within three continuous control forests (1050-5600 ha) in an old hyper-fragmented forest landscape in SW Germany. We assessed the impact of forest fragmentation, particularly edge effects, on PIHNs and the resulting differences in robustness against climate change by habitat-wise comparison of network topology and biologically realistic extinction cascades of networks following scores of vulnerability to climate change for the food plant species involved. Both the topological network metrics (complexity, nestedness, trophic niche redundancy) and robustness to climate change strongly increased in forest edges and fragments as opposed to the managed forest interior. The nature of the changes indicates that human impacts modify network structure mainly via host plant availability to insect herbivores. Improved robustness of PIHNs in forest edges/small fragments to climate-driven extinction cascades was attributable to an overall higher thermotolerance across plant communities, along with positive effects of network structure. The impoverishment of PIHNs in managed forest interiors and the suggested loss of insect diversity from climate-induced co-extinction highlight the need for further research efforts focusing on adequate silvicultural and conservation approaches.

Medium-sized tandem repeats represent an abundant component of the Drosophila virilis genome.

PubMed

Abdurashitov, Murat A; Gonchar, Danila A; Chernukhin, Valery A; Tomilov, Victor N; Tomilova, Julia E; Schostak, Natalia G; Zatsepina, Olga G; Zelentsova, Elena S; Evgen'ev, Michael B; Degtyarev, Sergey K H

2013-11-09

Previously, we developed a simple method for carrying out a restriction enzyme analysis of eukaryotic DNA in silico, based on the known DNA sequences of the genomes. This method allows the user to calculate lengths of all DNA fragments that are formed after a whole genome is digested at the theoretical recognition sites of a given restriction enzyme. A comparison of the observed peaks in distribution diagrams with the results from DNA cleavage using several restriction enzymes performed in vitro have shown good correspondence between the theoretical and experimental data in several cases. Here, we applied this approach to the annotated genome of Drosophila virilis which is extremely rich in various repeats. Here we explored the combined approach to perform the restriction analysis of D. virilis DNA. This approach enabled to reveal three abundant medium-sized tandem repeats within the D. virilis genome. While the 225 bp repeats were revealed previously in intergenic non-transcribed spacers between ribosomal genes of D. virilis, two other families comprised of 154 bp and 172 bp repeats were not described. Tandem Repeats Finder search demonstrated that 154 bp and 172 bp units are organized in multiple clusters in the genome of D. virilis. Characteristically, only 154 bp repeats derived from Helitron transposon are transcribed. Using in silico digestion in combination with conventional restriction analysis and sequencing of repeated DNA fragments enabled us to isolate and characterize three highly abundant families of medium-sized repeats present in the D. virilis genome. These repeats comprise a significant portion of the genome and may have important roles in genome function and structural integrity. Therefore, we demonstrated an approach which makes possible to investigate in detail the gross arrangement and expression of medium-sized repeats basing on sequencing data even in the case of incompletely assembled and/or annotated genomes.

Pitheciids in fragmented habitats: Land cover change and its implications for conservation.

PubMed

Boyle, Sarah A

2016-05-01

Pitheciids (Cacajao, Callicebus, Chiropotes, and Pithecia) have experienced habitat loss and fragmentation across their geographic range in South America. Some populations living in habitat fragments live in smaller groups, travel shorter distances, and consume items that are not regularly found in the diets of populations living in continuous habitat; however, these patterns are not consistent across species. I used the IUCN Red List of Threatened Species to delineate the geographic range and conservation status of 43 pitheciid species. I calculated the amount of modified land cover within the range of each species, as well as the extent to which the remaining habitat exists in small fragments and the amount of forest lost from 2000 to 2012. Mean forest fragment size ranged from 12 to 12,027 ha, and mean forest loss from 2000 to 2012 ranged from 10.7% for Chiropotes to 0.9% for Pithecia. Critically Endangered and Endangered species represented 20.9% of the pitheciid species, and 46.5% of these species had population trends documented as decreasing. Total modified land cover was greatest for Callicebus species (18.0% of geographic range), followed by Chiropotes (13.8%), Pithecia (4.4%), and Cacajao (1.1%). Species of greater conservation concern had smaller geographic ranges, and a greater percentage of their range consisting of modified land cover than species of lower conservation concern. Species of greater conservation concern also had a greater percentage of forest lost from 2000 to 2012 and a smaller percentage of the remaining forest being protected. Most studies of pitheciids in fragments have concentrated on census data; the behavior of pitheciids in fragments has been examined for only 9 of the 43 species. Increased data on the responses of pitheciid species to forest loss and fragmentation are necessary in order to address pitheciid conservation, especially in areas undergoing severe habitat loss. © 2014 Wiley Periodicals, Inc.

Aggravation of cold-induced injury in Vero-B4 cells by RPMI 1640 medium - identification of the responsible medium components.

PubMed

Pless-Petig, Gesine; Metzenmacher, Martin; Türk, Tobias R; Rauen, Ursula

2012-10-10

In modern biotechnology, there is a need for pausing cell lines by cold storage to adapt large-scale cell cultures to the variable demand for their products. We compared various cell culture media/solutions for cold storage of Vero-B4 kidney cells, a cell line widely used in biotechnology. Cold storage in RPMI 1640 medium, a recommended cell culture medium for Vero-B4 cells, surprisingly, strongly enhanced cold-induced cell injury in these cells in comparison to cold storage in Krebs-Henseleit buffer or other cell culture media (DMEM, L-15 and M199). Manufacturer, batch, medium supplements and the most likely components with concentrations outside the range of the other media/solutions (vitamin B12, inositol, biotin, p-aminobenzoic acid) did not cause this aggravation of cold-induced injury in RPMI 1640. However, a modified Krebs-Henseleit buffer with a low calcium concentration (0.42 mM), a high concentration of inorganic phosphate (5.6 mM), and glucose (11.1 mM; i.e. concentrations as in RPMI 1640) evoked a cell injury and loss of metabolic function corresponding to that observed in RPMI 1640. Deferoxamine improved cell survival and preserved metabolic function in modified Krebs-Henseleit buffer as well as in RPMI 1640. Similar Ca2+ and phosphate concentrations did not increase cold-induced cell injury in the kidney cell line LLC-PK1, porcine aortic endothelial cells or rat hepatocytes. However, more extreme conditions (Ca2+ was nominally absent and phosphate concentration raised to 25 mM as in the organ preservation solution University of Wisconsin solution) also increased cold-induced injury in rat hepatocytes and porcine aortic endothelial cells. These data suggest that the combination of low calcium and high phosphate concentrations in the presence of glucose enhances cold-induced, iron-dependent injury drastically in Vero-B4 cells, and that a tendency for this pathomechanism also exists in other cell types.

Flanking sequence determination and event-specific detection of genetically modified wheat B73-6-1.

PubMed

Xu, Junyi; Cao, Jijuan; Cao, Dongmei; Zhao, Tongtong; Huang, Xin; Zhang, Piqiao; Luan, Fengxia

2013-05-01

In order to establish a specific identification method for genetically modified (GM) wheat, exogenous insert DNA and flanking sequence between exogenous fragment and recombinant chromosome of GM wheat B73-6-1 were successfully acquired by means of conventional polymerase chain reaction (PCR) and thermal asymmetric interlaced (TAIL)-PCR strategies. Newly acquired exogenous fragment covered the full-length sequence of transformed genes such as transformed plasmid and corresponding functional genes including marker uidA, herbicide-resistant bar, ubiquitin promoter, and high-molecular-weight gluten subunit. The flanking sequence between insert DNA revealed high similarity with Triticum turgidum A gene (GenBank: AY494981.1). A specific PCR detection method for GM wheat B73-6-1 was established on the basis of primers designed according to the flanking sequence. This specific PCR method was validated by GM wheat, GM corn, GM soybean, GM rice, and non-GM wheat. The specifically amplified target band was observed only in GM wheat B73-6-1. This method is of high specificity, high reproducibility, rapid identification, and excellent accuracy for the identification of GM wheat B73-6-1.

Effects of FSH addition to an enriched medium containing insulin and EGF after long-term culture on functionality of equine ovarian biopsy tissue.

PubMed

Aguiar, F L N; Gastal, G D A; Ishak, G M; Gastal, M O; Teixeira, D I A; Feugang, J M; Figueiredo, J R; Gastal, E L

2017-09-01

The effect of FSH supplementation on an enriched cultured medium containing insulin (10 ng/mL) and EGF (50 ng/mL) was investigated on in vitro culture of equine ovarian biopsy tissue. Ovarian tissue fragments were collected from mares (n = 10) and distributed in the following treatments: noncultured control, cultured control, and cultured + FSH. Both treated groups were cultured for 7 or 15 days. The end points evaluated were: follicular morphology, estradiol levels in the culture medium, fluorescence intensity for TUNEL, EGFR and Ki-67 detection, and gene expression of GDF-9, BMP-15, and Cyclin-D2 in the ovarian tissue. After seven days of culture, medium supplemented with FSH had a similar (P > 0.05) percentage of morphologically normal follicles compared to the noncultured control group. Estradiol levels increased (P < 0.05) from Day 7 to Day 15 of culture for both treated groups. No difference (P > 0.05) was observed for TUNEL and EGFR intensity between the noncultured control group and the treated groups after 15 days of culture. Ki-67 intensity did not differ (P > 0.05) between treated groups after 15 days of culture, but decreased (P < 0.05) when compared with the noncultured control group. Similar (P > 0.05) mRNA expression for GDF-9, BMP-15, and Cyclin-D2 was observed among all treatments after 15 days of culture. In conclusion, an enriched medium supplemented or not with FSH was able to maintain the functionality of equine ovarian biopsy tissue after a long-term in vitro culture. Copyright © 2017 Elsevier Inc. All rights reserved.

Ultrasensitive direct impedimetric immunosensor for detection of serum HER2.

PubMed

Sharma, Shikha; Zapatero-Rodríguez, Julia; Saxena, Rahul; O'Kennedy, Richard; Srivastava, Sudha

2018-05-30

Assesment of human epidermal growth factor receptor 2 status is a key factor prompting definitive treatment decisions that help in reducing mortality rates associated with breast cancer. In this article, highly sensitive and low-cost impedimetric immunosensor using single-chain fragment variable antibody fragments was developed for quantitative detection of human epidermal growth factor receptor 2 from serum employing gold nanoparticle-modified disposable screen-printed carbon electrodes. The gold nanoparticles facilitate fast electron transfer and offer a biocompatible surface for immobilization of small antibody fragments in an oriented manner, resulting in improved antigen binding efficiency. The single-chain fragment variable antibody fragment-modified screen printed immunosensor exhibits wide dynamic range of 0.01-100 ng mL -1 and detection limit of 0.01 ng mL -1 . The advantages offered by this platform in terms of high sensitivity, broad dynamic range and low-cost demonstrates great potential for improved monitoring of human epidermal growth factor receptor 2 levels for the management of breast and other cancers. Copyright © 2018 Elsevier B.V. All rights reserved.

Heavy flavor puzzle at LHC: a serendipitous interplay of jet suppression and fragmentation.

PubMed

Djordjevic, Magdalena

2014-01-31

Both charged hadrons and D mesons are considered to be excellent probes of QCD matter created in ultrarelativistic heavy ion collisions. Surprisingly, recent experimental observations at LHC show the same jet suppression for these two probes, which--contrary to pQCD expectations--may suggest similar energy losses for light quarks and gluons in the QCD medium. We here use our recently developed energy loss formalism in a finite-size dynamical QCD medium to analyze this phenomenon that we denote as the "heavy flavor puzzle at LHC." We show that this puzzle is a consequence of an unusual combination of the suppression and fragmentation patterns and, in fact, does not require invoking the same energy loss for light partons. Furthermore, we show that this combination leads to a simple relationship between the suppressions of charged hadrons and D mesons and the corresponding bare quark suppressions. Consequently, a coincidental matching of jet suppression and fragmentation allows considerably simplifying the interpretation of the corresponding experimental data.

An evaluation of a new approach to the regeneration of Helichrysum italicum (Roth) G. Don, and the molecular characterization of the variation among sets of differently derived regenerants.

PubMed

Perrini, Rosaria; Alba, Vittorio; Ruta, Claudia; Morone-Fortunato, Irene; Blanco, Antonio; Montemurro, Cinzia

2009-01-01

A protocol for the induction of regeneration from leaves of Helichrysum italicum was established. Calli were found to form on the basal medium only when it was supplemented with thidiazuron (TDZ) alone or in combination with naphthalene acetic acid (NAA), with a percentage ranking of at least 80%. The hormone-free medium showed the highest percentage of shoot regeneration (62%) even though no callus formed. AFLP markers were employed to verify tissue culture-induced variation in the regenerated plantlets obtained by direct shoot regeneration or the indirect shoot regeneration process (callus formation). Seven out of the eleven AFLP primer pairs yielded polymorphic patterns. The average number of fragments per primer pair was 64.1. Singletons were represented by 12 (2.7%) fragments. Student's T-test was performed both on the average number of shared fragments and on the nucleotide diversity, and no significant statistical difference was observed between the two regeneration treatments.

rFN/Cad-11-Modified Collagen Type II Biomimetic Interface Promotes the Adhesion and Chondrogenic Differentiation of Mesenchymal Stem Cells

PubMed Central

Guo, Hongfeng; Zhang, Yuan; Li, Zhengsheng; Kang, Fei; Yang, Bo; Kang, Xia; Wen, Can; Yan, Yanfei; Jiang, Bo; Fan, Yujiang

2013-01-01

Properties of the cell-material interface are determining factors in the successful function of cells for cartilage tissue engineering. Currently, cell adhesion is commonly promoted through the use of polypeptides; however, due to their lack of complementary or modulatory domains, polypeptides must be modified to improve their ability to promote adhesion. In this study, we utilized the principle of matrix-based biomimetic modification and a recombinant protein, which spans fragments 7–10 of fibronectin module III (heterophilic motif ) and extracellular domains 1–2 of cadherin-11 (rFN/Cad-11) (homophilic motif ), to modify the interface of collagen type II (Col II) sponges. We showed that the designed material was able to stimulate cell proliferation and promote better chondrogenic differentiation of rabbit mesenchymal stem cells (MSCs) in vitro than both the FN modified surfaces and the negative control. Further, the Col II/rFN/Cad-11-MSCs composite stimulated cartilage formation in vivo; the chondrogenic effect of Col II alone was much less significant. These results suggested that the rFN/Cad-11-modified collagen type II biomimetic interface has dual biological functions of promoting adhesion and stimulating chondrogenic differentiation. This substance, thus, may serve as an ideal scaffold material for cartilage tissue engineering, enhancing repair of injured cartilage in vivo. PMID:23919505

78 FR 27995 - Notice of Inventory Completion for Native American Human Remains and Associated Funerary Objects...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-13

... fragments, 29 historic ceramic sherds, 1 prehistoric ceramic sherd, 128 unmodified faunal bone fragments, 1 modified deer rib, 3 bone buttons, 4 chipped stone flakes, 2 wooden buttons, 1 historic clay pipe bowl...

Evaluation of genetic diversity in jackfruit (Artocarpus heterophyllus Lam.) based on amplified fragment length polymorphism markers.

PubMed

Shyamalamma, S; Chandra, S B C; Hegde, M; Naryanswamy, P

2008-07-22

Artocarpus heterophyllus Lam., commonly called jackfruit, is a medium-sized evergreen tree that bears high yields of the largest known edible fruit. Yet, it has been little explored commercially due to wide variation in fruit quality. The genetic diversity and genetic relatedness of 50 jackfruit accessions were studied using amplified fragment length polymorphism markers. Of 16 primer pairs evaluated, eight were selected for screening of genotypes based on the number and quality of polymorphic fragments produced. These primer combinations produced 5976 bands, 1267 (22%) of which were polymorphic. Among the jackfruit accessions, the similarity coefficient ranged from 0.137 to 0.978; the accessions also shared a large number of monomorphic fragments (78%). Cluster analysis and principal component analysis grouped all jackfruit genotypes into three major clusters. Cluster I included the genotypes grown in a jackfruit region of Karnataka, called Tamaka, with very dry conditions; cluster II contained the genotypes collected from locations having medium to heavy rainfall in Karnataka; cluster III grouped the genotypes in distant locations with different environmental conditions. Strong coincidence of these amplified fragment length polymorphism-based groupings with geographical localities as well as morphological characters was observed. We found moderate genetic diversity in these jackfruit accessions. This information should be useful for tree breeding programs, as part of our effort to popularize jackfruit as a commercial crop.

Predicting primate local extinctions within "real-world" forest fragments: a pan-neotropical analysis.

PubMed

Benchimol, Maíra; Peres, Carlos A

2014-03-01

Understanding the main drivers of species extinction in human-modified landscapes has gained paramount importance in proposing sound conservation strategies. Primates play a crucial role in maintaining the integrity of forest ecosystem functions and represent the best studied order of tropical terrestrial vertebrates, yet primate species diverge widely in their responses to forest habitat disturbance and fragmentation. Here, we present a robust quantitative review on the synergistic effects of habitat fragmentation on Neotropical forest primates to pinpoint the drivers of species extinction across a wide range of forest patches from Mexico to Argentina. Presence-absence data on 19 primate functional groups were compiled from 705 forest patches and 55 adjacent continuous forest sites, which were nested within 61 landscapes investigated by 96 studies. Forest patches were defined in terms of their size, surrounding matrix and level of hunting pressure on primates, and each functional group was classified according to seven life-history traits. Generalized linear mixed models showed that patch size, forest cover, level of hunting pressure, home range size and trophic status were the main predictors of species persistence within forest isolates for all functional groups pooled together. However, patterns of local extinction varied greatly across taxa, with Alouatta and Callicebus moloch showing the highest occupancy rates even within tiny forest patches, whereas Brachyteles and Leontopithecus occupied fewer than 50% of sites, even in relatively large forest tracts. Our results uncover the main predictors of platyrrhine primate species extinction, highlighting the importance of considering the history of anthropogenic disturbances, the structure of landscapes, and species life-history attributes in predicting primate persistence in Neotropical forest patches. We suggest that large-scale conservation planning of fragmented forest landscapes should prioritize and set-aside large, well-connected and strictly protected forest reserves to maximize species persistence across the entire spectrum of primate life-history. © 2013 Wiley Periodicals, Inc.

Spermatogonial Culture Medium: An Effective and Efficient Nutrient Mixture for Culturing Rat Spermatogonial Stem Cells1

PubMed Central

Wu, Zhuoru; Falciatori, Ilaria; Molyneux, Laura A.; Richardson, Timothy E.; Chapman, Karen M.; Hamra, F. Kent

2009-01-01

An economical and simplified procedure to derive and propagate fully functional lines of undifferentiated rat spermatogonia in vitro is presented. The procedure is based on the formulation of a new spermatogonial culture medium termed SG medium. The SG medium is composed of a 1:1 mixture of Dulbecco modified Eagle medium:Ham F12 nutrient, 20 ng/ml of GDNF, 25 ng/ml of FGF2, 100 μM 2-mercaptoethanol, 6 mM l-glutamine, and a 1× concentration of B27 Supplement Minus Vitamin A solution. Using SG medium, six individual spermatogonial lines were derived from the testes of six separate Sprague-Dawley rats. After proliferating over a 120-day period in SG medium, stem cells within the spermatogonial cultures effectively regenerated spermatogenesis in testes of busulfan-treated recipient rats, which transmitted the donor cell haplotype to more than 75% of progeny by natural breeding. Subculturing in SG medium did not require protease treatment and was achieved by passaging the loosely bound spermatogonial cultures at 1:3 dilutions onto fresh monolayers of irradiated DR4 mouse fibroblasts every 12 days. Spermatogonial lines derived and propagated using SG medium were characterized as homogeneous populations of ZBTB16+ DAZL+ cells endowed with spermatogonial stem cell potential. PMID:19299316

Chlamydia Hijacks ARF GTPases To Coordinate Microtubule Posttranslational Modifications and Golgi Complex Positioning.

PubMed

Wesolowski, Jordan; Weber, Mary M; Nawrotek, Agata; Dooley, Cheryl A; Calderon, Mike; St Croix, Claudette M; Hackstadt, Ted; Cherfils, Jacqueline; Paumet, Fabienne

2017-05-02

The intracellular bacterium Chlamydia trachomatis develops in a parasitic compartment called the inclusion. Posttranslationally modified microtubules encase the inclusion, controlling the positioning of Golgi complex fragments around the inclusion. The molecular mechanisms by which Chlamydia coopts the host cytoskeleton and the Golgi complex to sustain its infectious compartment are unknown. Here, using a genetically modified Chlamydia strain, we discovered that both posttranslationally modified microtubules and Golgi complex positioning around the inclusion are controlled by the chlamydial inclusion protein CT813/CTL0184/InaC and host ARF GTPases. CT813 recruits ARF1 and ARF4 to the inclusion membrane, where they induce posttranslationally modified microtubules. Similarly, both ARF isoforms are required for the repositioning of Golgi complex fragments around the inclusion. We demonstrate that CT813 directly recruits ARF GTPases on the inclusion membrane and plays a pivotal role in their activation. Together, these results reveal that Chlamydia uses CT813 to hijack ARF GTPases to couple posttranslationally modified microtubules and Golgi complex repositioning at the inclusion. IMPORTANCE Chlamydia trachomatis is an important cause of morbidity and a significant economic burden in the world. However, how Chlamydia develops its intracellular compartment, the so-called inclusion, is poorly understood. Using genetically engineered Chlamydia mutants, we discovered that the effector protein CT813 recruits and activates host ADP-ribosylation factor 1 (ARF1) and ARF4 to regulate microtubules. In this context, CT813 acts as a molecular platform that induces the posttranslational modification of microtubules around the inclusion. These cages are then used to reposition the Golgi complex during infection and promote the development of the inclusion. This study provides the first evidence that ARF1 and ARF4 play critical roles in controlling posttranslationally modified microtubules around the inclusion and that Chlamydia trachomatis hijacks this novel function of ARF to reposition the Golgi complex. Copyright © 2017 Wesolowski et al.

Exploration of particle production mechanisms via angular correlations of π, K, p, Λ with ALICE in pp collisions at √S = 7 TeV

NASA Astrophysics Data System (ADS)

Janik, Małgorzata Anna

2018-02-01

Two-particle correlations as a function of Δη and Δφ are used in many colliding systems to study a wide range of physical phenomena. Examples include the collective behavior of the quark-gluon plasma medium, jets, quantum statistics or Coulomb effects, conservation laws, and resonance decays. In this work, measurements of the correlations of identified particles and their antiparticles (for π, K, p, Λ) are reported in pp collisions at √s = 7 TeV at low transverse momenta. The analysis reveals differences in particle production between baryons and mesons. The correlation functions for mesons exhibit the expected peak dominated by the effects of mini-jet fragmentation and are reproduced well by general purpose Monte Carlo generators. For baryon pairs where both particles have the same baryon number, an anti-correlation structure is observed instead of a peak centered at (Δη, Δφ) = (0, 0); an observation which presents a challenge to models typically used to describe pp data (PYTHIA, PHOJET). This baryon anti-correlation is further interpreted in the context of baryon production mechanisms in the fragmentation processes.

RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids

PubMed Central

Sample, Paul J.; Gaston, Kirk W.; Alfonzo, Juan D.; Limbach, Patrick A.

2015-01-01

Ribosomal ribonucleic acid (RNA), transfer RNA and other biological or synthetic RNA polymers can contain nucleotides that have been modified by the addition of chemical groups. Traditional Sanger sequencing methods cannot establish the chemical nature and sequence of these modified-nucleotide containing oligomers. Mass spectrometry (MS) has become the conventional approach for determining the nucleotide composition, modification status and sequence of modified RNAs. Modified RNAs are analyzed by MS using collision-induced dissociation tandem mass spectrometry (CID MS/MS), which produces a complex dataset of oligomeric fragments that must be interpreted to identify and place modified nucleosides within the RNA sequence. Here we report the development of RoboOligo, an interactive software program for the robust analysis of data generated by CID MS/MS of RNA oligomers. There are three main functions of RoboOligo: (i) automated de novo sequencing via the local search paradigm. (ii) Manual sequencing with real-time spectrum labeling and cumulative intensity scoring. (iii) A hybrid approach, coined ‘variable sequencing’, which combines the user intuition of manual sequencing with the high-throughput sampling of automated de novo sequencing. PMID:25820423

Recombinational inactivation of the gene encoding nitrate reductase in Aspergillus parasiticus.

PubMed Central

Wu, T S; Linz, J E

1993-01-01

Functional disruption of the gene encoding nitrate reductase (niaD) in Aspergillus parasiticus was conducted by two strategies, one-step gene replacement and the integrative disruption. Plasmid pPN-1, in which an internal DNA fragment of the niaD gene was replaced by a functional gene encoding orotidine monophosphate decarboxylase (pyrG), was constructed. Plasmid pPN-1 was introduced in linear form into A. parasiticus CS10 (ver-1 wh-1 pyrG) by transformation. Approximately 25% of the uridine prototrophic transformants (pyrG+) were chlorate resistant (Chlr), demonstrating their inability to utilize nitrate as a sole nitrogen source. The genetic block in nitrate utilization was confirmed to occur in the niaD gene by the absence of growth of the A. parasiticus CS10 transformants on medium containing nitrate as the sole nitrogen source and the ability to grow on several alternative nitrogen sources. Southern hybridization analysis of Chlr transformants demonstrated that the resident niaD locus was replaced by the nonfunctional allele in pPN-1. To generate an integrative disruption vector (pSKPYRG), an internal fragment of the niaD gene was subcloned into a plasmid containing the pyrG gene as a selectable marker. Circular pSKPYRG was transformed into A. parasiticus CS10. Chlr pyrG+ transformants were screened for nitrate utilization and by Southern hybridization analysis. Integrative disruption of the genomic niaD gene occurred in less than 2% of the transformants. Three gene replacement disruption transformants and two integrative disruption transformants were tested for mitotic stability after growth under nonselective conditions. All five transformants were found to stably retain the Chlr phenotype after growth on nonselective medium.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:8215371

Inferring Resilience to Fragmentation-Induced Changes in Plant Communities in a Semi-Arid Mediterranean Ecosystem

PubMed Central

de Frutos, Ángel; Navarro, Teresa; Pueyo, Yolanda; Alados, Concepción L.

2015-01-01

Predicting the capacity of ecosystems to absorb impacts from disturbance events (resilience), including land-use intensification and landscape fragmentation, is challenging in the face of global change. Little is known about the impacts of fragmentation on ecosystem functioning from a multi-dimensional perspective (multiple traits). This study used 58 500-m linear transects to quantify changes in the functional composition and resilience of vascular plant communities in response to an increase in landscape fragmentation in 18 natural scrubland fragments embedded within a matrix of abandoned crop fields in Cabo de Gata-Níjar Natural Park, Almería, Spain. Changes in functional community composition were measured using functional diversity indices (functional richness and functional dispersion) that were based on 12 plant traits. Resilience was evaluated using the functional redundancy and response diversity from the perspective of plant dispersal, which is important, particularly, in fragmented landscapes. Scrubland fragmentation was measured using the Integral Index of Connectivity (IIC). The functional richness of the plant communities was higher in the most fragmented scrubland. Conversely, the functional dispersion (i.e., spread) of trait values among species in the functional trait space was lower at the most fragmented sites; consequently, the ecological tolerance of the vegetation to scrubland fragmentation decreased. Classifying the plant species into four functional groups indicated that fragmentation favoured an increase in functional redundancy in the ‘short basal annual forbs and perennial forbs’ group, most of which are species adapted to degraded soils. An assessment based on the traits associated with plant dispersal indicated that the resilience of ‘woody plants’, an important component in the Mediterranean scrubland, and habitat fragmentation were negatively correlated; however, the correlation was positive in the ‘short basal annual forbs and perennial forbs’ and the ‘grasses’ groups. PMID:25790432

Mitochondrial morphology transitions and functions: implications for retrograde signaling?

PubMed Central

Picard, Martin; Shirihai, Orian S.; Gentil, Benoit J.

2013-01-01

In response to cellular and environmental stresses, mitochondria undergo morphology transitions regulated by dynamic processes of membrane fusion and fission. These events of mitochondrial dynamics are central regulators of cellular activity, but the mechanisms linking mitochondrial shape to cell function remain unclear. One possibility evaluated in this review is that mitochondrial morphological transitions (from elongated to fragmented, and vice-versa) directly modify canonical aspects of the organelle's function, including susceptibility to mitochondrial permeability transition, respiratory properties of the electron transport chain, and reactive oxygen species production. Because outputs derived from mitochondrial metabolism are linked to defined cellular signaling pathways, fusion/fission morphology transitions could regulate mitochondrial function and retrograde signaling. This is hypothesized to provide a dynamic interface between the cell, its genome, and the fluctuating metabolic environment. PMID:23364527

Taxane recovery from cells of Taxus in micro- and hypergravity

NASA Technical Reports Server (NTRS)

Durzan, D. J.; Ventimiglia, F.; Havel, L.

1998-01-01

Cell suspension cultures of Taxus cuspidata produce taxanes that are released from the outer surface of cells into the culture medium as free and bound alkaloids. Paclitaxel (Taxol (TM)), is an anti-cancer drug in short supply. It has a taxane ring derived from baccatin III and a C-13 phenylisoserine side-chain. This drug is produced over a wide range of gravitational forces. Monoclonal and polyclonal antibodies to paclitaxel, baccatin III, and the C-13 phenylisoserine side chain were combined in multiple-labeling studies to localize taxanes and paclitaxel on cell surfaces or on particles released into the culture medium. Bioreactor vessel design altered the composition of taxanes recovered from cells in simulated microgravity. At 10(-2) and 2x10(-4)g, taxane recovery was reduced but biomass growth and percent paclitaxel was significantly increased. At 1 to 24g, growth was reduced with a significant recovery of total taxanes with low percent paclitaxel. Bound paclitaxel was also localized in endonuclease-rich fragmenting nuclei of individual apoptotic cells. A model is presented comprising TCH (touch) genes encoding enzymes that modify taxane-bearing xylan residues in cell walls, the calcium-sensing of gravitational forces by the cytoplasm, and the predisposition of nuclei to apoptosis. This integrates the adaptive physiological and biochemical responses of drug-producing genomes with gravitational forces.

Functional traits variation explains the distribution of Aextoxicon punctatum (Aextoxicaceae) in pronounced moisture gradients within fog-dependent forest fragments.

PubMed

Salgado-Negret, Beatriz; Canessa, Rafaella; Valladares, Fernando; Armesto, Juan J; Pérez, Fernanda

2015-01-01

Climate change and fragmentation are major threats to world forests. Understanding how functional traits related to drought tolerance change across small-scale, pronounced moisture gradients in fragmented forests is important to predict species' responses to these threats. In the case of Aextoxicon punctatum, a dominant canopy tree in fog-dependent rain forest patches in semiarid Chile, we explored how the magnitude, variability and correlation patterns of leaf and xylem vessel traits and hydraulic conductivity varied across soil moisture (SM) gradients established within and among forest patches of different size, which are associated with differences in tree establishment and mortality patterns. Leaf traits varied across soil-moisture gradients produced by fog interception. Trees growing at drier leeward edges showed higher leaf mass per area, trichome and stomatal density than trees from the wetter core and windward zones. In contrast, xylem vessel traits (vessels diameter and density) did not vary producing loss of hydraulic conductivity at drier leeward edges. We also detected higher levels of phenotypic integration and variability at leeward edges. The ability of A. punctatum to modify leaf traits in response to differences in SM availability established over short distances (<500 m) facilitates its persistence in contrasting microhabitats within forest patches. However, xylem anatomy showed limited plasticity, which increases cavitation risk at leeward edges. Greater patch fragmentation, together with fluctuations in irradiance and SM in small patches, could result in higher risk of drought-related tree mortality, with profound impacts on hydrological balances at the ecosystem scale.

Functional traits variation explains the distribution of Aextoxicon punctatum (Aextoxicaceae) in pronounced moisture gradients within fog-dependent forest fragments

PubMed Central

Salgado-Negret, Beatriz; Canessa, Rafaella; Valladares, Fernando; Armesto, Juan J.; Pérez, Fernanda

2015-01-01

Climate change and fragmentation are major threats to world forests. Understanding how functional traits related to drought tolerance change across small-scale, pronounced moisture gradients in fragmented forests is important to predict species’ responses to these threats. In the case of Aextoxicon punctatum, a dominant canopy tree in fog-dependent rain forest patches in semiarid Chile, we explored how the magnitude, variability and correlation patterns of leaf and xylem vessel traits and hydraulic conductivity varied across soil moisture (SM) gradients established within and among forest patches of different size, which are associated with differences in tree establishment and mortality patterns. Leaf traits varied across soil-moisture gradients produced by fog interception. Trees growing at drier leeward edges showed higher leaf mass per area, trichome and stomatal density than trees from the wetter core and windward zones. In contrast, xylem vessel traits (vessels diameter and density) did not vary producing loss of hydraulic conductivity at drier leeward edges. We also detected higher levels of phenotypic integration and variability at leeward edges. The ability of A. punctatum to modify leaf traits in response to differences in SM availability established over short distances (<500 m) facilitates its persistence in contrasting microhabitats within forest patches. However, xylem anatomy showed limited plasticity, which increases cavitation risk at leeward edges. Greater patch fragmentation, together with fluctuations in irradiance and SM in small patches, could result in higher risk of drought-related tree mortality, with profound impacts on hydrological balances at the ecosystem scale. PMID:26257746

Living biointerfaces based on non-pathogenic bacteria support stem cell differentiation

NASA Astrophysics Data System (ADS)

Hay, Jake J.; Rodrigo-Navarro, Aleixandre; Hassi, Karoliina; Moulisova, Vladimira; Dalby, Matthew J.; Salmeron-Sanchez, Manuel

2016-02-01

Lactococcus lactis, a non-pathogenic bacteria, has been genetically engineered to express the III7-10 fragment of human fibronectin as a membrane protein. The engineered L. lactis is able to develop biofilms on different surfaces (such as glass and synthetic polymers) and serves as a long-term substrate for mammalian cell culture, specifically human mesenchymal stem cells (hMSC). This system constitutes a living interface between biomaterials and stem cells. The engineered biofilms remain stable and viable for up to 28 days while the expressed fibronectin fragment induces hMSC adhesion. We have optimised conditions to allow long-term mammalian cell culture, and found that the biofilm is functionally equivalent to a fibronectin-coated surface in terms of osteoblastic differentiation using bone morphogenetic protein 2 (BMP-2) added to the medium. This living bacteria interface holds promise as a dynamic substrate for stem cell differentiation that can be further engineered to express other biochemical cues to control hMSC differentiation.

Creation of forest edges has a global impact on forest vertebrates.

PubMed

Pfeifer, M; Lefebvre, V; Peres, C A; Banks-Leite, C; Wearn, O R; Marsh, C J; Butchart, S H M; Arroyo-Rodríguez, V; Barlow, J; Cerezo, A; Cisneros, L; D'Cruze, N; Faria, D; Hadley, A; Harris, S M; Klingbeil, B T; Kormann, U; Lens, L; Medina-Rangel, G F; Morante-Filho, J C; Olivier, P; Peters, S L; Pidgeon, A; Ribeiro, D B; Scherber, C; Schneider-Maunoury, L; Struebig, M; Urbina-Cardona, N; Watling, J I; Willig, M R; Wood, E M; Ewers, R M

2017-11-09

Forest edges influence more than half of the world's forests and contribute to worldwide declines in biodiversity and ecosystem functions. However, predicting these declines is challenging in heterogeneous fragmented landscapes. Here we assembled a global dataset on species responses to fragmentation and developed a statistical approach for quantifying edge impacts in heterogeneous landscapes to quantify edge-determined changes in abundance of 1,673 vertebrate species. We show that the abundances of 85% of species are affected, either positively or negatively, by forest edges. Species that live in the centre of the forest (forest core), that were more likely to be listed as threatened by the International Union for Conservation of Nature (IUCN), reached peak abundances only at sites farther than 200-400 m from sharp high-contrast forest edges. Smaller-bodied amphibians, larger reptiles and medium-sized non-volant mammals experienced a larger reduction in suitable habitat than other forest-core species. Our results highlight the pervasive ability of forest edges to restructure ecological communities on a global scale.

Creation of forest edges has a global impact on forest vertebrates

NASA Astrophysics Data System (ADS)

Pfeifer, M.; Lefebvre, V.; Peres, C. A.; Banks-Leite, C.; Wearn, O. R.; Marsh, C. J.; Butchart, S. H. M.; Arroyo-Rodríguez, V.; Barlow, J.; Cerezo, A.; Cisneros, L.; D'Cruze, N.; Faria, D.; Hadley, A.; Harris, S. M.; Klingbeil, B. T.; Kormann, U.; Lens, L.; Medina-Rangel, G. F.; Morante-Filho, J. C.; Olivier, P.; Peters, S. L.; Pidgeon, A.; Ribeiro, D. B.; Scherber, C.; Schneider-Maunoury, L.; Struebig, M.; Urbina-Cardona, N.; Watling, J. I.; Willig, M. R.; Wood, E. M.; Ewers, R. M.

2017-11-01

Forest edges influence more than half of the world’s forests and contribute to worldwide declines in biodiversity and ecosystem functions. However, predicting these declines is challenging in heterogeneous fragmented landscapes. Here we assembled a global dataset on species responses to fragmentation and developed a statistical approach for quantifying edge impacts in heterogeneous landscapes to quantify edge-determined changes in abundance of 1,673 vertebrate species. We show that the abundances of 85% of species are affected, either positively or negatively, by forest edges. Species that live in the centre of the forest (forest core), that were more likely to be listed as threatened by the International Union for Conservation of Nature (IUCN), reached peak abundances only at sites farther than 200-400 m from sharp high-contrast forest edges. Smaller-bodied amphibians, larger reptiles and medium-sized non-volant mammals experienced a larger reduction in suitable habitat than other forest-core species. Our results highlight the pervasive ability of forest edges to restructure ecological communities on a global scale.

Synthesis of the human insulin gene. Part II. Further improvements in the modified phosphotriester method and the synthesis of seventeen deoxyribooligonucleotide fragments constituting human insulin chains B and mini-CDNA.

PubMed Central

Sung, W L; Hsiung, H M; Brousseau, R; Michniewicz, J; Wu, R; Narang, S A

1979-01-01

The purification of protected deoxyribooligonucleotides containing phosphotriester internucleotidic linkages has been improved by developing a deactivated silica gel chromatographic technique. The efficiency of this technique as applied in the modified phosphotriester approach has been demonstrated in the rapid synthesis of seventeen pure fragments constituting the sequence of human insulin B and mini-C DNA. The sequence of each oligomer was confirmed by the two-dimensional mobility shift method of fingerprinting. Images PMID:230464

Clinical and radiographic outcomes of femoral head fractures: excision vs. fixation of fragment in Pipkin type I: what is the optimal choice for femoral head fracture?

PubMed

Park, Kyung-Soon; Lee, Keun-Bae; Na, Bo-Ram; Yoon, Taek-Rim

2015-07-01

In this work, we present relatively long-term results of femoral head fractures with a specific focus on Pipkin type I fractures. Fifty-nine femoral head fractures were treated according to modified Pipkin's classification as follows: type I, small fragment distal to the fovea centralis (FC); type II, large fragment distal to the FC; type III, large fragment proximal to the FC; type IV, comminuted fracture. There were 15 cases of type I, 28 of type II, 9 of type III, and 7 of type IV fractures. Conservative treatment with skeletal traction was performed in 4 type II cases, excision of the fragment in 15 type I and 10 type II cases, fixation of the fragment in 14 type II and all 9 type III cases, and total hip replacement in all 7 type IV cases. The overall clinical and radiographic outcomes were evaluated using previously published criteria, focusing on the results in Pipkin type I fractures with relatively large fragments. Based on Epstein criteria, in type II fractures, excellent or good clinical results were seen in 6 of 10 patients (60.0 %) treated by excision of the fragment and 12 of 14 patients (85.7 %) treated by internal fixation (p = 0.05). Also, excellent or good radiologic results were seen in 4 of 10 (40.0 %) patients treated by excision of the fragment and 12 of 14 (85.7 %) patients treated by internal fixation (p = 0.03). Even in Pipkin type I fractures, if the fragment is large (modified Pipkin type II), early reduction and internal fixation can produce good results.

Enhancing Effects of Carbon Dioxide on the Primary Isolation of Acid-Fast Bacilli in a Modified Lowenstein-Jensen Medium

PubMed Central

Gruft, Howard; Loder, Arthur

1971-01-01

Specimens inoculated on modified Lowenstein-Jensen medium were incubated aerobically and in an atmosphere of 8% CO2. Sixteen per cent of the positive specimens grew Mycobacterium tuberculosis only after incubation in CO2. PMID:5002315

High production of llama variable heavy-chain antibody fragment (VHH) fused to various reader proteins by Aspergillus oryzae.

PubMed

Hisada, Hiromoto; Tsutsumi, Hiroko; Ishida, Hiroki; Hata, Yoji

2013-01-01

Llama variable heavy-chain antibody fragment (VHH) fused to four different reader proteins was produced and secreted in culture medium by Aspergillus oryzae. These fusion proteins consisted of N-terminal reader proteins, VHH, and a C-terminal his-tag sequence which facilitated purification using one-step his-tag affinity chromatography. SDS-PAGE analysis of the deglycosylated purified fusion proteins confirmed that the molecular weight of each corresponded to the expected sum of VHH and the respective reader proteins. The apparent high molecular weight reader protein glucoamylase (GlaB) was found to be suitable for efficient VHH production. The GlaB-VHH-His protein bound its antigen, human chorionic gonadotropin, and was detectable by a new ELISA-based method using a coupled assay with glucoamylase, glucose oxidase, peroxidase, maltose, and 3,3',5,5'-tetramethylbenzidine as substrates. Addition of potassium phosphate to the culture medium induced secretion of 0.61 mg GlaB-VHH-His protein/ml culture medium in 5 days.

Shikonin Production by Callus Culture of Onosma bulbotrichom as Active Pharmaceutical Ingredient

PubMed Central

Bagheri, Fereshteh; Tahvilian, Reza; Karimi, Naser; Chalabi, Maryam; Azami, Mahsa

2018-01-01

The objective of this research was in-vitro germination and callus induction of Onosma bulbotrichum (O. bulbotrichum) as a medicinal herb which belongs to Boraginaceae family. For germination, the seeds were cultured on growth regulator-free MS medium and for callus induction, seeds were sown on modified MS medium containing different concentrations of kinetin (kn)- Indole-3-acetic acid (IAA) and kn- 2,4-D (2,4-dichlorophenoxyacetic acid), respectively. The plates were maintained in the dark at growth chamber. After 7 days seed germination on hormone-free medium and after 10 days callus initiation on modified medium in the presence of hormones was occurred. The maximum pigmented callus (100%) was observed on modified MS medium with a combination of 0.2 mg.L-1 IAA + 2.10 mg.L-1 kn. Shikonin determination was performed by HPLC method. In addition, total hydroxynaphtoquinons as polyphenols in sum of callus and culture medium were measured by spectrophotometric method and revealed that total naphtoquinones content at IAA was more than 2, 4-D. PMID:29881407

Repositioning the substrate activity screening (SAS) approach as a fragment-based method for identification of weak binders.

PubMed

Gladysz, Rafaela; Cleenewerck, Matthias; Joossens, Jurgen; Lambeir, Anne-Marie; Augustyns, Koen; Van der Veken, Pieter

2014-10-13

Fragment-based drug discovery (FBDD) has evolved into an established approach for "hit" identification. Typically, most applications of FBDD depend on specialised cost- and time-intensive biophysical techniques. The substrate activity screening (SAS) approach has been proposed as a relatively cheap and straightforward alternative for identification of fragments for enzyme inhibitors. We have investigated SAS for the discovery of inhibitors of oncology target urokinase (uPA). Although our results support the key hypotheses of SAS, we also encountered a number of unreported limitations. In response, we propose an efficient modified methodology: "MSAS" (modified substrate activity screening). MSAS circumvents the limitations of SAS and broadens its scope by providing additional fragments and more coherent SAR data. As well as presenting and validating MSAS, this study expands existing SAR knowledge for the S1 pocket of uPA and reports new reversible and irreversible uPA inhibitor scaffolds. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Medium-induced gluon radiation and colour decoherence beyond the soft approximation

NASA Astrophysics Data System (ADS)

Apolinário, Liliana; Armesto, Néstor; Milhano, José Guilherme; Salgado, Carlos A.

2015-02-01

We derive the in-medium gluon radiation spectrum off a quark within the path integral formalism at finite energies, including all next-to-eikonal corrections in the propagators of quarks and gluons. Results are computed for finite formation times, including interference with vacuum amplitudes. By rewriting the medium averages in a convenient manner we present the spectrum in terms of dipole cross sections and a colour decoherence parameter with the same physical origin as that found in previous studies of the antenna radiation. This factorisation allows us to present a simple physical picture of the medium-induced radiation for any value of the formation time, that is of interest for a probabilistic implementation of the modified parton shower. Known results are recovered for the particular cases of soft radiation and eikonal quark and for the case of a very long medium, with length much larger than the average formation times for medium-induced radiation. Technical details of the computation of the relevant n-point functions in colour space and of the required path integrals in transverse space are provided. The final result completes the calculation of all finite energy corrections for the radiation off a quark in a QCD medium that exist in the small angle approximation and for a recoilless medium.

Variable Gene Dispersal Conditions and Spatial Deforestation Patterns Can Interact to Affect Tropical Tree Conservation Outcomes

PubMed Central

Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H.

2015-01-01

Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with ‘Near’ distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal regimens will be a likely outcome of fragmentation. Conservation implications include possible manual interventions (manual manipulations of offspring dispersers and/or pollinators) in forest fragments to increase population recovery and genetic diversity retention. PMID:26000951

Variable gene dispersal conditions and spatial deforestation patterns can interact to affect tropical tree conservation outcomes.

PubMed

Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H

2015-01-01

Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with 'Near' distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal regimens will be a likely outcome of fragmentation. Conservation implications include possible manual interventions (manual manipulations of offspring dispersers and/or pollinators) in forest fragments to increase population recovery and genetic diversity retention.

Intrinsic Tau Acetylation Is Coupled to Auto-Proteolytic Tau Fragmentation

PubMed Central

Cohen, Todd J.; Constance, Brian H.; Hwang, Andrew W.; James, Michael; Yuan, Chao-Xing

2016-01-01

Tau proteins are abnormally aggregated in a range of neurodegenerative tauopathies including Alzheimer’s disease (AD). Recently, tau has emerged as an extensively post-translationally modified protein, among which lysine acetylation is critical for normal tau function and its pathological aggregation. Here, we demonstrate that tau isoforms have different propensities to undergo lysine acetylation, with auto-acetylation occurring more prominently within the lysine-rich microtubule-binding repeats. Unexpectedly, we identified a unique intrinsic property of tau in which auto-acetylation induces proteolytic tau cleavage, thereby generating distinct N- and C-terminal tau fragments. Supporting a catalytic reaction-based mechanism, mapping and mutagenesis studies showed that tau cysteines, which are required for acetyl group transfer, are also essential for auto-proteolytic tau processing. Further mass spectrometry analysis identified the C-terminal 2nd and 4th microtubule binding repeats as potential sites of auto-cleavage. The identification of acetylation-mediated auto-proteolysis provides a new biochemical mechanism for tau self-regulation and warrants further investigation into whether auto-catalytic functions of tau are implicated in AD and other tauopathies. PMID:27383765

Intrinsic Tau Acetylation Is Coupled to Auto-Proteolytic Tau Fragmentation.

PubMed

Cohen, Todd J; Constance, Brian H; Hwang, Andrew W; James, Michael; Yuan, Chao-Xing

2016-01-01

Tau proteins are abnormally aggregated in a range of neurodegenerative tauopathies including Alzheimer's disease (AD). Recently, tau has emerged as an extensively post-translationally modified protein, among which lysine acetylation is critical for normal tau function and its pathological aggregation. Here, we demonstrate that tau isoforms have different propensities to undergo lysine acetylation, with auto-acetylation occurring more prominently within the lysine-rich microtubule-binding repeats. Unexpectedly, we identified a unique intrinsic property of tau in which auto-acetylation induces proteolytic tau cleavage, thereby generating distinct N- and C-terminal tau fragments. Supporting a catalytic reaction-based mechanism, mapping and mutagenesis studies showed that tau cysteines, which are required for acetyl group transfer, are also essential for auto-proteolytic tau processing. Further mass spectrometry analysis identified the C-terminal 2nd and 4th microtubule binding repeats as potential sites of auto-cleavage. The identification of acetylation-mediated auto-proteolysis provides a new biochemical mechanism for tau self-regulation and warrants further investigation into whether auto-catalytic functions of tau are implicated in AD and other tauopathies.

Anthropogenic Habitats Facilitate Dispersal of an Early Successional Obligate: Implications for Restoration of an Endangered Ecosystem.

PubMed

Amaral, Katrina E; Palace, Michael; O'Brien, Kathleen M; Fenderson, Lindsey E; Kovach, Adrienne I

2016-01-01

Landscape modification and habitat fragmentation disrupt the connectivity of natural landscapes, with major consequences for biodiversity. Species that require patchily distributed habitats, such as those that specialize on early successional ecosystems, must disperse through a landscape matrix with unsuitable habitat types. We evaluated landscape effects on dispersal of an early successional obligate, the New England cottontail (Sylvilagus transitionalis). Using a landscape genetics approach, we identified barriers and facilitators of gene flow and connectivity corridors for a population of cottontails in the northeastern United States. We modeled dispersal in relation to landscape structure and composition and tested hypotheses about the influence of habitat fragmentation on gene flow. Anthropogenic and natural shrubland habitats facilitated gene flow, while the remainder of the matrix, particularly development and forest, impeded gene flow. The relative influence of matrix habitats differed between study areas in relation to a fragmentation gradient. Barrier features had higher explanatory power in the more fragmented site, while facilitating features were important in the less fragmented site. Landscape models that included a simultaneous barrier and facilitating effect of roads had higher explanatory power than models that considered either effect separately, supporting the hypothesis that roads act as both barriers and facilitators at all spatial scales. The inclusion of LiDAR-identified shrubland habitat improved the fit of our facilitator models. Corridor analyses using circuit and least cost path approaches revealed the importance of anthropogenic, linear features for restoring connectivity between the study areas. In fragmented landscapes, human-modified habitats may enhance functional connectivity by providing suitable dispersal conduits for early successional specialists.

Anthropogenic Habitats Facilitate Dispersal of an Early Successional Obligate: Implications for Restoration of an Endangered Ecosystem

PubMed Central

Amaral, Katrina E.; Palace, Michael; O’Brien, Kathleen M.; Fenderson, Lindsey E.; Kovach, Adrienne I.

2016-01-01

Landscape modification and habitat fragmentation disrupt the connectivity of natural landscapes, with major consequences for biodiversity. Species that require patchily distributed habitats, such as those that specialize on early successional ecosystems, must disperse through a landscape matrix with unsuitable habitat types. We evaluated landscape effects on dispersal of an early successional obligate, the New England cottontail (Sylvilagus transitionalis). Using a landscape genetics approach, we identified barriers and facilitators of gene flow and connectivity corridors for a population of cottontails in the northeastern United States. We modeled dispersal in relation to landscape structure and composition and tested hypotheses about the influence of habitat fragmentation on gene flow. Anthropogenic and natural shrubland habitats facilitated gene flow, while the remainder of the matrix, particularly development and forest, impeded gene flow. The relative influence of matrix habitats differed between study areas in relation to a fragmentation gradient. Barrier features had higher explanatory power in the more fragmented site, while facilitating features were important in the less fragmented site. Landscape models that included a simultaneous barrier and facilitating effect of roads had higher explanatory power than models that considered either effect separately, supporting the hypothesis that roads act as both barriers and facilitators at all spatial scales. The inclusion of LiDAR-identified shrubland habitat improved the fit of our facilitator models. Corridor analyses using circuit and least cost path approaches revealed the importance of anthropogenic, linear features for restoring connectivity between the study areas. In fragmented landscapes, human-modified habitats may enhance functional connectivity by providing suitable dispersal conduits for early successional specialists. PMID:26954014

Application of mucilage from Dicerocaryum eriocarpum plant as biosorption medium in the removal of selected heavy metal ions.

PubMed

Jones, Bassey O; John, Odiyo O; Luke, Chimuka; Ochieng, Aoyi; Bassey, Bridget J

2016-07-15

The ability of mucilage from Dicerocaryum eriocarpum (DE) plant to act as biosorption medium in the removal of metals ions from aqueous solution was investigated. Functional groups present in the mucilage were identified using Fourier transform infrared spectroscopy (FTIR). Mucilage was modified with sodium and potassium chlorides. This was aimed at assessing the biosorption efficiency of modified mucilage: potassium mucilage (PCE) and sodium mucilage (SCE) and comparing it with non-modified deionised water mucilage (DCE) in the uptake of metal ions. FTIR results showed that the functional groups providing the active sites in PCE and SCE and DCE include: carboxyl, hydroxyl and carbonyl groups. The chloride used in the modification of the mucilage did not introduce new functional groups but increased the intensity of the already existing functional groups in the mucilage. Results from biosorption experiment showed that DE mucilage displays good binding affinity with metals ions [Zn(II), Cd(II) Ni(II), Cr(III) and Fe(II)] in the aqueous solution. Increase in the aqueous solution pH, metal ions initial concentration and mucilage concentration increased the biosorption efficiency of DE mucilage. The maximum contact time varied with each species of metal ions. Optimum pH for [Zn(II), Cd(II) Ni(II) and Fe(II)] occurred at pH 4 and pH 6 for Cr(III). Kinetic models result fitted well to pseudo-second-order with a coefficient values of R(2) = 1 for Cd(II), Ni(II), Cr(III), Fe(II) and R(2) = 0.9974 for Zn(II). Biosorption isotherms conforms best with Freundlich model for all the metal ions with correlation factors of 0.9994, 0.9987, 0.9554, 0.9621 and 0.937 for Zn(II), Ni(II), Fe(II), Cr(III) and Cd(II), respectively. Biosorption capacity of DE mucilage was 0.010, 2.387, 4.902, 0688 and 0.125 for Zn(II), Cr(III), Fe(II), Cd(II) and Ni(II) respectively. The modified mucilage was found to be highly efficient in the removal of metal ions than the unmodified mucilage. Copyright © 2016 Elsevier Ltd. All rights reserved.

Gravitation in Material Media

ERIC Educational Resources Information Center

Ridgely, Charles T.

2011-01-01

When two gravitating bodies reside in a material medium, Newton's law of universal gravitation must be modified to account for the presence of the medium. A modified expression of Newton's law is known in the literature, but lacks a clear connection with existing gravitational theory. Newton's law in the presence of a homogeneous material medium…

Modification of Einstein A Coefficient in Dissipative Gas Medium

NASA Technical Reports Server (NTRS)

Cao, Chang-Qi; Cao, Hui; Qin, Ke-Cheng

1996-01-01

Spontaneous radiation in dissipative gas medium such as plasmas is investigated by Langevin equations and the modified Weisskopf-Wigner approximation. Since the refractive index of gas medium is expected to be nearly unity, we shall first neglect the medium polarization effect. We show that absorption in plasmas may in certain case modify the Einstein A coefficient significantly and cause a pit in the A coefficient-density curves for relatively low temperature plasmas and also a pit in the A coefficient-temperature curves. In the next, the effect of medium polarization is taken into account in addition. To our surprise, its effect in certain case is quite significant. The dispersive curves show different behaviors in different region of parameters.

Functional Silver-Silicone-Nanofilament-Composite Material for Water Disinfection.

PubMed

Meier, Margrith; Suppiger, Angela; Eberl, Leo; Seeger, Stefan

2017-01-01

The roughness of superhydrophobic silicone nanofilaments (SNFs) is exploited to enlarge the contact area of conventional filter material. As an efficient wetting of the filter material is crucial for water treatment, the wettability of SNFs is readily modified from superhydrophobic to hydrophilic during the functionalization process. SNFs are coated on glass beads and subsequently modified with biocidal silver nanoparticles (AgNPs). The enlarged surface area of SNFs allows a 30 times higher loading of AgNPs in comparison to glass beads without SNF coating. Thus, in column experiments, the AgNP-SNF-nanocomposite-modified glass beads exert superior antibacterial activity towards suspensions of E. coli K12 compared to AgNP functionalized glass beads without SNFs. Additionally, reusing the AgNP-SNF-nanocomposite-coated glass beads with fresh bacteria contaminated medium increases their efficacy and reduces the colony forming units by ≈6 log units. Thereby, the silver loss during percolation is below 0.1 μg mL -1 . These results highlight, first, the potential of AgNP-SNF-nanocomposite-modified glass beads as an effective filter substrate for water disinfection, and second, the efficiency of SNF coating in increasing the contact area of conventional filter material. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Critical thresholds in species` responses to landscape structure

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

With, K.A.; Crist, T.O.

1995-12-01

Critical thresholds are transition ranges across which small changes in spatial pattern produce abrupt shifts in ecological responses. Habitat fragmentation provides a familiar example of a critical threshold. As the landscape becomes dissected into smaller parcels of habitat. landscape connectivity-the functional linkage among habitat patches - may suddenly become disrupted, which may have important consequences for the distribution and persistence of populations. Landscape connectivity depends not only on the abundance and spatial patterning of habitat. but also on the habitat specificity and dispersal abilities of species. Habitat specialists with limited dispersal capabilities presumably have a much lower threshold to habitatmore » fragmentation than highly vagile species, which may perceive the landscape as functionally connected across a greater range of fragmentation severity. To determine where threshold effects in species, responses to landscape structure are likely to occur, a simulation model modified from percolation theory was developed. Our simulations predicted the distributional patterns of populations in different landscape mosaics, which we tested empirically using two grasshopper species (Orthoptera: Acrididae) that occur in the shortgrass prairie of north-central Colorado. The distribution of these two species in this grassland mosaic matched the predictions from our simulations. By providing quantitative predictions of threshold effects, this modelling approach may prove useful in the formulation of conservation strategies and assessment of land-use changes on species` distributional patterns and persistence.« less

Surgical correction of severe strabismus and enophthalmos secondary to zygomatic arch fracture in a dog.

PubMed

Konrade, Kricket A; Clode, Alison B; Michau, Tammy M; Roe, Simon C; Trumpatori, Brian J; Krug, William V; Gilger, Brian C

2009-01-01

A grossly displaced segmental zygomatic arch fracture with marked ventro-lateral deviation of the left globe was diagnosed in a 3-month-old male German Shepherd dog following a bite injury. The fracture was approached via a modified lateral orbitotomy and a fragment of the lacrimal bone removed. The rostral portion of the fracture was stabilized with a 5-hole 2.0 dynamic compression plate bone plate. The surgical correction achieved sufficient skeletal fixation for proper anatomical reduction of the globe and excellent cosmetic and functional outcomes.

[Genotoxic modification of nucleic acid bases and biological consequences of it. Review and prospects of experimental and computational investigations

NASA Technical Reports Server (NTRS)

Poltev, V. I.; Bruskov, V. I.; Shuliupina, N. V.; Rein, R.; Shibata, M.; Ornstein, R.; Miller, J.

1993-01-01

The review is presented of experimental and computational data on the influence of genotoxic modification of bases (deamination, alkylation, oxidation) on the structure and biological functioning of nucleic acids. Pathways are discussed for the influence of modification on coding properties of bases, on possible errors of nucleic acid biosynthesis, and on configurations of nucleotide mispairs. The atomic structure of nucleic acid fragments with modified bases and the role of base damages in mutagenesis and carcinogenesis are considered.

Effects of clonal fragmentation on intraspecific competition of a stoloniferous floating plant.

PubMed

Wang, P; Xu, Y-S; Dong, B-C; Xue, W; Yu, F-H

2014-11-01

Disturbance is common and can fragment clones of plants. Clonal fragmentation may affect the density and growth of ramets so that it could alter intraspecific competition. To test this hypothesis, we grew one (low density), five (medium density) or nine (high density) parent ramets of the floating invasive plant Pistia stratiotes in buckets, and newly produced offspring ramets were either severed (with fragmentation) or remained connected to parent ramets (no fragmentation). Increasing density reduced biomass of the whole clone (i.e. parent ramet plus its offspring ramets), showing intense intraspecific competition. Fragmentation decreased biomass of offspring ramets, but increased biomass of parent ramets and the whole clone, suggesting significant resource translocation from parent to offspring ramets when clones were not fragmented. There was no interaction effect of density x fragmentation on biomass of the whole clone, and fragmentation did not affect competition intensity index. We conclude that clonal fragmentation does not alter intraspecific competition between clones of P. stratiotes, but increases biomass production of the whole clone. Thus, fragmentation may contribute to its interspecific competitive ability and invasiveness, and intentional fragmentation should not be recommended as a measure to stop the rapid growth of this invasive species. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Enzymes and chelating agent in cotton pretreatment.

PubMed

Csiszár, E; Losonczi, A; Szakács, G; Rusznák, I; Bezúr, L; Reicher, J

2001-08-23

Desized cotton fabric and cotton seed-coat fragments (impurities) have been treated with commercial cellulase (Celluclast 1.5 L), hemicellulase-pectinase (Viscozyme 120 L) and xylanase (Pulpzyme HC) enzymes. Seed-coat fragments hydrolyzed much faster than the cotton fabric itself. This relative difference in hydrolysis rates makes possible a direct enzymatic removal of seed-coat fragments from desized cotton fabric. Addition of chelating agents such as ethylenediamine-tetra-acetic acid (EDTA) markedly enhanced the directed enzyme action. Pretreatments carried out in acidic solution at pH 5 increased the lightness of seed-coat fragments, contrary to the samples treated in neutral medium at pH 7. Alkaline scouring resulted in darker seed-coat fragments except for the samples pretreated with Pulpzyme HC plus EDTA. This effect is similar to that observed in the biobleaching process in pulp and paper industry.

Detection of Sulphate-Reducing Bacteria and Others Cultivable Facultative Bacteria in Dental Tissues

PubMed Central

Gonçalves, Lúcio de Souza; Dias, Eliane Pedra; Heggendorn, Christiane; Lutterbach, Márcia T. S.

2014-01-01

Aim To detect for the presence of sulphate-reducing bacteria (SRB) and evaluate the possible association between SRB and cultivable facultative bacterial of oral sites with different periodontal conditions. Methods The study was carried out on 9 samples from different oral sites in 8 patients (two samples were collected from the same patient). Material was collected using modified Postgate E culture medium, indicated for the growth and isolation of SRB. In addition, a reducing solution for anaerobic bacteria was used as a transport solution for facultative bacteria and identified by polymerase chain reaction amplification (PCR) and sequencing of the 16S rRNA gene. Results SRB was found in 3 patient samples: the first in a root fragment, the second in a root fragment and a healthy tooth with vertical bone loss and a mobility degree of 3; and the third in a healthy tooth extracted for orthodontic treatment. In the final patient, the cultivable facultative species Lactobacillus casei was identified. Other facultative bacterial species were identified in patient 5 (Kurthia Gibsonii) and patient 7 (Pseudomonas aeruginosa). Conclusions The detection of SRB in different dental tissues with distinct periodontal features demonstrated that new studies need to be developed in order to determine the true role of SRB in the oral microbiota. In addition, it was possible to verify the presence of Lactobacillus casei together with SRB in one sample. PMID:27688355

Cholecystokinin octa- and tetrapeptide degradation by synaptic membranes. I. Evidence for competition with enkephalins for in vitro common degradation pathways.

PubMed

Deschodt-Lanckman, M; Bui, N D

1981-01-01

Degradation of CCK-4 and -8 by purified synaptic membranes was followed by measuring the fluorescence of tryptophan released from the peptides after separation of degradation products by HPLC. For enkephalins and related fragments, the release of tyrosine was monitored using the same method. Kinetics of hydrolysis of CCK-like peptides indicated a rapid processing of CCK-4 and a slower breakdown of CCK-8 (with a greater resistance of the sulfated form of CCK-8 as compared to the unsulfated peptide). Leu- and met-enkephalins were degraded at the same rate while their N-terminal tri- and dipeptides were hydrolysed more slowly. When CCK-4 or CCK-8 were incubated in the presence of leu-enkephalin, a dose-dependent inhibition of the release of tryptophan was observed. Enkaphalin fragments do not modify the kinetics of degradation of CCK-4. The degradation of leu-enkephalin was inhibited in a dose-dependent manner by the presence of CCK-related peptides in the medium. After solubilization of membrane-bound enzymes by Triton X-100 followed by chromatography on DEAE cellulose, five peaks of CCK-4 degrading activity were detected (two minor and three major peaks). With enkephalin as substrate, five peaks were also observed; the three major activities were the same as those detected for CCK-4.

Characterization of Tyrosine Nitration and Cysteine Nitrosylation Modifications by Metastable Atom-Activation Dissociation Mass Spectrometry

NASA Astrophysics Data System (ADS)

Cook, Shannon L.; Jackson, Glen P.

2011-02-01

The fragmentation behavior of nitrated and S-nitrosylated peptides were studied using collision induced dissociation (CID) and metastable atom-activated dissociation mass spectrometry (MAD-MS). Various charge states, such as 1+, 2+, 3+, 2-, of modified and unmodified peptides were exposed to a beam of high kinetic energy helium (He) metastable atoms resulting in extensive backbone fragmentation with significant retention of the post-translation modifications (PTMs). Whereas the high electron affinity of the nitrotyrosine moiety quenches radical chemistry and fragmentation in electron capture dissociation (ECD) and electron transfer dissociation (ETD), MAD does produce numerous backbone cleavages in the vicinity of the modification. Fragment ions of nitrosylated cysteine modifications typically exhibit more abundant neutral losses than nitrated tyrosine modifications because of the extremely labile nature of the nitrosylated cysteine residues. However, compared with CID, MAD produced between 66% and 86% more fragment ions, which preserved the labile -NO modification. MAD was also able to differentiate I/L residues in the modified peptides. MAD is able to induce radical ion chemistry even in the presence of strong radical traps and therefore offers unique advantages to ECD, ETD, and CID for determination of PTMs such as nitrated and S-nitrosylated peptides.

Identification of Small Peptides in Human Cerebrospinal Fluid upon Amyloid-β Degradation.

PubMed

Mizuta, Naoki; Yanagida, Kanta; Kodama, Takashi; Tomonaga, Takeshi; Takami, Mako; Oyama, Hiroshi; Kudo, Takashi; Ikeda, Manabu; Takeda, Masatoshi; Tagami, Shinji; Okochi, Masayasu

2017-01-01

Amyloid-β (Aβ) degradation in brains of Alzheimer disease patients is a crucial focus for the clarification of disease pathogenesis. Nevertheless, the mechanisms underlying Aβ degradation in the human brain remain unclear. This study aimed to quantify the levels of small C-terminal Aβ fragments generated upon Aβ degradation in human cerebrospinal fluid (CSF). A fraction containing small peptides was isolated and purified from human CSF by high-pressure liquid chromatography. Degradation products of Aβ C termini were identified and measured by liquid chromatography-tandem mass spectrometry. The C-terminal fragments of Aβ in the conditioned medium of cultured cells transfected with the Swedish variant of βAPP (sw βAPP) were analyzed. These fragments in brains of PS1 I213T knock-in transgenic mice, overexpressing sw βAPP, were also analyzed. The peptide fragments GGVV and GVV, produced by the cleavage of Aβ40, were identified in human CSF as well as in the brains of the transgenic mice and in the conditioned medium of the cultured cells. Relative to Aβ40 levels, GGVV and GVV levels were 7.6 ± 0.81 and 1.5 ± 0.18%, respectively, in human CSF. Levels of the GGVV fragment did not increase by the introduction of genes encoding neprilysin and insulin-degrading enzyme to the cultured cells. Our results indicate that a substantial amount of Aβ40 in human brains is degraded via a neprilysin- or insulin-degrading enzyme-independent pathway. © 2017 S. Karger AG, Basel.

Regioselective chemical modification of monoclonal antibodies

DOEpatents

Ranadive, Girish; Rosenzweig, Howard S.; Epperly, Michael; Bloomer, William

1993-01-01

A method of selectively modifying an immunoglobulin having at least one Fab region and at least one Fc region, each region having an isoelectric point wherein said isoelectric point of the Fab fragment of said immunoglobulin is different than the isoelectric point of the Fc fragment of the immunoglobulin, said method comprising modification of the immunoglobulin at a pH between the respective isoelectric points of the Fab and Fc fragments of the immunoglobulin.

An innovative strategy to clone positive modifier genes of defects caused by mtDNA mutations: MRPS18C as suppressor gene of m.3946G>A mutation in MT-ND1 gene.

PubMed

Rodríguez-García, María Elena; Cotrina-Vinagre, Francisco Javier; Carnicero-Rodríguez, Patricia; Martínez-Azorín, Francisco

2017-07-01

We have developed a new functional complementation approach to clone modifier genes which overexpression is able to suppress the biochemical defects caused by mtDNA mutations (suppressor genes). This strategy consists in transferring human genes into respiratory chain-deficient fibroblasts, followed by a metabolic selection in a highly selective medium. We used a normalized expression cDNA library in an episomal vector (pREP4) to transfect the fibroblasts, and a medium with glutamine and devoid of any carbohydrate source to select metabolically. Growing the patient's fibroblasts in this selective medium, the deficient cells rapidly disappear unless they are rescued by the cDNA of a suppressor gene. The use of an episomal vector allows us to carry out several rounds of transfection/selection (cyclical phenotypic rescue) to enrich the rescue with true clones of suppressor genes. Using fibroblasts from a patient with epileptic encephalopathy with the m.3946G>A (p.E214K) mutation in the MT-ND1 gene, several candidate genes were identified and one of them was characterized functionally. Thus, overexpression of MRPS18C gene (that encode for bS18m protein) suppressed the molecular defects produced by this mtDNA mutation, recovering the complex I activity and reducing the ROS produced by this complex to normal levels. We suggest that modulation of bS18m expression may be an effective therapeutic strategy for the patients with this mutation.

Nonviral RNA transfection to transiently modify T cells with chimeric antigen receptors for adoptive therapy.

PubMed

Riet, Tobias; Holzinger, Astrid; Dörrie, Jan; Schaft, Niels; Schuler, Gerold; Abken, Hinrich

2013-01-01

Redirecting T cells with a chimeric antigen receptor (CAR) of predefined specificity showed remarkable efficacy in the adoptive therapy trials of malignant diseases. The CAR consists of a single chain fragment of variable region (scFv) antibody targeting domain covalently linked to the CD3ζ signalling domain of the T cell receptor complex to mediate T cell activation upon antigen engagement. By using an antibody-derived targeting domain a CAR can potentially redirect T cells towards any target expressed on the cell surface as long as a binding domain is available. Antibody-mediated targeting moreover circumvents MHC restriction of the targeted antigen, thereby broadening the potential of applicability of adoptive T cell therapy. While T cells were so far genetically modified by viral transduction, transient modification with a CAR by RNA transfection gained increasing interest during the last years. This chapter focuses on methods to modify human T cells from peripheral blood with a CAR by electroporation of in vitro transcribed RNA and to test modified T cells for function for use in adoptive immunotherapy.

Emerging Ecosystems Change the Spatial Distribution of Top Carnivores Even in Poorly Populated Areas

PubMed Central

Barbar, Facundo; Werenkraut, Victoria; Morales, Juan Manuel; Lambertucci, Sergio Agustín

2015-01-01

Humans affect biological diversity and species distribution patterns by modifying resource availability and generating novel environments where generalist species benefit and specialist species are rare. In particular, cities create local homogenization while roads fragment habitat, although both processes can increase food availability for some species that may be able to take advantage of this new source. We studied space use by birds of prey in relation to human construction, hypothesizing that these birds would be affected even in poorly populated areas. We worked in Northwestern Patagonia, Argentina, which is experiencing a high population growth, but still having very large unpopulated areas. We related the presence of raptors with different sources of human disturbance and found that both the abundance and richness of these birds were positively associated with anthropogenic environments. These results are driven mostly by a strong association between the medium-sized generalist species and these novel environments (mainly roads and cities). This may create an imbalance in intra-guild competitive abilities, modifying the normal structures of top carnivore hierarchies. Indeed, the structure of raptor communities seems to be changing, even in poorly populated areas, with anthropogenic constructions seemingly producing changes in wild areas more promptly than thought, a cause for concern in ecosystems conservation issues. PMID:25799547

Multi-Stage Mass Spectrometry Analysis of Sugar-Conjugated β-Turn Structures to be Used as Probes in Autoimmune Diseases

NASA Astrophysics Data System (ADS)

Giangrande, Chiara; Auberger, Nicolas; Rentier, Cédric; Papini, Anna Maria; Mallet, Jean-Maurice; Lavielle, Solange; Vinh, Joëlle

2016-04-01

Synthetic sugar-modified peptides were identified as antigenic probes in the context of autoimmune diseases. The aim of this work is to provide a mechanistic study on the fragmentation of different glycosylated analogs of a synthetic antigenic probe able to detect antibodies in a subpopulation of multiple sclerosis patients. In particular the N-glucosylated type I' β-turn peptide structure called CSF114(Glc) was used as a model to find signature fragmentations exploring the potential of multi-stage mass spectrometry by MALDI-LTQ Orbitrap. Here we compare the fragmentation of the glucosylated form of the synthetic peptide CSF114(Glc), bearing a glucose moiety on an asparagine residue, with less or non- immunoreactive forms, bearing different sugar-modifications, such as CSF114(GlcNAc), modified with a residue of N-acetylglucosamine, and CSF114[Lys7(1-deoxyfructopyranosyl)], this last one modified with a 1-deoxyfructopyranosyl moiety on a lysine at position 7. The analysis was set up using a synthetic compound specifically deuterated on the C-1 to compare its fragmentation with the fragmentation of the undeuterated form, and thus ascertain with confidence the presence on an Asn(Glc) within a peptide sequence. At the end of the study, our analysis led to the identification of signature neutral losses inside the sugar moieties to characterize the different types of glycosylation/glycation. The interest of this study lies in the possibility of applyimg this approach to the discovery of biomarkers and in the diagnosis of autoimmune diseases.

Multi-Stage Mass Spectrometry Analysis of Sugar-Conjugated β-Turn Structures to be Used as Probes in Autoimmune Diseases.

PubMed

Giangrande, Chiara; Auberger, Nicolas; Rentier, Cédric; Papini, Anna Maria; Mallet, Jean-Maurice; Lavielle, Solange; Vinh, Joëlle

2016-04-01

Synthetic sugar-modified peptides were identified as antigenic probes in the context of autoimmune diseases. The aim of this work is to provide a mechanistic study on the fragmentation of different glycosylated analogs of a synthetic antigenic probe able to detect antibodies in a subpopulation of multiple sclerosis patients. In particular the N-glucosylated type I' β-turn peptide structure called CSF114(Glc) was used as a model to find signature fragmentations exploring the potential of multi-stage mass spectrometry by MALDI-LTQ Orbitrap. Here we compare the fragmentation of the glucosylated form of the synthetic peptide CSF114(Glc), bearing a glucose moiety on an asparagine residue, with less or non- immunoreactive forms, bearing different sugar-modifications, such as CSF114(GlcNAc), modified with a residue of N-acetylglucosamine, and CSF114[Lys(7)(1-deoxyfructopyranosyl)], this last one modified with a 1-deoxyfructopyranosyl moiety on a lysine at position 7. The analysis was set up using a synthetic compound specifically deuterated on the C-1 to compare its fragmentation with the fragmentation of the undeuterated form, and thus ascertain with confidence the presence on an Asn(Glc) within a peptide sequence. At the end of the study, our analysis led to the identification of signature neutral losses inside the sugar moieties to characterize the different types of glycosylation/glycation. The interest of this study lies in the possibility of applyimg this approach to the discovery of biomarkers and in the diagnosis of autoimmune diseases. Graphical Abstract .

Medium-energy electrons and heavy ions in Jupiter's magnetosphere - Effects of lower hybrid wave-particle interactions

NASA Technical Reports Server (NTRS)

Barbosa, D. D.

1986-01-01

A theory of medium-energy (about keV) electrons and heavy ions in Jupiter's magnetosphere is presented. Lower hybrid waves are generated by the combined effects of a ring instability of neutral wind pickup ions and the modified two-stream instability associated with transport of cool Iogenic plasma. The quasi-linear energy diffusion coefficient for lower hybrid wave-particle interactions is evaluated, and several solutions to the diffusion equation are given. Calculations based on measured wave properties show that the noise substantially modifies the particle distribution functions. The effects are to accelerate superthermal ions and electrons to keV energies and to thermalize the pickup ions on time scales comparable to the particle residence time. The S(2+)/S(+) ratio at medium energies is a measure of the relative contribution from Iogenic thermal plasma and neutral wind ions, and this important quantity should be determined from future measurements. The theory also predicts a preferential acceleration of heavy ions with an accleration time that scales inversely with the root of the ion mass. Electrons accelerated by the process contribute to further reionization of the neutral wind by electron impact, thus providing a possible confirmation of Alfven's critical velocity effect in the Jovian magnetosphere.

A coupled analytical model for hydrostatic response of 1-3 piezocomposites.

PubMed

Rajapakse, Nimal; Chen, Yue

2008-08-01

This study presents a fully coupled analysis of a unit cell of a 1-3 piezocomposite under hydrostatic loading. The governing equations for coupled axisymmetric electroelastic field of a transversely isotropic piezoelectric medium and a transversely isotropic elastic medium are used. A reduced form of the analytical general solutions expressed in terms of series of modified Bessel functions of the first and second kind are used. The solution of the boundary-value problem corresponding to a unit cell is presented. The effective properties of a 1-3 piezocomposite are obtained for different fiber volume fractions, polymer and piezoceramic properties, and fiber aspect ratios. Comparisons with previously reported simplified and uncoupled models are made.

Fusion proteins useful for producing pinene

DOEpatents

Peralta-Yahya, Pamela P.; Keasling, Jay D

2016-06-28

The present invention provides for a modified host cell comprising a heterologous pinene synthase (PS), or enzymatically active fragment or variant thereof, and optionally a geranyl pyrophosphate synthase (GPPS), or enzymatically active fragment or variant thereof, or a fusion protein comprising: (a) a PS and (b) a GPPS linked by a linker.

Transformation of PRT6 RNAi construct into tomato (Solanum lycopersicum) cv. Micro-Tom

NASA Astrophysics Data System (ADS)

Suka, Intan Elya; Chew, Bee Lynn; Goh, Hoe-Han; Isa, Nurulhikma Md

2018-04-01

PROTEOLYSIS 6 plays major role in the N-end rule pathway as N-recognin which functions as E3 ligase enzyme. It mediates ubiquitin processes that lead to degradation of unstable substrate protein. The aim of the current study is to transform the PRT6 gene into tomato (Solanum lycopersicum) from the cultivar Micro-Tom and to investigate its function in regulating ripening in tomato fruits. The PRT6_RNAi construct was successfully transformed into Agrobacterium C58 via heat shock method and transformed into seven days old cotyledon explants. Factors affecting transformation efficiency such as co-cultivation time and type of plant growth regulator combination were evaluated. Results from this study found that pre-cultured cotyledons from seven days old seedlings incubated for 2 days in co-cultivation medium increased shoot regeneration. Plant growth hormones zeatin combine with auxin produced a higher number of callus formation but lower shoot proliferation and transformation frequency compared to treatments of single plant hormone in the selection medium. Polymerase chain reaction (PCR) was performed on the regenerated shoots to confirm the integration of PRT6 fragment into the genome of transgenic plants. Based on PCR analysis, all putative shoots were positive transformants.

Tablet fragmentation without a disintegrant: A novel design approach for accelerating disintegration and drug release from 3D printed cellulosic tablets.

PubMed

Arafat, Basel; Wojsz, Magdalena; Isreb, Abdullah; Forbes, Robert T; Isreb, Mohammad; Ahmed, Waqar; Arafat, Tawfiq; Alhnan, Mohamed A

2018-06-15

Fused deposition modelling (FDM) 3D printing has shown the most immediate potential for on-demand dose personalisation to suit particular patient's needs. However, FDM 3D printing often involves employing a relatively large molecular weight thermoplastic polymer and results in extended release pattern. It is therefore essential to fast-track drug release from the 3D printed objects. This work employed an innovative design approach of tablets with unique built-in gaps (Gaplets) with the aim of accelerating drug release. The novel tablet design is composed of 9 repeating units (blocks) connected with 3 bridges to allow the generation of 8 gaps. The impact of size of the block, the number of bridges and the spacing between different blocks was investigated. Increasing the inter-block space reduced mechanical resistance of the unit, however, tablets continued to meet pharmacopeial standards for friability. Upon introduction into gastric medium, the 1 mm spaces gaplet broke into mini-structures within 4 min and met the USP criteria of immediate release products (86.7% drug release at 30 min). Real-time ultraviolet (UV) imaging indicated that the cellulosic matrix expanded due to swelling of hydroxypropyl cellulose (HPC) upon introduction to the dissolution medium. This was followed by a steady erosion of the polymeric matrix at a rate of 8 μm/min. The design approach was more efficient than a comparison conventional formulation approach of adding disintegrants to accelerate tablet disintegration and drug release. This work provides a novel example where computer-aided design was instrumental at modifying the performance of solid dosage forms. Such an example may serve as the foundation for a new generation of dosage forms with complicated geometric structures to achieve functionality that is usually achieved by a sophisticated formulation approach. Copyright © 2018 Elsevier B.V. All rights reserved.

Modified suture-bridge technique to prevent a marginal dog-ear deformity improves structural integrity after rotator cuff repair.

PubMed

Ryu, Keun Jung; Kim, Bang Hyun; Lee, Yohan; Lee, Yoon Seok; Kim, Jae Hwa

2015-03-01

The arthroscopic suture-bridge technique has proved to provide biomechanically firm fixation of the torn rotator cuff to the tuberosity by increasing the footprint contact area and pressure. However, a marginal dog-ear deformity is encountered not infrequently when this technique is used, impeding full restoration of the torn cuff. To evaluate the structural and functional outcomes of the use of a modified suture-bridge technique to prevent a marginal dog-ear deformity compared with a conventional suture-bridge method in rotator cuff repair. Cohort study; Level of evidence 2. A consecutive series of 71 patients aged 50 to 65 years who underwent arthroscopic rotator cuff repair for full-thickness medium-sized to massive tears was evaluated. Patients were divided into 2 groups according to repair technique: a conventional suture-bridge technique (34 patients; group A) versus a modified suture-bridge technique to prevent a marginal dog-ear deformity (37 patients; group B). Radiographic evaluations included postoperative cuff integrity using MRI. Functional evaluations included pre- and postoperative range of motion (ROM), pain visual analog scale (VAS), the University of California, Los Angeles (UCLA) shoulder rating scale, the Constant score, and the American Shoulder and Elbow Surgeons (ASES) score. All patients were followed up clinically at a minimum of 1 year. When the 2 surgical techniques were compared, postoperative structural integrity by Sugaya classification showed the distribution of types I:II:III:IV:V to be 4:20:2:4:4 in group A and 20:12:4:0:1 in group B. More subjects in group B had a favorable Sugaya type compared with group A (P < .001). The postoperative healed:retear rate was 26:8 in group A and 36:1 in group B, with a significantly lower retear rate in group B (P = .011). However, there were no significant differences in ROM and all functional outcome scores between the 2 groups postoperatively. When surgical techniques were compared across healed (n = 62) and retear (n = 9) groups, significantly fewer modified suture-bridge technique repairs were found in the retear group (P = .03). There were significant differences between healed and retear groups in functional outcome scores, with worse results in the retear group. A modified suture-bridge technique to prevent a marginal dog-ear deformity provided better structural outcomes than a conventional suture-bridge technique for medium-sized to massive rotator cuff tears. This technique may ultimately provide better functional outcomes by decreasing the retear rate. © 2014 The Author(s).

Alterations in protein kinase C activity and processing during zinc-deficiency-induced cell death.

PubMed

Chou, Susan S; Clegg, Michael S; Momma, Tony Y; Niles, Brad J; Duffy, Jodie Y; Daston, George P; Keen, Carl L

2004-10-01

Protein kinases C (PKCs) are a family of serine/threonine kinases that are critical for signal transduction pathways involved in growth, differentiation and cell death. All PKC isoforms have four conserved domains, C1-C4. The C1 domain contains cysteine-rich finger-like motifs, which bind two zinc atoms. The zinc-finger motifs modulate diacylglycerol binding; thus, intracellular zinc concentrations could influence the activity and localization of PKC family members. 3T3 cells were cultured in zinc-deficient or zinc-supplemented medium for up to 32 h. Cells cultured in zinc-deficient medium had decreased zinc content, lowered cytosolic classical PKC activity, increased caspase-3 processing and activity, and reduced cell number. Zinc-deficient cytosols had decreased activity and expression levels of PKC-alpha, whereas PKC-alpha phosphorylation was not altered. Inhibition of PKC-alpha with Gö6976 had no effect on cell number in the zinc-deficient group. Proteolysis of the novel PKC family member, PKC-delta, to its 40-kDa catalytic fragment occurred in cells cultured in the zinc-deficient medium. Occurrence of the PKC-delta fragment in mitochondria was co-incident with caspase-3 activation. Addition of the PKC-delta inhibitor, rottlerin, or zinc to deficient medium reduced or eliminated proteolysis of PKC-delta, activated caspase-3 and restored cell number. Inhibition of caspase-3 processing by Z-DQMD-FMK (Z-Asp-Gln-Met-Asp-fluoromethylketone) did not restore cell number in the zinc-deficient group, but resulted in processing of full-length PKC-delta to a 56-kDa fragment. These results support the concept that intracellular zinc concentrations influence PKC activity and processing, and that zinc-deficiency-induced apoptosis occurs in part through PKC-dependent pathways.

Quark fragmentation functions in NJL-jet model

NASA Astrophysics Data System (ADS)

Bentz, Wolfgang; Matevosyan, Hrayr; Thomas, Anthony

2014-09-01

We report on our studies of quark fragmentation functions in the Nambu-Jona-Lasinio (NJL) - jet model. The results of Monte-Carlo simulations for the fragmentation functions to mesons and nucleons, as well as to pion and kaon pairs (dihadron fragmentation functions) are presented. The important role of intermediate vector meson resonances for those semi-inclusive deep inelastic production processes is emphasized. Our studies are very relevant for the extraction of transverse momentum dependent quark distribution functions from measured scattering cross sections. We report on our studies of quark fragmentation functions in the Nambu-Jona-Lasinio (NJL) - jet model. The results of Monte-Carlo simulations for the fragmentation functions to mesons and nucleons, as well as to pion and kaon pairs (dihadron fragmentation functions) are presented. The important role of intermediate vector meson resonances for those semi-inclusive deep inelastic production processes is emphasized. Our studies are very relevant for the extraction of transverse momentum dependent quark distribution functions from measured scattering cross sections. Supported by Grant in Aid for Scientific Research, Japanese Ministry of Education, Culture, Sports, Science and Technology, Project No. 20168769.

Synthesis of the human insulin gene. Part III. Chemical synthesis of 5'-phosphomonoester group containing deoxyribooligonucleotides by the modified phosphotriester method. Its application in the synthesis of seventeen fragments constituting human insulin C-chain DNA.

PubMed Central

Hsiung, H M; Sung, W L; Brousseau, R; Wu, R; Narang, S A

1980-01-01

A method for phosphorylating a protected deoxyribooligonucleotide containing phosphotriester linkages is described. The modified phosphotriester method of chemical synthesis is further refined in terms of (i) better final deblocking conditions and (ii) new chromatography solvent systems containing acetone-water-ethyl acetate to yield pure oligomers. The effectiveness of these improvements has been demonstrated in the rapid and efficient synthesis of seventeen fragments constituting the sequence of human insulin C-chain DNA. Images PMID:7008029

System and method for introduction and stabilization of genes in Thermus sp.

DOEpatents

Kayser, Kevin J.; Park, Ho-Shin; Kilbane, II, John J.

2005-03-01

A method for introducing and stabilizing heterologous and recombinant genes in a thermophilic host in which a characteristic gene defining a detectable host characteristic is inactivated or deleted from the thermophilic host, resulting in a modified thermophilic host expressing an absence of the detectable host characteristic. A DNA fragment of interest is inserted into the modified thermophilic host together with an intact characteristic gene, whereby the detectable host characteristic is restored to the thermophilic host, thereby enabling detection and confirmation of successful transformation using plasmid vectors and integration of the DNA fragment into the chromosome of the thermophilic host.

Development of modified flyash as a permeable reactive barrier medium for a former manufactured gas plant site, Northern Ireland

NASA Astrophysics Data System (ADS)

Doherty, R.; Phillips, D. H.; McGeough, K. L.; Walsh, K. P.; Kalin, R. M.

2006-05-01

A sequential biological permeable reactive barrier (PRB) was determined to be the best option for remediating groundwater that has become contaminated with a wide range of organic contaminants (i.e., benzene, toluene, ethylbenzene, xylene and polyaromatic hydrocarbons), heavy metals (i.e., lead and arsenic), and cyanide at a former manufactured gas plant after 150 years of operation in Portadown, Northern Ireland. The objective of this study was to develop a modified flyash that could be used in the initial cell within a sequential biological PRB to filter complex contaminated groundwater containing ammonium. Flyash modified with lime (CaOH) and alum was subjected to a series of batch tests which investigated the modified cation exchange capacity (CEC) and rate of removal of anions and cations from the solution. These tests showed that a high flyash composition medium (80%) could remove 8.65 mol of ammonium contaminant for every kilogram of medium. The modified CEC procedure ruled out the possibility of cation exchange as the major removal mechanism. The medium could also adsorb anions as well as cations (i.e., Pb and Cr), but not with the same capacity. The initial mechanism for Pb and Cr removal is probably precipitation. This is followed by sorption, which is possibly the only mechanism for the removal of dichromate anions. Scanning electron microscopic analysis revealed very small (<1 μm) cubic highly crystalline precipitates on the flyash, although this new crystalline zeolite growth did not occur rapidly enough to enable productive zeolite formation. Surface area measurements showed that biofilm growth on the medium could be a major factor in the comparative reduction of surface area between real and synthetic contaminant groundwaters. The modified flyash was found to be a highly sorptive granular material that did not inhibit microbiological activity, however, leaching tests revealed that the medium would fail as a long-term barrier material.

Surface functionalization of quantum dots with fine-structured pH-sensitive phospholipid polymer chains.

PubMed

Liu, Yihua; Inoue, Yuuki; Ishihara, Kazuhiko

2015-11-01

To add novel functionality to quantum dots (QDs), we synthesized water-soluble and pH-responsive block-type polymers by reversible addition-fragmentation chain transfer (RAFT) polymerization. The polymers were composed of cytocompatible 2-methacryloyloxyethyl phosphorylcholine (MPC) polymer segments, which contain a small fraction of active ester groups and can be used to conjugate biologically active compounds to the polymer, and pH-responsive poly(2-(N,N-diethylamino) ethyl methacrylate (DEAEMA)) segments. One terminal of the polymer chain had a hydrophobic alkyl group that originated from the RAFT initiator. This hydrophobic group can bind to the hydrophobic layer on the QD surface. A fluorescent dye was conjugated to the polymer chains via the active ester group. The block-type polymers have an amphiphilic nature in aqueous medium. The polymers were thus easily bound to the QD surface upon evaporation of the solvent from a solution containing the block-type polymer and QDs, yielding QD/fluorescence dye-conjugated polymer hybrid nanoparticles. Fluorescence resonance energy transfer (FRET) between the QDs (donors) and the fluorescent dye molecules (acceptors) was used to obtain information on the conformational dynamics of the immobilized polymers. Higher FRET efficiency of the QD/fluorescent dye-conjugated polymer hybrid nanoparticles was observed at pH 7.4 as compared to pH 5.0 due to a stretching-shrinking conformational motion of the poly(DEAEMA) segments in response to changes in pH. We concluded that the block-type MPC polymer-modified nanoparticles could be used to evaluate the pH of cells via FRET fluorescence based on the cytocompatibility of the MPC polymer. Copyright © 2015 Elsevier B.V. All rights reserved.

[Protein S3 fragments neighboring mRNA during elongation and translation termination on the human ribosome].

PubMed

Khaĭrulina, Iu S; Molotkov, M V; Bulygin, K N; Graĭfer, D M; Ven'yaminova, A G; Frolova, L Iu; Stahl, J; Karpova, G G

2008-01-01

Protein S3 fragments were determined that crosslink to modified mRNA analogues in positions +5 to +12 relative to the first nucleotide in the P-site binding codon in model complexes mimicking states of ribosomes at the elongation and translation termination steps. The mRNA analogues contained a Phe codon UUU/UUC at the 5'-termini that could predetermine the position of the tRNA(Phe) on the ribosome by the location of P-site binding and perfluorophenylazidobenzoyl group at a nucleotide in various positions 3' of the UUU/UUC codon. The crosslinked S3 protein was isolated from 80S ribosomal complexes irradiated with mild UV light and subjected to cyanogen bromide-induced cleavage at methionine residues with subsequent identification of the crosslinked oligopeptides. An analysis of the positions of modified oligopeptides resulting from the cleavage showed that, in dependence on the positions of modified nucleotides in the mRNA analogue, the crosslinking sites were found in the N-terminal half of the protein (fragment 2-127) and/or in the C-terminal fragment 190-236; the latter reflects a new peculiarity in the structure of the mRNA binding center in the ribosome, unknown to date. The results of crosslinking did not depend on the type of A-site codon or on the presence of translation termination factor eRF1.

Fragment Production and Survival in Irradiated Disks: A Comprehensive Cooling Criterion

NASA Astrophysics Data System (ADS)

Kratter, Kaitlin M.; Murray-Clay, Ruth A.

2011-10-01

Accretion disks that become gravitationally unstable can fragment into stellar or substellar companions. The formation and survival of these fragments depends on the precarious balance between self-gravity, internal pressure, tidal shearing, and rotation. Disk fragmentation depends on two key factors: (1) whether the disk can get to the fragmentation boundary of Q = 1 and (2) whether fragments can survive for many orbital periods. Previous work suggests that to reach Q = 1, and have fragments survive, a disk must cool on an orbital timescale. Here we show that disks heated primarily by external irradiation always satisfy the standard cooling time criterion. Thus, even though irradiation heats disks and makes them more stable in general, once they reach the fragmentation boundary, they fragment more easily. We derive a new cooling criterion that determines fragment survival and calculate a pressure-modified Hill radius, which sets the maximum size of pressure-supported objects in a Keplerian disk. We conclude that fragmentation in protostellar disks might occur at slightly smaller radii than previously thought and recommend tests for future simulations that will better predict the outcome of fragmentation in real disks.

Regioselective chemical modification of monoclonal antibodies

DOEpatents

Ranadive, G.; Rozenzweig, H.S.; Epperly, M.; Bloomer, W.

1993-05-04

A method is presented of selectively modifying an immunoglobulin having at least one Fab region and at least one Fc region. Each region has an isoelectric point where the isoelectric point of the Fab fragment of the immunoglobulin is different from the isoelectric point of the Fc fragment of the immunoglobulin. The method comprises of a modification of the immunoglobulin at a pH between the respective isoelectric points of the Fab and Fc fragments of the immunoglobulin.

A hypervelocity launcher for simulated large fragment space debris impacts at 10 km/s

NASA Technical Reports Server (NTRS)

Tullos, R. J.; Gray, W. M.; Mullin, S. A.; Cour-Palais, B. G.

1989-01-01

The background, design, and testing of two explosive launchers for simulating large fragment space debris impacts are presented. The objective was to develop a launcher capable of launching one gram aluminum fragments at velocities of 10 km/s. The two launchers developed are based on modified versions of an explosive shaped charge, common in many military weapons. One launcher design has yielded a stable fragment launch of approximately one gram of aluminum at 8.93 km/s velocity. The other design yielded velocities in excess of 10 km/s, but failed to produce a cohesive fragment launch. This work is ongoing, and future plans are given.

Effect of different procedures of ejaculate collection, extenders and packages on DNA integrity of boar spermatozoa following freezing-thawing.

PubMed

Fraser, L; Strzezek, J

2007-06-01

Whole ejaculate or sperm-rich fraction, collected from four sexually mature boars, was frozen in an extender containing lactose-hen egg yolk with glycerol (lactose-HEY-G) or extender containing lactose, lyophilized lipoprotein fractions isolated from ostrich egg yolk and glycerol (lactose-LPFo-G), and Orvus Es Paste, respectively. The sperm samples were also frozen in a standard boar semen extender (Kortowo-3), without the addition of cryoprotective substances. Sperm DNA integrity was assessed using a modified neutral comet assay. Sperm characteristics such as motility, plasma membrane integrity (SYBR-14/PI), mitochondrial function (rhodamine 123) and acrosome integrity were monitored. Freezing-thawing caused a significant increase (P<0.05) in sperm DNA fragmentation, irrespective of the procedures of ejaculate collection and extender type. Sperm DNA fragmentation was significantly lower (P<0.05) in the whole ejaculate compared with the sperm-rich fraction, indicating that spermatozoa maintained in the whole seminal plasma prior to its removal for freezing-thawing procedure were less vulnerable to cryo-induced DNA fragmentation. Furthermore, spermatozoa frozen in lactose-HEY-G or lactose-LPFo-G extender exhibited lower (P<0.05) DNA fragmentation than those frozen in the absence of cryoprotective substances. The levels of sperm DNA damage, as expressed by comet tail length and tail moment values, were significantly higher (P<0.05) in sperm samples frozen in the absence of cryoprotective substances. The deterioration in post-thaw sperm DNA integrity was concurrent with reduced sperm characteristics. It can be suggested that evaluation of DNA integrity, coupled with different sperm characteristics such as motility, plasma membrane integrity and mitochondrial function, may aid in determining the quality of frozen-thawed boar semen.

Influence of Space Flight Factors on the Genetic Properties of Streptomyces Lividans 66 (PIJ702)

NASA Technical Reports Server (NTRS)

Tabakov, V. Yu.; Voeikova, T. A.; Tairbekov, M. G.; Goins, T. L.; Martinson, V. G.; Pyle, B. H.

2006-01-01

Gram-positive Streptomyces bacteria display genetic instability in response to external factors. Strain S. lividans 66 harbors the multicopy plasmid pIJ702 with selective and differential marker genes for antibiotic thiostrepton resistance and melanin production. Culture plates of modified ISP agar medium with and without thiostrepton were flown on Foton-M2. Suboptimal flight temperatures, which were simulated for asynchronous ground controls, resulted in slow growth and failure to differentiate and sporulate. Flight samples and asynchronous controls showed a high frequency of failing to express plasmid markers compared to laboratory controls. This was associated with loss of plasmid DNA and likely resulted from suboptimal temperatures for flight cultures and controls. Neither restriction fragment length polymorphism, nor polymerase chain reaction amplification coupled with denaturing gradient gel electrophoresis, revealed differences between pIJ702 DNA from flight vs. control clones. Mutations of the plasmid marker genes resulting from specific spaceflight factors, e.g., microgravity and radiation, were not detected.

Modification of citrus and apple pectin by power ultrasound: Effects of acid and enzymatic treatment.

PubMed

Muñoz-Almagro, Nerea; Montilla, Antonia; Moreno, F Javier; Villamiel, Mar

2017-09-01

Pectin-derived oligosaccharides are emerging as a new generation of functional ingredients with new or improved technological and/or bioactive properties as compared to pectin. This work addresses the impact of power ultrasound (US) on the structure of citrus and apple pectin under different experimental conditions of power, amplitude and pectin concentration in aqueous and acid media, as well as in the presence of a pectinase. Results indicated that depolymerisation of both pectin increased with time and intensity of US in aqueous media and their polydispersity decreased. In general, a higher depolymerisation was observed in pectin treated by US in the presence of nitric and citric acids than in water, and hardly any difference was detected between both types of acids. Most of the assays gave rise to high-methoxylated pectin with a degree of esterification above 50%, pointing out their suitability for potential gelling agents. Finally, US did not have any impact in assisted enzymatic hydrolysis on the degree and/or rate of depolymerisation at low and medium levels of pectin concentration (0.5 and 2%), whereas a higher diversity of pectin fragments was found at 5% which could be indicative of a more controlled depolymerisation. These findings highlight the importance of the selection of appropriate US processing conditions to diversify the applications of modified pectin, as well as the potential of US as a prospective alternative to currently used depolymerisation techniques. Copyright © 2016 Elsevier B.V. All rights reserved.

Targeting α-synuclein oligomers by protein-fragment complementation for drug discovery in synucleinopathies.

PubMed

Moussaud, Simon; Malany, Siobhan; Mehta, Alka; Vasile, Stefan; Smith, Layton H; McLean, Pamela J

2015-05-01

Reducing the burden of α-synuclein oligomeric species represents a promising approach for disease-modifying therapies against synucleinopathies such as Parkinson's disease and dementia with Lewy bodies. However, the lack of efficient drug discovery strategies that specifically target α-synuclein oligomers has been a limitation to drug discovery programs. Here we describe an innovative strategy that harnesses the power of bimolecular protein-fragment complementation to monitor synuclein-synuclein interactions. We have developed two robust models to monitor α-synuclein oligomerization by generating novel stable cell lines expressing α-synuclein fusion proteins for either fluorescent or bioluminescent protein-fragment complementation under the tetracycline-controlled transcriptional activation system. A pilot screen was performed resulting in the identification of two potential hits, a p38 MAPK inhibitor and a casein kinase 2 inhibitor, thereby demonstrating the suitability of our protein-fragment complementation assay for the measurement of α-synuclein oligomerization in living cells at high throughput. The application of the strategy described herein to monitor α-synuclein oligomer formation in living cells with high throughput will facilitate drug discovery efforts for disease-modifying therapies against synucleinopathies and other proteinopathies.

Construction of an agglutination tool: recombinant Fab fragments biotinylated in vitro.

PubMed

Czerwinski, Marcin; Krop-Watorek, Anna; Wasniowska, Kazimiera; Smolarek, Dorota; Spitalnik, Steven L

2009-11-30

The pComb3H vector system is used for constructing and panning recombinant antibody libraries. It allows for expression of monovalent Fab fragments, either on the surface of M13 phage, or in the form of soluble proteins secreted into the periplasmic space of bacteria. We constructed a modified pComb3H vector containing cDNA encoding for a 23-amino acid fragment of the Escherichia coli biotin carboxy carrier protein (BCCP), which is an acceptor sequence for biotinylation. The vector was used to express the Fab fragment recognizing human glycophorin A. The purified Fab fragment containing this biotin acceptor sequence was effectively biotinylated in vitro using biotin ligase (BirA). The specificity and avidity of the biotinylated Fab fragments were similar to the previously produced, unmodified Fab fragments. An avidin-alkaline phosphatase conjugate was used to detect the recombinant Fab fragments, instead of secondary antibody. In addition, when biotinylated Fab fragments were mixed with avidin, red blood cells were directly agglutinated.

Pore-scale Investigation of Surfactant Induced Mobilization for the Remediation of LNAPL

NASA Astrophysics Data System (ADS)

Ghosh, J.; Tick, G. R.

2011-12-01

The presence of nonaqueous phase liquids within the subsurface can significantly limit the effectiveness of groundwater remediation. Specifically, light nonaqueous phase liquids (LNAPLs) present unique challenges as they can become "smeared" within zones above and below the water table. The aim of this research is to understand the interfacial phenomena at the pore scale influencing residual saturation of LNAPL distribution as function of media heterogeneity and remediation processes from various aquifer systems. A series of columns were packed with three types of unconsolidated sand of increasing heterogeneity in grain size distribution and were established with residual saturations of light and heavy crude oil fractions, respectively. These columns were then subjected to flooding with 0.1% anionic surfactant solution in various episodes to initiate mobilization and enhanced recovery of NAPL phase contamination. Synchrotron X-ray microtomography (SXM) imaging technology was used to study three-dimensional (3-D) distributions of crude-oil-blobs before and after sequential surfactant flooding events. Results showed that LNAPL blob distributions became more heterogeneous after each subsequent surfactant flooding episode for all porous-media systems. NAPL recovery was most effective from the homogenous porous medium whereby 100% recovery resulted after 5 pore volumes (PVs) of flushing. LNAPL within the mildly heterogeneous porous medium produced a limited but consistent reduction in saturation after each surfactant flooding episode (23% and 43% recovery for light and heavy after the 5-PV flood). The highly heterogeneous porous medium showed greater NAPL recovery potential (42% and 16% for light and heavy) only after multiple pore volumes of flushing, at which point the NAPL blobs become fragmented into the smaller fragments in response to the reduced interfacial tension. The heterogeneity of the porous media (i.e. grain-size distribution) was a dominant control on the NAPL-blob-size-distribution trapped as residual saturation. The mobility of the NAPL blobs, as a result of surfactant flooding, was primarily controlled by the relative permeability of the medium and the reduction of interfacial tension between the wetting phase (water) and NAPL phase.

Effect of palladium doping on the stability and fragmentation patterns of cationic gold clusters

NASA Astrophysics Data System (ADS)

Ferrari, P.; Hussein, H. A.; Heard, C. J.; Vanbuel, J.; Johnston, R. L.; Lievens, P.; Janssens, E.

2018-05-01

We analyze in detail how the interplay between electronic structure and cluster geometry determines the stability and the fragmentation channels of single Pd-doped cationic Au clusters, PdA uN-1+ (N =2 -20 ). For this purpose, a combination of photofragmentation experiments and density functional theory calculations was employed. A remarkable agreement between the experiment and the calculations is obtained. Pd doping is found to modify the structure of the Au clusters, in particular altering the two-dimensional to three-dimensional transition size, with direct consequences on the stability of the clusters. Analysis of the electronic density of states of the clusters shows that depending on cluster size, Pd delocalizes one 4 d electron, giving an enhanced stability to PdA u6 + , or remains with all 4 d10 electrons localized, closing an electronic shell in PdA u9 + . Furthermore, it is observed that for most clusters, Au evaporation is the lowest-energy decay channel, although for some sizes Pd evaporation competes. In particular, PdA u7 + and PdA u9 + decay by Pd evaporation due to the high stability of the A u7 + and A u9 + fragmentation products.

Degradation testing of Mg alloys in Dulbecco's modified eagle medium: Influence of medium sterilization.

PubMed

Marco, Iñigo; Feyerabend, Frank; Willumeit-Römer, Regine; Van der Biest, Omer

2016-05-01

This work studies the in vitro degradation of Mg alloys for bioabsorbable implant applications under near physiological conditions. For this purpose, the degradation behaviour of Mg alloys in Dulbecco's modified eagle medium (DMEM) which is a commonly used cell culture medium is analysed. Unfortunately, DMEM can be contaminated by microorganisms, acidifying the medium and accelerating the Mg degradation process by dissolution of protective degradation layers, such as (Mgx,Cay)(PO4)z. In this paper the influence of sterilization by applying UV-C radiation and antibiotics (penicillin/streptomycin) is analysed with two implant material candidates: Mg-Gd and Mg-Ag alloys; and pure magnesium as well as Mg-4Y-3RE as a reference. Copyright © 2016 Elsevier B.V. All rights reserved.

The Momentum Kick Model Description of the Near-Side Ridge and Jet Quenching

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

Wong, Cheuk-Yin

2008-12-01

In the momentum kick model, a near-side jet parton occurs near the surface, kicks medium partons, loses energy, and fragments into the trigger particle and fragmentation products. The kicked medium partons subsequently materialize as the observed ridge particles which cary direct information on the magnitude of the momentum kick and the initial parton momentum distribution at the moment of jet-parton collision. The initial parton momentum distribution, extracted from the STAR ridge data for central Au-Au collisions at \\sqrt{s_NN} = 200 GeV, has a thermal-like transverse momentum distribution, but a non-Gaussian, relatively flat rapidity distribution at mid-rapidity with sharp kinematic boundariesmore » at large rapidities. The degree of jet quenching and the centrality dependence of the ridge yield can also be described by the momentum kick model.« less

Chlamydia Hijacks ARF GTPases To Coordinate Microtubule Posttranslational Modifications and Golgi Complex Positioning

PubMed Central

Wesolowski, Jordan; Weber, Mary M.; Nawrotek, Agata; Dooley, Cheryl A.; Calderon, Mike; St. Croix, Claudette M.; Hackstadt, Ted; Cherfils, Jacqueline

2017-01-01

ABSTRACT The intracellular bacterium Chlamydia trachomatis develops in a parasitic compartment called the inclusion. Posttranslationally modified microtubules encase the inclusion, controlling the positioning of Golgi complex fragments around the inclusion. The molecular mechanisms by which Chlamydia coopts the host cytoskeleton and the Golgi complex to sustain its infectious compartment are unknown. Here, using a genetically modified Chlamydia strain, we discovered that both posttranslationally modified microtubules and Golgi complex positioning around the inclusion are controlled by the chlamydial inclusion protein CT813/CTL0184/InaC and host ARF GTPases. CT813 recruits ARF1 and ARF4 to the inclusion membrane, where they induce posttranslationally modified microtubules. Similarly, both ARF isoforms are required for the repositioning of Golgi complex fragments around the inclusion. We demonstrate that CT813 directly recruits ARF GTPases on the inclusion membrane and plays a pivotal role in their activation. Together, these results reveal that Chlamydia uses CT813 to hijack ARF GTPases to couple posttranslationally modified microtubules and Golgi complex repositioning at the inclusion. PMID:28465429

Energetic and optical consequences in isotropic curved space and time.

PubMed

Ben-Abdallah, P

2001-10-20

In numerous media (nonlinear material, moving dielectrics, superfluids, Bose-Einstein condensates, and others) and different in vacuo states (nontrivial quantum electrodynamics in vacuo) matter or vacuum fluctuations modify light propagation in the same way that an effective gravitational field does. This nonlinear optical behavior affects not only the energy paths but also the form of the energetic invariant. However, such a function plays a key role when we try to develop a phenomenological kinetic theory for participating media. I analyze how modification of light propagation transforms the energetic invariant and modifies its transport inside a participating medium. A semianalytical method is presented to solve the radiative transfer equation for any spherically symmetric problems.

The behavior limestone under explosive load

NASA Astrophysics Data System (ADS)

Orlov, M. Yu; Orlova, Yu N.; Bogomolov, G. N.

2016-11-01

Limestone behavior under explosive loading was investigated. The behavior of the limestone by the action of the three types of explosives, including granular, ammonite and emulsion explosives was studied in detail. The shape and diameter of the explosion craters were obtained. The observed fragments after the blast have been classified as large, medium and small fragments. Three full-scale experiments were carried out. The research results can be used as a qualitative test for the approbation of numerical methods.

A comparative study on effects of heterotrophic microbial activity on the stability of bivalve and coral carbonate during early diagenesis.

NASA Astrophysics Data System (ADS)

Lange, Skadi M.; Krause, Stefan; Immenhauser, Adrian; Ritter, Ann-Christin; Gorb, Stanislav N.; Kleinteich, Thomas; Treude, Tina

2016-04-01

Following deposition and shallow burial, marine biogenic carbonates are exposed to an environment that is geochemically affected by a manifold of bacterial metabolic redox processes. To allow for comparison of potential microbe-mediated alteration effects on carbonates, we used aragonitic bivalve shell samples and porous aragonitic coral fragments for incubation experiments in oxic- and anoxic seawater media. The media contained marine sediment slurries or bacterial cultures to mimic the natural processes in vitro. The results for anoxic experimental media containing bivalve shell samples or coral fragments displayed considerable changes in carbonate-system parameters (pH, AT, CA, DIC) and divalent-cation ratios (Mg/Ca, Mg/Sr, Sr/Ca) over time. Furthermore, incubated bivalve shell samples were altered in morphology, elemental composition and isotopic signature. Coral-fragment bearing oxic incubations were run at two temperature regimes and divalent-cation ratios of the high-temperature bacterial medium displayed withdrawal of Ca2+ and Sr2+ from the medium, thus indicating microbe-induced secondary aragonite precipitation. Analyses of coral fragments include electron-microprobe mapping and X-ray microtomography to resolve elemental sample composition and pore-space alteration features, respectively. Up to this point our results indicate that heterotrophic bacterial activity has the potential to affect surficial or open pore space in carbonate archives by increasing rates of alteration relative to sterile environments.

Assessing and monitoring the risk of desertification in Dobrogea, Romania, using Landsat data and decision tree classifier.

PubMed

Vorovencii, Iosif

2015-04-01

The risk of the desertification of a part of Romania is increasingly evident, constituting a serious problem for the environment and the society. This article attempts to assess and monitor the risk of desertification in Dobrogea using Landsat Thematic Mapper (TM) satellite images acquired in 1987, 1994, 2000, 2007 and 2011. In order to assess the risk of desertification, we used as indicators the Modified Soil Adjustment Vegetation Index 1 (MSAVI1), the Moving Standard Deviation Index (MSDI) and the albedo, indices relating to the vegetation conditions, the landscape pattern and micrometeorology. The decision tree classifier (DTC) was also used on the basis of pre-established rules, and maps displaying six grades of desertification risk were obtained: non, very low, low, medium, high and severe. Land surface temperature (LST) was also used for the analysis. The results indicate that, according to pre-established rules for the period of 1987-2011, there are two grades of desertification risk that have an ascending trend in Dobrogea, namely very low and medium desertification. An investigation into the causes of the desertification risk revealed that high temperature is the main factor, accompanied by the destruction of forest shelterbelts and of the irrigation system and, to a smaller extent, by the fragmentation of agricultural land and the deforestation in the study area.

A Modified Constitutive Model for Tensile Flow Behaviors of BR1500HS Ultra-High-Strength Steel at Medium and Low Temperature Regions

NASA Astrophysics Data System (ADS)

Zhao, Jun; Quan, Guo-Zheng; Pan, Jia; Wang, Xuan; Wu, Dong-Sen; Xia, Yu-Feng

2018-01-01

Constitutive model of materials is one of the most requisite mathematical model in the finite element analysis, which describes the relationships of flow behaviors with strain, strain rate and temperature. In order to construct such constitutive relationships of ultra-high-strength BR1500HS steel at medium and low temperature regions, the true stress-strain data over a wide temperature range of 293-873 K and strain rate range of 0.01-10 s-1 were collected from a series of isothermal uniaxial tensile tests. The experimental results show that stress-strain relationships are highly non-linear and susceptible to three parameters involving temperature, strain and strain rate. By considering the impacts of strain rate and temperature on strain hardening, a modified constitutive model based on Johnson-Cook model was proposed to characterize flow behaviors in medium and low temperature ranges. The predictability of the improved model was also evaluated by the relative error (W(%)), correlation coefficient (R) and average absolute relative error (AARE). The R-value and AARE-value for modified constitutive model at medium and low temperature regions are 0.9915 & 1.56 % and 0.9570 & 5.39 %, respectively, which indicates that the modified constitutive model can precisely estimate the flow behaviors for BR1500HS steel in the medium and low temperature regions.

Lysozyme immobilization onto PVC catheters grafted with NVCL and HEMA for reduction of bacterial adhesion

NASA Astrophysics Data System (ADS)

Guadarrama-Zempoalteca, Yesica; Díaz-Gómez, Luis; Meléndez-Ortiz, H. Iván; Concheiro, Angel; Alvarez-Lorenzo, Carmen; Bucio, Emilio

2016-09-01

The aim of the present work was to functionalize poly(vinyl chloride) (PVC) urinary catheters with grafted copolymers that can improve the biocompatibility and serve as binding points of lysozyme. PVC catheters were modified by grafting a mixture of N-vinylcaprolactam (NVCL) and 2-hydroxyethylmethacrylate (HEMA) applying a gamma-ray pre-irradiation method. The effect of absorbed dose, monomer concentration, temperature, and reaction time on the grafting percentage was evaluated. The grafted catheters were characterized regarding surface composition (FTIR-ATR spectroscopy), thermal properties (DSC and TGA) and swelling in aqueous medium. Lysozyme was directly coupled onto PVC-g-(NVCL/HEMA) previously activated using carbonyldiimidazole. Antimicrobial lytic activity of the modified catheters over time was tested against Micrococcus lysodeikticus. Lysozyme diminished the adhesion of Staphylococcus aureus onto the functionalized catheters, which may be suitable to prevent biofilm formation.

System configured for applying a modifying agent to a non-equidimensional substrate

DOEpatents

Janikowski,; Stuart K. , Argyle; Mark D. , Fox; Robert V. , Propp; W Alan, Toth [Idaho Falls, ID; William J. , Ginosar; Daniel M. , Allen; Charles A. , Miller; David, L [Idaho Falls, ID

2007-07-10

The present invention is related to systems and methods for modifying various non-equidimensional substrates with modifying agents. The system comprises a processing chamber configured for passing the non-equidimensional substrate therethrough, wherein the processing chamber is further configured to accept a treatment mixture into the chamber during movement of the non-equidimensional substrate through the processing chamber. The treatment mixture can comprise of the modifying agent in a carrier medium, wherein the carrier medium is selected from the group consisting of a supercritical fluid, a near-critical fluid, a superheated fluid, a superheated liquid, and a liquefied gas. Thus, the modifying agent can be applied to the non-equidimensional substrate upon contact between the treatment mixture and the non-equidimensional substrate.

System configured for applying a modifying agent to a non-equidimensional substrate

DOEpatents

Janikowski, Stuart K.; Toth, William J.; Ginosar, Daniel M.; Allen, Charles A.; Argyle, Mark D.; Fox, Robert V.; Propp, W. Alan; Miller, David L.

2003-09-23

The present invention is related to systems and methods for modifying various non-equidimensional substrates with modifying agents. The system comprises a processing chamber configured for passing the non-equidimensional substrate therethrough, wherein the processing chamber is further configured to accept a treatment mixture into the chamber during movement of the non-equidimensional substrate through the processing chamber. The treatment mixture can comprise of the modifying agent in a carrier medium, wherein the carrier medium is selected from the group consisting of a supercritical fluid, a near-critical fluid, a superheated fluid, a superheated liquid, and a liquefied gas. Thus, the modifying agent can be applied to the non-equidimensional substrate upon contact between the treatment mixture and the non-equidimensional substrate.

Low functional richness and redundancy of a predator assemblage in native forest fragments of Chiloe island, Chile.

PubMed

Farias, Ariel A; Jaksic, Fabian M

2011-07-01

1. Changes in land use and habitat fragmentation are major drivers of global change, and studying their effects on biodiversity constitutes a major research programme. However, biodiversity is a multifaceted concept, with a functional component linking species richness to ecosystem function. Currently, the interaction between functional and taxonomic components of biodiversity under realistic scenarios of habitat degradation is poorly understood. 2. The expected functional richness (FR)-species richness relationship (FRSR) is positive, and attenuated for functional redundancy in species-rich assemblages. Further, environmental filters are expected to flatten that association by sorting species with similar traits. Thus, analysing FRSR can inform about the response of biodiversity to environmental gradients and habitat fragmentation, and its expected functional consequences. 3. Top predators affect ecosystem functioning through prey consumption and are particularly vulnerable to changes in land use and habitat fragmentation, being good indicators of ecosystem health and suitable models for assessing the effects of habitat fragmentation on their FR. 4. Thus, this study analyses the functional redundancy of a vertebrate predator assemblage at temperate forest fragments in a rural landscape of Chiloe island (Chile), testing the existence of environmental filters by contrasting an empirically derived FRSR against those predicted from null models, and testing the association between biodiversity components and the structure of forest fragments. 5. Overall, contrasts against null models indicate that regional factors determine low levels of FR and redundancy for the vertebrate predator assemblage studied, while recorded linear FRSR indicates proportional responses of the two biodiversity components to the structure of forest fragments. Further, most species were positively associated with either fragment size or shape complexity, which are highly correlated. This, and the absence of ecological filters at the single-fragment scale, rendered taxonomically and functionally richer predator assemblages at large complex-shaped fragments. 6. These results predict strong effects of deforestation on both components of biodiversity, potentially affecting the functioning of remnants of native temperate forest ecosystems. Thus, the present study assesses general responses of functional and taxonomic components of biodiversity to a specific human-driven process. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.

The effect of nanofiber based filter morphology on bacteria deactivation during water filtration

NASA Astrophysics Data System (ADS)

Kimmer, Dusan; Vincent, Ivo; Lev, Jaroslav; Kalhotka, Libor; Mikula, Premysl; Korinkova, Radka; Sambaer, Wannes; Zatloukal, Martin

2013-04-01

Procedures permitting to prepare homogeneous functionalized nanofibre structures based on polyurethanes modified by phthalocyanines (PCs) by employing a suitable combination of variables during the electrospinning process are presented. Compared are filtration and bacteria deactivation properties of open and planar nanostructures with PCs embedded into polyurethane chain by a covalent bond protecting the release of active organic compound during the filtration process. Finding that the morphology of functionalized nanofibre structures have an effect on bacterial growth was confirmed by microbiological and physico-chemical analyses, such as the inoculation in a nutrient agar culture medium and flow cytometry.

Particle-size distribution modified effective medium theory and validation by magneto-dielectric Co-Ti substituted BaM ferrite composites

NASA Astrophysics Data System (ADS)

Li, Qifan; Chen, Yajie; Harris, Vincent G.

2018-05-01

This letter reports an extended effective medium theory (EMT) including particle-size distribution functions to maximize the magnetic properties of magneto-dielectric composites. It is experimentally verified by Co-Ti substituted barium ferrite (BaCoxTixFe12-2xO19)/wax composites with specifically designed particle-size distributions. In the form of an integral equation, the extended EMT formula essentially takes the size-dependent parameters of magnetic particle fillers into account. It predicts the effective permeability of magneto-dielectric composites with various particle-size distributions, indicating an optimal distribution for a population of magnetic particles. The improvement of the optimized effective permeability is significant concerning magnetic particles whose properties are strongly size dependent.

Optimization of culture conditions and medium composition for the production of micrococcin GO5 by Micrococcus sp. GO5.

PubMed

Kim, Mi-Hee; Kong, Yoon-Jung; Baek, Hong; Hyun, Hyung-Hwan

2006-01-02

To enhance the production of micrococcin GO5, a bacteriocin produced by Micrococcus sp. GO5, cultivation conditions and medium composition were optimized. The optimal initial pH and temperature for bacteriocin production were 7.0-9.0 and 37 degrees C, respectively. Micrococcus sp. GO5 displayed the highest micrococcin GO5 activity when grown in modified MRS medium that contained lactose or sucrose, rather than glucose, as a carbon source. The maximum bacteriocin activity was obtained in modified MRS medium containing 0.5% tryptone and 1.0% yeast extract as nitrogen sources instead of the other nitrogen sources present in MRS medium. Bacteriocin production was greatly affected by the concentration of K(2)HPO(4); strain GO5 produced eight-fold more bacteriocin in medium containing 2.0-2.5% K(2)HPO(4) than in medium containing 0.2% K(2)HPO(4). The optimal concentration of MgSO(4).7H(2)O for bacteriocin production was 0.5%. The production of micrococcin GO5 was increased 32-fold in shake flask culture and 16-fold in a bioreactor using the optimized medium (TY medium), compared with culturing in MRS medium.

Analysis of Bending Strength of Resin Mortars That Are at Risk of Long-Term Exposure to Environmental Corrosives

NASA Astrophysics Data System (ADS)

Debska, Bernardeta; Licholai, Lech

2017-12-01

The results of the article are part of an extensive research on new building materials including cement-free polymer composites where the binder is epoxy resin modified with glycolyzates obtained from poly (ethylene terephthalate) waste (PET). The investigation conducted con-firmed that there is a possibility of using waste materials in the production of mortar. Since they have always been an environmental problem, their utilization will help to apply the principles of sustainable development in the processes of obtaining new materials. The article discusses the results of a study of flexural strength of polymer mortars. Mortar specimens modified with propylene glycol and PET waste based glycolyzate were exposed to a 10% NaCl solution and their strength parameters were then examined after one month, six months and twelve months of immersion in this aggressive medium. The same characteristics were also determined for specimens that were not exposed to the NaCl solution. The results were presented as the trend function. The sections of the curve corresponding to the particular periods of exposure in aggressive medium vary in shape. Due to this, an attempt was made to adjust the spline function to the experimental data. The composites obtained show a deterioration in their strength properties which grows with the extension of their exposure to a corrosive medium. However, the chemical corrosion resistance of the mortars under investigation can be considered very good as it is still much higher than that of conventional cement mortars. Even after a year exposure to a corrosive substance, the mortars obtained still show high mean flexural strength values which equal about 30 MPa.

Functionalization of multi-walled carbon nanotubes with thermo-responsive azide-terminated poly(N-isopropylacrylamide) via click reactions.

PubMed

Su, Xin; Shuai, Ya; Guo, Zanru; Feng, Yujun

2013-04-18

Covalently functionalized multi-walled carbon nanotubes (MWNTs) were prepared by grafting well-defined thermo-responsive poly(N-isopropylacrylamide) (PNIPAM) via click reactions. First, azide-terminated poly(N-isopropylacrylamide) (N3-PNIPAM) was synthesized by reversible addition fragmentation chain-transfer (RAFT) polymerization, and then the N₃-PNIPAM moiety was connected onto MWNTs by click chemistry. The products were characterized by means of FT-IR, TGA and TEM. The results show that the modification of MWNTs is very successful and MWNTs functionalized by N₃-PNIPAM (MWNTs-PNIPAM) have good solubility and stability in water. TEM images show the functionalized MWNTs are dispersed individually, indicating that the bundles of original MWNTs are separated into individual tubes by surface modification with polymer chains. These MWNTs modified with PNIPAM represent a potential nano-material for preparation of hydrophilic composite materials.

Direct connection between the different QCD orders for parton distribution and fragmentation functions

NASA Astrophysics Data System (ADS)

Shevchenko, O. Yu.

2013-06-01

The formulas directly connecting parton distribution functions and fragmentation functions at the next-to-leading-order QCD with the same quantities at the leading order are derived. These formulas are universal, i.e., have the same form for all kinds of parton distribution functions and fragmentation functions, differing only in the respective splitting functions entering there.

Effective medium model for a granular monolayer on an elastic substrate

NASA Astrophysics Data System (ADS)

Maznev, Alexei

Effective medium models have been shown to work well in describing experimental observations of the interaction of surface Rayleigh waves with contact vibrations of a monolayer of microspheres . However, these models contain intrinsic conceptual problems: for example, the local displacement of the substrate at the contact point is equated to the effective medium average value of the surface displacement. I will present a rigorous derivation of the effective medium model for a random arrangement of mass-spring oscillators on an elastic half-space using elastodynamic surface Green's function formalism. We will see that the model equating the local surface displacement to the effective medium displacement is indeed valid if the spring constant of the oscillators is modified to include the stiffness of the contact calculated in the quasistatic approximation. In the case of contact vibrations of microspheres, this means using the spring constant calculated using the Hertzian contact model. Thus the results obtained in the prior work were correct despite the apparent inconsistencies in the model. The presented analysis will provide a solid foundation for effective medium models used to describe dynamics of microparticle arrays adhered to a solid substrate. This work was supported by the U. S. Army Research Office through the Institute for Soldier Nanotechnologies under Grant W911NF-13-D-0001.

A novel magneto-DNA duplex probe for bacterial DNA detection based on exonuclease III-aided cycling amplification.

PubMed

Zeng, Yan; Wan, Yi; Zhang, Dun; Qi, Peng

2015-01-01

A novel magneto-DNA duplex probe for bacterial DNA detection based on exonuclease III (Exo-III) aided cycling amplification has been developed. This magneto-DNA duplex probe contains a partly hybrid fluorophore-modified capture probe and a fluorophore-modified signal probe with magnetic microparticle as carrier. In the presence of a perfectly matched target bacterial DNA, blunt 3'-terminus of the capture probe is formed, activating the Exo-III aided cycling amplification. Thus, Exo-III catalyzes the stepwise removal of mononucleotides from this terminus, releasing both fluorophore-modified signal probe, fluorescent dyes of the capture probe and target DNA. The released target DNA then starts a new cycle, while released fluorescent fragments are recovered with magnetic separation for fluorescence signal collection. This system exhibited sensitive detection of bacterial DNA, with a detection limit of 14 pM because of the unique cleavage function of Exo-III, high fluorescence intensity, and separating function of magneto-DNA duplex probes. Besides this sensitivity, this strategy exhibited excellent selectivity with mismatched bacterial DNA targets and other bacterial species targets and good applicability in real seawater samples, hence, this strategy could be potentially used for qualitative and quantitative analysis of bacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantum-chemical study of the effect of ligands on the structure and properties of gold clusters

NASA Astrophysics Data System (ADS)

Golosnaya, M. N.; Pichugina, D. A.; Oleinichenko, A. V.; Kuz'menko, N. E.

2017-02-01

The structures of [Au4(dpmp)2X2]2+clusters, where X =-C≡CH,-CH3,-SCH3,-F,-Cl,-Br,-I, dpmp is bis((diphenylphosphino)methyl)(phenyl)phosphine, are calculated at the level of density functional theory with the PBE functional and a modified Dirac-Coulomb-Breit Hamiltonian in an all-electron basis set (Λ). Using the example of [Au4(dpmp)2(C≡CC6H5)2]2+, the interatomic distances and bond angles calculated by means of PBE0/LANL2DZ, TPSS/LANL2DZ, TPSSh/LANL2DZ, and PBE/Λ are compared to X-ray crystallography data. It is shown that PBE/Λ yields the most accurate calculation of the geometrical parameters of this cluster. The ligand effect on the electronic stability of a cluster and the stability in reactions of decomposition into different fragments is studied, along with the capability of ligand exchange. Stability is predicted for [Au4(dpmp)2F2]2+ and [Au4(dpmp)2(SCH3)2]2+, while [Au4(dpmp)2I2]2+ cluster is unstable and its decomposes into two identical fragments is supposed.

Sporothrix schenckii Sensu Lato identification in fragments of skin lesion cultured in NNN medium for differential diagnosis of cutaneous leishmaniasis.

PubMed

Antonio, Liliane de Fátima; Pimentel, Maria Inês Fernandes; Lyra, Marcelo Rosandiski; Madeira, Maria de Fátima; Miranda, Luciana de Freitas Campos; Paes, Rodrigo Almeida; Brito-Santos, Fábio; Carvalho, Maria Helena Galdino Figueredo; Schubach, Armando de Oliveira

2017-02-01

Eighty-nine patients with clinical suspicion of leishmaniasis were referred for differential diagnosis. Sporothrix schenckii sensu lato was isolated in Novy-MacNeal-Nicolle + Schneider media in 98% of 64 patients with final diagnosis of sporotrichosis. This medium may be suitable for diagnosis of sporotrichosis in areas where cutaneous leishmaniasis is also endemic. Copyright © 2016 Elsevier Inc. All rights reserved.

Cloning, Sequencing, and Characterization of the cgmB Gene of Sinorhizobium meliloti Involved in Cyclic β-Glucan Biosynthesis

PubMed Central

Wang, Ping; Ingram-Smith, Cheryl; Hadley, Jill A.; Miller, Karen J.

1999-01-01

Periplasmic cyclic β-glucans of Rhizobium species provide important functions during plant infection and hypo-osmotic adaptation. In Sinorhizobium meliloti (also known as Rhizobium meliloti), these molecules are highly modified with phosphoglycerol and succinyl substituents. We have previously identified an S. meliloti Tn5 insertion mutant, S9, which is specifically impaired in its ability to transfer phosphoglycerol substituents to the cyclic β-glucan backbone (M. W. Breedveld, J. A. Hadley, and K. J. Miller, J. Bacteriol. 177:6346–6351, 1995). In the present study, we have cloned, sequenced, and characterized this mutation at the molecular level. By using the Tn5 flanking sequences (amplified by inverse PCR) as a probe, an S. meliloti genomic library was screened, and two overlapping cosmid clones which functionally complement S9 were isolated. A 3.1-kb HindIII-EcoRI fragment found in both cosmids was shown to fully complement mutant S9. Furthermore, when a plasmid containing this 3.1-kb fragment was used to transform Rhizobium leguminosarum bv. trifolii TA-1JH, a strain which normally synthesizes only neutral cyclic β-glucans, anionic glucans containing phosphoglycerol substituents were produced, consistent with the functional expression of an S. meliloti phosphoglycerol transferase gene. Sequence analysis revealed the presence of two major, overlapping open reading frames within the 3.1-kb fragment. Primer extension analysis revealed that one of these open reading frames, ORF1, was transcribed and its transcription was osmotically regulated. This novel locus of S. meliloti is designated the cgm (cyclic glucan modification) locus, and the product encoded by ORF1 is referred to as CgmB. PMID:10419956

In vivo Monitoring of Serotonin by Nanomaterial Functionalized Acupuncture Needle

NASA Astrophysics Data System (ADS)

Li, Yu-Tao; Tang, Li-Na; Ning, Yong; Shu, Qing; Liang, Feng-Xia; Wang, Hua; Zhang, Guo-Jun

2016-06-01

Acupuncture treatment is amazing but controversial. Up to now, the mechanism of treating diseases by acupuncture and moxibustion is still unclear, especially the occurrence of the molecular events in local acupoints. Herein, we report an extremely stable microsensor by modifying carbon nanotube (CNT) to the tip surface of acupuncture needle and applying this CNT-modified acupuncture needle for real time monitoring of serotonin (5-HT) in vivo. To stabilize CNT modification on the needle tip surface, poly(3,4-ethylenedioxythiophene)(PEDOT) was employed as glue water to stick CNT on the needle. The detection limit of the CNT-modified needle was found to be approximately 50 nM and 78 nM in the PBS and the cell medium, respectively. In addition, the needle showed good selectivity to some inflammatory mediators and some electroactive molecules. For the first time, the CNT-modified needle could be directly probed into rat body for real time monitoring of 5-HT in vivo, showing a great potential for better understanding the mechanism of acupuncture treatment.

Escherichia coli cytotoxic necrotizing factor 1: evidence for induction of actin assembly by constitutive activation of the p21 Rho GTPase.

PubMed Central

Fiorentini, C; Donelli, G; Matarrese, P; Fabbri, A; Paradisi, S; Boquet, P

1995-01-01

Cytotoxic necrotizing factor type 1 (CNF1) induces in HEp-2 cells an increase in F-actin structures, which was detectable by fluorescence-activated cell sorter analysis 24 h after addition of this factor to the culture medium. Increase in F-actin was correlated with the augmentation of both the cell volume and the total cell actin content. Actin assembly-disassembly is controlled by small GTP-binding proteins of the Rho family, which have been reported recently to be modified by CNF1 treatment. Clostridium difficile toxin B and Clostridium botulinum exoenzyme C3, both known to act on the Rho GTPase, were used as biological tools to study the effect of CNF1 on this protein. CNF1 incubated before, during, or after exposure to the chimeric toxin C3B (which is the product of a genetic fusion between the DNA coding for C3 and the one coding for the B fragment of diphtheria toxin) protected HEp-2 cells from the disruption of F-actin structures caused by inactivation of the Rho GTPase through its ADP-ribosylation. On the other hand, C. difficile toxin B cytopathic effect was not observed upon preincubation of cells with CNF1. Toxins acting through a Rho-independent mechanism, such as cytochalasin D and Clostridium spiroforme iota-like toxin, could not be modified in their cellular activities by CNF1 treatment. All of our results suggest that CNF1 modifies the Rho molecule, thus probably protecting this GTPase from further bacterial toxin modification. PMID:7558302

Escherichia coli cytotoxic necrotizing factor 1: evidence for induction of actin assembly by constitutive activation of the p21 Rho GTPase.

PubMed

Fiorentini, C; Donelli, G; Matarrese, P; Fabbri, A; Paradisi, S; Boquet, P

1995-10-01

Cytotoxic necrotizing factor type 1 (CNF1) induces in HEp-2 cells an increase in F-actin structures, which was detectable by fluorescence-activated cell sorter analysis 24 h after addition of this factor to the culture medium. Increase in F-actin was correlated with the augmentation of both the cell volume and the total cell actin content. Actin assembly-disassembly is controlled by small GTP-binding proteins of the Rho family, which have been reported recently to be modified by CNF1 treatment. Clostridium difficile toxin B and Clostridium botulinum exoenzyme C3, both known to act on the Rho GTPase, were used as biological tools to study the effect of CNF1 on this protein. CNF1 incubated before, during, or after exposure to the chimeric toxin C3B (which is the product of a genetic fusion between the DNA coding for C3 and the one coding for the B fragment of diphtheria toxin) protected HEp-2 cells from the disruption of F-actin structures caused by inactivation of the Rho GTPase through its ADP-ribosylation. On the other hand, C. difficile toxin B cytopathic effect was not observed upon preincubation of cells with CNF1. Toxins acting through a Rho-independent mechanism, such as cytochalasin D and Clostridium spiroforme iota-like toxin, could not be modified in their cellular activities by CNF1 treatment. All of our results suggest that CNF1 modifies the Rho molecule, thus probably protecting this GTPase from further bacterial toxin modification.

Simulation of dependence of the cross section of deuterons beam fragmentation into cumulative pions and protons on the mass of the target nucleus

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

Litvinenko, A. G., E-mail: alitvin@jinr.ru; Litvinenko, E. I.

2015-03-15

We have studied the mechanisms influencing production of cumulative pions and protons in the fragmentation of the incident deuterons into cumulative pions and protons emitted at zero angle. We argue that the peripheral dependence on the atomic mass of the target nucleus, which was obtained in the experiments for medium and heavy nuclei, can be explained by scattering on target nucleons without introducing additional parameters.

Efficient heterologous expression and secretion in Aspergillus oryzae of a llama variable heavy-chain antibody fragment V(HH) against EGFR.

PubMed

Okazaki, Fumiyoshi; Aoki, Jun-ichi; Tabuchi, Soichiro; Tanaka, Tsutomu; Ogino, Chiaki; Kondo, Akihiko

2012-10-01

We have constructed a filamentous fungus Aspergillus oryzae that secretes a llama variable heavy-chain antibody fragment (V(HH)) that binds specifically to epidermal growth factor receptor (EGFR) in a culture medium. A major improvement in yield was achieved by fusing the V(HH) with a Taka-amylase A signal sequence (sTAA) and a segment of 28 amino acids from the N-terminal region of Rhizopus oryzae lipase (N28). The yields of secreted, immunologically active anti-EGFR V(HH) reached 73.8 mg/1 in a Sakaguchi flask. The V(HH) fragments were released from the sTAA or N28 proteins by an indigenous A. oryzae protease during cultivation. The purified recombinant V(HH) fragment was specifically recognized and could bind to the EGFR with a high affinity.

Increased cellular uptake of peptide-modified PEGylated gold nanoparticles.

PubMed

He, Bo; Yang, Dan; Qin, Mengmeng; Zhang, Yuan; He, Bing; Dai, Wenbing; Wang, Xueqing; Zhang, Qiang; Zhang, Hua; Yin, Changcheng

2017-12-09

Gold nanoparticles are promising drug delivery vehicles for nucleic acids, small molecules, and proteins, allowing various modifications on the particle surface. However, the instability and low bioavailability of gold nanoparticles compromise their clinical application. Here, we functionalized gold nanoparticles with CPP fragments (CALNNPFVYLI, CALRRRRRRRR) through sulfhydryl PEG to increase their stability and bioavailability. The resulting gold nanoparticles were characterized with transmission electron microscopy (TEM), dynamic light scattering (DLS), UV-visible spectrometry and X-ray photoelectron spectroscopy (XPS), and the stability in biological solutions was evaluated. Comparing to PEGylated gold nanoparticles, CPP (CALNNPFVYLI, CALRRRRRRRR)-modified gold nanoparticles showed 46 folds increase in cellular uptake in A549 and B16 cell lines, as evidenced by the inductively coupled plasma atomic emission spectroscopy (ICP-AES). The interactions between gold nanoparticles and liposomes indicated CPP-modified gold nanoparticles bind to cell membrane more effectively than PEGylated gold nanoparticles. Surface plasmon resonance (SPR) was used to measure interactions between nanoparticles and the membrane. TEM and uptake inhibitor experiments indicated that the cellular entry of gold nanoparticles was mediated by clathrin and macropinocytosis. Other energy independent endocytosis pathways were also identified. Our work revealed a new strategy to modify gold nanoparticles with CPP and illustrated the cellular uptake pathway of CPP-modified gold nanoparticles. Copyright © 2017 Elsevier Inc. All rights reserved.

Executive Dysfunction in OSA Before and After Treatment: A Meta-Analysis

PubMed Central

Olaithe, Michelle; Bucks, Romola S.

2013-01-01

Study Objectives: Obstructive sleep apnea (OSA) is a frequent and often underdiagnosed condition that is associated with upper airway collapse, oxygen desaturation, and sleep fragmentation leading to cognitive dysfunction. There is meta-analytic evidence that subdomains of attention and memory are affected by OSA. However, a thorough investigation of the impact of OSA on different subdomains of executive function is yet to be conducted. This report investigates the impact of OSA and its treatment, in adult patients, on 5 theorized subdomains of executive function. Design: An extensive literature search was conducted of published and unpublished materials, returning 35 studies that matched selection criteria. Meta-analysis was used to synthesize the results from studies examining the impact of OSA on executive functioning compared to controls (21 studies), and before and after treatment (19 studies); 5 studies met inclusion in both categories. Measurements: Research papers were selected which assessed 5 subdomains of executive function: Shifting, Updating, Inhibition, Generativity, and Fluid Reasoning. Results: All 5 domains of executive function demonstrated medium to very large impairments in OSA independent of age and disease severity. Furthermore, all subdomains of executive function demonstrated small to medium improvements with CPAP treatment. Discussion: Executive function is impaired across all five domains in OSA; these difficulties improved with CPAP treatment. Age and disease severity did not moderate the effects found; however, further studies are needed to explore the extent of primary and secondary effects, and the impact of age and premorbid intellectual ability (cognitive reserve). Citation: Olaithe M; Bucks RS. Executive dysfunction in OSA before and after treatment: a meta-analysis. SLEEP 2013;36(9):1297-1305. PMID:23997362

Influence of plasmon coupling on the photoluminescence of ZnS/Ag nanoparticles obtained by laser irradiation in liquid

NASA Astrophysics Data System (ADS)

Moos, Rafaela; Graff, Ismael L.; de Oliveira, Vinicius S.; Schreiner, Wido H.; Bezerra, Arandi G.

2017-10-01

We investigate the photoluminescence, optical absorption and structural properties of ZnS submitted to laser irradiation in water and isopropyl alcohol. Nanoparticles were produced by irradiating micro-sized ZnS particles dispersed in both liquids, with and without the addition of Ag nanoparticles, taking advantage of the laser-assisted fragmentation effect. When ZnS microparticles are irradiated either in pure water or isopropyl alcohol a considerable size reduction is achieved (from micra to few nanometers). The photoluminescence of these nanoparticles mainly occurs in the UV, centered at 350 nm, and with smaller intensity in the visible, centered at 600 nm. Irradiation of ZnS microparticles dispersed in colloidal silver triggers a reaction between both materials, modifying its optical absorption and photoluminescent properties. After irradiation of ZnS in alcohol containing Ag nanoparticles, a giant increase of the UV photoluminescence is observed. Interestingly, when the irradiation is performed in aqueous Ag nanoparticles colloids, the photoluminescence suffers a red-shift towards the violet-blue. The data show that core-shell (Ag-ZnO) nanostructures are formed after irradiation and the visible emission likely originates from the ZnO shell grown around silver nanoparticles. The presence of Ag nanoparticles in the liquid medium promotes a stronger absorption of the laser beam during irradiation due to the coupling with the surface plasmon resonance, fostering intense reactions among ZnS, Ag nanoparticles, and the liquid medium. Our study shows that with a simple change of the liquid medium wherein the irradiation is conducted the photoluminescence can be tuned from UV to visible and core-shell nanostructures can be obtained.

Gravitation in material media

NASA Astrophysics Data System (ADS)

Ridgely, Charles T.

2011-03-01

When two gravitating bodies reside in a material medium, Newton's law of universal gravitation must be modified to account for the presence of the medium. A modified expression of Newton's law is known in the literature, but lacks a clear connection with existing gravitational theory. Newton's law in the presence of a homogeneous material medium is herein derived on the basis of classical, Newtonian gravitational theory and by a general relativistic use of Archimedes' principle. It is envisioned that the techniques presented herein will be most useful to graduate students and those undergraduate students having prior experience with vector analysis and potential theory.

Utilization of hydrotalcite modified with 3,4,5-trihydroxybenzoic acid for the treatment of silver-containing wastewater

NASA Astrophysics Data System (ADS)

Yanti, I.; Winata, W. F.; Anugrahwati, M.

2018-04-01

Utilization of hydrotalcite modified with 3,4,5-trihydroxybenzoic acid as a medium for the treatment of silver-containing wastewater has been done by using adsorption method. The modified hydrotalcite was prepared by direct precipitation using Mg and Al metals precursor and an organic compound of 3,4,5-trihydroxybenzoic acid. The modified material was then used for the treatment of silver-containing wastewater through adsorption method together with the determination of adsorption capacity, kinetics study as well as the material characterization after the treatment process. It could be observed from the results that the adsorption of silver onto the modified hydrotalcite was in accordance with Langmuir adsorption model with the adsorption capacity (qmax) of 400 mg.g-1. Moreover, the adsorption kinetics of the treatment showed that the process followed the kinetics model of pseudo-second-order of Ho with the velocity constant (k) of 1.15x10-4g.mg-1.minute-1. The adsorption process exhibited an exergonic property with the adsorption energy of 28.10x103 J.mol-1. All of the adsorption processes were conducted in the condition of pHadsorption = 3. Meanwhile, results from the characterization using FTIR showed the functional groups of C=C, -OH and NO3 - on the modified hydrotalcite underwent some alteration after the adsorption process of Ag(I). Therefore it can be observed that the functional groups of COOH and OH had an important role in the adsorption of silver from wastewater.

Anthropogenic Matrices Favor Homogenization of Tree Reproductive Functions in a Highly Fragmented Landscape.

PubMed

Carneiro, Magda Silva; Campos, Caroline Cambraia Furtado; Beijo, Luiz Alberto; Ramos, Flavio Nunes

2016-01-01

Species homogenization or floristic differentiation are two possible consequences of the fragmentation process in plant communities. Despite the few studies, it seems clear that fragments with low forest cover inserted in anthropogenic matrices are more likely to experience floristic homogenization. However, the homogenization process has two other components, genetic and functional, which have not been investigated. The purpose of this study was to verify whether there was homogenization of tree reproductive functions in a fragmented landscape and, if found, to determine how the process was influenced by landscape composition. The study was conducted in eight fragments in southwest Brazil. The study was conducted in eight fragments in southwestern Brazil. In each fragment, all individual trees were sampled that had a diameter at breast height ≥3 cm, in ten plots (0.2 ha) and, classified within 26 reproductive functional types (RFTs). The process of functional homogenization was evaluated using additive partitioning of diversity. Additionally, the effect of landscape composition on functional diversity and on the number of individuals within each RFT was evaluated using a generalized linear mixed model. appeared to be in a process of functional homogenization (dominance of RFTs, alpha diversity lower than expected by chance and and low beta diversity). More than 50% of the RFTs and the functional diversity were affected by the landscape parameters. In general, the percentage of forest cover has a positive effect on RFTs while the percentage of coffee matrix has a negative one. The process of functional homogenization has serious consequences for biodiversity conservation because some functions may disappear that, in the long term, would threaten the fragments. This study contributes to a better understanding of how landscape changes affect the functional diversity, abundance of individuals in RFTs and the process of functional homogenization, as well as how to manage fragmented landscapes.

Anthropogenic Matrices Favor Homogenization of Tree Reproductive Functions in a Highly Fragmented Landscape

PubMed Central

2016-01-01

Species homogenization or floristic differentiation are two possible consequences of the fragmentation process in plant communities. Despite the few studies, it seems clear that fragments with low forest cover inserted in anthropogenic matrices are more likely to experience floristic homogenization. However, the homogenization process has two other components, genetic and functional, which have not been investigated. The purpose of this study was to verify whether there was homogenization of tree reproductive functions in a fragmented landscape and, if found, to determine how the process was influenced by landscape composition. The study was conducted in eight fragments in southwest Brazil. The study was conducted in eight fragments in southwestern Brazil. In each fragment, all individual trees were sampled that had a diameter at breast height ≥3 cm, in ten plots (0.2 ha) and, classified within 26 reproductive functional types (RFTs). The process of functional homogenization was evaluated using additive partitioning of diversity. Additionally, the effect of landscape composition on functional diversity and on the number of individuals within each RFT was evaluated using a generalized linear mixed model. appeared to be in a process of functional homogenization (dominance of RFTs, alpha diversity lower than expected by chance and and low beta diversity). More than 50% of the RFTs and the functional diversity were affected by the landscape parameters. In general, the percentage of forest cover has a positive effect on RFTs while the percentage of coffee matrix has a negative one. The process of functional homogenization has serious consequences for biodiversity conservation because some functions may disappear that, in the long term, would threaten the fragments. This study contributes to a better understanding of how landscape changes affect the functional diversity, abundance of individuals in RFTs and the process of functional homogenization, as well as how to manage fragmented landscapes. PMID:27760218

Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA.

PubMed

Prati, Federica; Zuccotto, Fabio; Fletcher, Daniel; Convery, Maire A; Fernandez-Menendez, Raquel; Bates, Robert; Encinas, Lourdes; Zeng, Jingkun; Chung, Chun-Wa; De Dios Anton, Paco; Mendoza-Losana, Alfonso; Mackenzie, Claire; Green, Simon R; Huggett, Margaret; Barros, David; Wyatt, Paul G; Ray, Peter C

2018-04-06

Our findings reported herein provide support for the benefits of including functional group complexity (FGC) within fragments when screening against protein targets such as Mycobacterium tuberculosis InhA. We show that InhA fragment actives with FGC maintained their binding pose during elaboration. Furthermore, weak fragment hits with functional group handles also allowed for facile fragment elaboration to afford novel and potent InhA inhibitors with good ligand efficiency metrics for optimization. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Cosmic-Ray Source Composition Determined from ACE

NASA Technical Reports Server (NTRS)

Wiedenbeck, M.

2000-01-01

The cosmic rays arriving at Earth comprise a mix of material produced by stellar sources and ejected into the interstellar medium (primary cosmic rays) and particles produced by fragmentation of heavier nuclei during transport through the Galaxy.

Anthropogenic disturbances jeopardize biodiversity conservation within tropical rainforest reserves.

PubMed

Martínez-Ramos, Miguel; Ortiz-Rodríguez, Iván A; Piñero, Daniel; Dirzo, Rodolfo; Sarukhán, José

2016-05-10

Anthropogenic disturbances affecting tropical forest reserves have been documented, but their ecological long-term cumulative effects are poorly understood. Habitat fragmentation and defaunation are two major anthropogenic threats to the integrity of tropical reserves. Based on a long-term (four decades) study, we document how these disturbances synergistically disrupt ecological processes and imperil biodiversity conservation and ecosystem functioning at Los Tuxtlas, the northernmost tropical rainforest reserve in the Americas. Deforestation around this reserve has reduced the reserve to a medium-sized fragment (640 ha), leading to an increased frequency of canopy-gap formation. In addition, hunting and habitat loss have caused the decline or local extinction of medium and large herbivores. Combining empirical, experimental, and modeling approaches, we support the hypothesis that such disturbances produced a demographic explosion of the long-lived (≈120 y old, maximum height of 7 m) understory palm Astrocaryum mexicanum, whose population has increased from 1,243-4,058 adult individuals per hectare in only 39 y (annual growth rate of ca 3%). Faster gap formation increased understory light availability, enhancing seed production and the growth of immature palms, whereas release from mammalian herbivory and trampling increased survival of seedlings and juveniles. In turn, the palm's demographic explosion was followed by a reduction of tree species diversity, changing forest composition, altering the relative contribution of trees to forest biomass, and disrupting litterfall dynamics. We highlight how indirect anthropogenic disturbances (e.g., palm proliferation) on otherwise protected areas threaten tropical conservation, a phenomenon that is currently eroding the planet's richest repositories of biodiversity.

Anthropogenic disturbances jeopardize biodiversity conservation within tropical rainforest reserves

PubMed Central

Martínez-Ramos, Miguel; Ortiz-Rodríguez, Iván A.; Piñero, Daniel; Dirzo, Rodolfo; Sarukhán, José

2016-01-01

Anthropogenic disturbances affecting tropical forest reserves have been documented, but their ecological long-term cumulative effects are poorly understood. Habitat fragmentation and defaunation are two major anthropogenic threats to the integrity of tropical reserves. Based on a long-term (four decades) study, we document how these disturbances synergistically disrupt ecological processes and imperil biodiversity conservation and ecosystem functioning at Los Tuxtlas, the northernmost tropical rainforest reserve in the Americas. Deforestation around this reserve has reduced the reserve to a medium-sized fragment (640 ha), leading to an increased frequency of canopy-gap formation. In addition, hunting and habitat loss have caused the decline or local extinction of medium and large herbivores. Combining empirical, experimental, and modeling approaches, we support the hypothesis that such disturbances produced a demographic explosion of the long-lived (≈120 y old, maximum height of 7 m) understory palm Astrocaryum mexicanum, whose population has increased from 1,243–4,058 adult individuals per hectare in only 39 y (annual growth rate of ca. 3%). Faster gap formation increased understory light availability, enhancing seed production and the growth of immature palms, whereas release from mammalian herbivory and trampling increased survival of seedlings and juveniles. In turn, the palm’s demographic explosion was followed by a reduction of tree species diversity, changing forest composition, altering the relative contribution of trees to forest biomass, and disrupting litterfall dynamics. We highlight how indirect anthropogenic disturbances (e.g., palm proliferation) on otherwise protected areas threaten tropical conservation, a phenomenon that is currently eroding the planet’s richest repositories of biodiversity. PMID:27071122

Biosorption properties of citrus peel derived oligogalacturonides, enzyme-modified pectin and peel hydrolysis residues

USDA-ARS?s Scientific Manuscript database

Data is presented on the biosorption properties of modified pectins and pectin fragments using lead as a model cation. Samples tested for their sorption capacity are Narrow-Range Size-Classes of galacturonic acid oligomers, well characterized homogalacturonan demethylations series produced at pH 7....

Changes in Tree Reproductive Traits Reduce Functional Diversity in a Fragmented Atlantic Forest Landscape

PubMed Central

Girão, Luciana Coe; Lopes, Ariadna Valentina; Tabarelli, Marcelo; Bruna, Emilio M.

2007-01-01

Functional diversity has been postulated to be critical for the maintenance of ecosystem functioning, but the way it can be disrupted by human-related disturbances remains poorly investigated. Here we test the hypothesis that habitat fragmentation changes the relative contribution of tree species within categories of reproductive traits (frequency of traits) and reduces the functional diversity of tree assemblages. The study was carried out in an old and severely fragmented landscape of the Brazilian Atlantic forest. We used published information and field observations to obtain the frequency of tree species and individuals within 50 categories of reproductive traits (distributed in four major classes: pollination systems, floral biology, sexual systems, and reproductive systems) in 10 fragments and 10 tracts of forest interior (control plots). As hypothesized, populations in fragments and control plots differed substantially in the representation of the four major classes of reproductive traits (more than 50% of the categories investigated). The most conspicuous differences were the lack of three pollination systems in fragments-pollination by birds, flies and non-flying mammals-and that fragments had a higher frequency of both species and individuals pollinated by generalist vectors. Hermaphroditic species predominate in both habitats, although their relative abundances were higher in fragments. On the contrary, self-incompatible species were underrepresented in fragments. Moreover, fragments showed lower functional diversity (H' scores) for pollination systems (−30.3%), floral types (−23.6%), and floral sizes (−20.8%) in comparison to control plots. In contrast to the overwhelming effect of fragmentation, patch and landscape metrics such as patch size and forest cover played a minor role on the frequency of traits. Our results suggest that habitat fragmentation promotes a marked shift in the relative abundance of tree reproductive traits and greatly reduces the functional diversity of tree assemblages in fragmented landscapes. PMID:17878943

Development of zwitterionic sulfobetaine block copolymer conjugation strategies for reduced platelet deposition in respiratory assist devices.

PubMed

Malkin, Alexander D; Ye, Sang-Ho; Lee, Evan J; Yang, Xiguang; Zhu, Yang; Gamble, Lara J; Federspiel, William J; Wagner, William R

2018-02-09

Respiratory assist devices, that utilize ∼2 m 2 of hollow fiber membranes (HFMs) to achieve desired gas transfer rates, have been limited in their adoption due to such blood biocompatibility limitations. This study reports two techniques for the functionalization and subsequent conjugation of zwitterionic sulfobetaine (SB) block copolymers to polymethylpentene (PMP) HFM surfaces with the intention of reducing thrombus formation in respiratory assist devices. Amine or hydroxyl functionalization of PMP HFMs (PMP-A or PMP-H) was accomplished using plasma-enhanced chemical vapor deposition. The generated functional groups were conjugated to low molecular weight SB block copolymers with N-hydroxysuccinimide ester or siloxane groups (SBNHS or SBNHSi) that were synthesized using reversible addition fragmentation chain transfer polymerization. The modified HFMs (PMP-A-SBNHS or PMP-H-SBNHSi) showed 80-95% reduction in platelet deposition from whole ovine blood, stability under the fluid shear of anticipated operating conditions, and uninhibited gas exchange performance relative to non-modified HFMs (PMP-C). Additionally, the functionalization and SBNHSi conjugation technique was shown to reduce platelet deposition on polycarbonate and poly(vinyl chloride), two other materials commonly found in extracorporeal circuits. The observed thromboresistance and stability of the SB modified surfaces, without degradation of HFM gas transfer performance, indicate that this approach is promising for longer term pre-clinical testing in respiratory assist devices and may ultimately allow for the reduction of anticoagulation levels in patients being supported for extended periods. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2018. © 2018 Wiley Periodicals, Inc.

Acute flexor tendon injury following midshaft radius and ulna fractures in a paediatric patient.

PubMed

Williams, James; Wharton, Rupert; Peev, Peter; Horwitz, Maxim

2018-06-01

Delayed rupture of the extensor and flexor tendons are recognised complications of distal radius fractures. However, acute flexor tendon rupture in the context of forearm fractures is rare. A twelve-year-old female sustained midshaft fractures of the radius and ulna. Intra-operatively the flexor pollicis longus (FPL) was found to be stripped from its musculotendinous junction at the level of the fracture fragment. The ruptured tendon was repaired using a modified Krackow technique at the time of fracture fixation. The repair was protected in plaster of Paris prior to referral to the paediatric hand clinic. The patient made a full recovery. Flexor tendon injury is a rare but potentially devastating consequence of acute forearm fractures. High energy trauma, significant volar angulation of the fracture fragment and clinical signs of flexor tendon injury should raise suspicion of this injury. A high index of suspicion in conjunction with repeat clinical examination of flexor tendon function should be performed before opting for closed management or intramedullary nailing in paediatric patients.

Polydopamine-Coated Magnetic Molecularly Imprinted Polymers with Fragment Template for Identification of Pulsatilla Saponin Metabolites in Rat Feces with UPLC-Q-TOF-MS.

PubMed

Zhang, Yu-Zhen; Zhang, Jia-Wei; Wang, Chong-Zhi; Zhou, Lian-Di; Zhang, Qi-Hui; Yuan, Chun-Su

2018-01-24

In this work, a modified pretreatment method using magnetic molecularly imprinted polymers (MMIPs) was successfully applied to study the metabolites of an important botanical with ultraperformance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). The MMIPs for glucoside-specific adsorption was used to identify metabolites of Pulsatilla chinensis in rat feces. Polymers were prepared by using Fe 3 O 4 nanoparticles as the supporting matrix, d-glucose as fragment template, and dopamine as the functional monomer and cross-linker. Results showed that MMIPs exhibited excellent extraction performance, large adsorption capacity (5.65 mg/g), fast kinetics (60 min), and magnetic separation. Furthermore, the MMIPs coupled with UPLC-Q-TOF-MS were successfully utilized for the identification of 17 compounds including 15 metabolites from the Pulsatilla saponin metabolic pool. This study provides a reliable protocol for the separation and identification of saponin metabolites in a complex biological sample, including those from herbal medicines.

Development of a potent and selective FLT3 kinase inhibitor by systematic expansion of a non-selective fragment-screening hit.

PubMed

Nakano, Hirofumi; Hasegawa, Tsukasa; Imamura, Riyo; Saito, Nae; Kojima, Hirotatsu; Okabe, Takayoshi; Nagano, Tetsuo

2016-05-01

A non-selective inhibitor (1) of FMS-like tyrosine kinase-3 (FLT3) was identified by fragment screening and systematically modified to afford a potent and selective inhibitor 26. We confirmed that 26 inhibited the growth of FLT-3-activated human acute myeloid leukemia cell line MV4-11. Our design strategy enabled rapid development of a novel type of FLT3 inhibitor from the hit fragment in the absence of target-structural information. Copyright © 2016 Elsevier Ltd. All rights reserved.

Consumption of bee pollen affects rat ovarian functions.

PubMed

Kolesarova, A; Bakova, Z; Capcarova, M; Galik, B; Juracek, M; Simko, M; Toman, R; Sirotkin, A V

2013-12-01

The aim of this study was to examine possible effects of bee pollen added to the feed mixture (FM) on rat ovarian functions (secretion activity and apoptosis). We evaluated the bee pollen effect on the release of insulin-like growth factor I (IGF-I) and steroid hormones (progesterone and estradiol), as well as on the expression of markers of apoptosis (Bcl-2, Bax and caspase-3) in rat ovarian fragments. Female rats (n = 15) were fed during 90 days by FM without or with rape seed bee pollen in dose either 3 kg/1000 kg FM or 5 kg/1000 kg FM. Fragments of ovaries isolated from rats of each group (totally 72 pieces) were incubated for 24 h. Hormonal secretion into the culture medium was detected by RIA. The markers of apoptosis were evaluated by Western blotting. It was observed that IGF-I release by rat ovarian fragments was significantly (p < 0.05) decreased; on the other hand, progesterone and estradiol secretion was increased after bee pollen treatment at dose 5 kg/1000 kg FM but not at 3 kg/1000 FM. Accumulation of Bcl-2 was increased by bee pollen added at 3 kg/1000 kg FM, but not at higher dose. Accumulation of Bax was increased in ovaries of rats fed by bee pollen at doses either 3 or 5 kg/1000 kg FM, whilst accumulation of caspase-3 increased after feeding with bee pollen at dose 5 kg/1000 kg FM, but not at 3 kg/1000 kg FM. Our results contribute to new insights regarding the effect of bee pollen on both secretion activity (release of growth factor IGF-I and steroid hormones progesterone and estradiol) and apoptosis (anti- and pro-apoptotic markers Bcl-2, Bax and caspase-3). Bee pollen is shown to be a potent regulator of rat ovarian functions. © 2012 Blackwell Verlag GmbH.

The role of porosity and annealing in the impact fragmentation of an aluminum reactive material

NASA Astrophysics Data System (ADS)

Hooper, Joseph

2017-06-01

A reactive fragment has a unique structural requirement to survive explosive launch but then fragment catastrophically and combust upon impact. Suitable materials for this application tend to be metal composites with high ductility in compression but elastic-brittle behavior in tension. Characterizing the dynamic fragmentation of such materials is key for understanding their lethality. Here we consider a prototypical aluminum reactive frag material, formed via cold isostatic pressing of micron-scale powder followed by annealing. Samples were gun-launched into a target and recovered in a soft-catch medium of artificial snow, allowing for excellent recovery down to micron sizes and minimal contamination. Recovered fragment distributions were analyzed and compared to standard energy-balance theories. We study the effect of compaction pressure and annealing conditions on the fragmentation behavior at 500-800 m/s impacts, and find a particularly strong effect from short annealing periods. Though dynamic fracture occurs entirely along original particle boundaries in this material, recovery processes within the Al microstructure during annealing lead to a rapid decrease in the extent of fragmentation. This work was funded by the Office of Naval Research, program director Cliff Bedford.

Molecular photoionization processes of astrophysical and aeronomical interest

NASA Technical Reports Server (NTRS)

Langhoff, P. W.

1985-01-01

An account is given of aspects of photoionization processes in molecules, with particular reference to recent theoretical and experimental studies of partial cross sections for production of specific final electronic states and of parent and fragment ions. Such cross sections help provide a basis for specifying the state of excitation of the ionized medium, are useful for estimating the kinetic energy distributions of photoejected electrons and fragment ions, provide parent-and fragment-ion yields, and clarify the possible origins of neutral fragments in highly excited rovibronic states. A descriptive account is given of photoionization phenomena, including tabulation of valence- and inner-shell potentials for some molecules of astrophysical and aeronomical interest. Cross sectional expressions are given. Various approximations currently employed in computational studies are described briefly, threshold laws and high-energy limits are indicated, and distinction is drawn between resonant and direct photoionization phenomena. Recent experimental and theoretical studies of partial photoionization cross sections in selected compounds of astrophysical and aeronomical relevance are described and discussed.

Analytical Model of Large Data Transactions in CoAP Networks

PubMed Central

Ludovici, Alessandro; Di Marco, Piergiuseppe; Calveras, Anna; Johansson, Karl H.

2014-01-01

We propose a novel analytical model to study fragmentation methods in wireless sensor networks adopting the Constrained Application Protocol (CoAP) and the IEEE 802.15.4 standard for medium access control (MAC). The blockwise transfer technique proposed in CoAP and the 6LoWPAN fragmentation are included in the analysis. The two techniques are compared in terms of reliability and delay, depending on the traffic, the number of nodes and the parameters of the IEEE 802.15.4 MAC. The results are validated trough Monte Carlo simulations. To the best of our knowledge this is the first study that evaluates and compares analytically the performance of CoAP blockwise transfer and 6LoWPAN fragmentation. A major contribution is the possibility to understand the behavior of both techniques with different network conditions. Our results show that 6LoWPAN fragmentation is preferable for delay-constrained applications. For highly congested networks, the blockwise transfer slightly outperforms 6LoWPAN fragmentation in terms of reliability. PMID:25153143

Accurate reconstruction of the optical parameter distribution in participating medium based on the frequency-domain radiative transfer equation

NASA Astrophysics Data System (ADS)

Qiao, Yao-Bin; Qi, Hong; Zhao, Fang-Zhou; Ruan, Li-Ming

2016-12-01

Reconstructing the distribution of optical parameters in the participating medium based on the frequency-domain radiative transfer equation (FD-RTE) to probe the internal structure of the medium is investigated in the present work. The forward model of FD-RTE is solved via the finite volume method (FVM). The regularization term formatted by the generalized Gaussian Markov random field model is used in the objective function to overcome the ill-posed nature of the inverse problem. The multi-start conjugate gradient (MCG) method is employed to search the minimum of the objective function and increase the efficiency of convergence. A modified adjoint differentiation technique using the collimated radiative intensity is developed to calculate the gradient of the objective function with respect to the optical parameters. All simulation results show that the proposed reconstruction algorithm based on FD-RTE can obtain the accurate distributions of absorption and scattering coefficients. The reconstructed images of the scattering coefficient have less errors than those of the absorption coefficient, which indicates the former are more suitable to probing the inner structure. Project supported by the National Natural Science Foundation of China (Grant No. 51476043), the Major National Scientific Instruments and Equipment Development Special Foundation of China (Grant No. 51327803), and the Foundation for Innovative Research Groups of the National Natural Science Foundation of China (Grant No. 51121004).

The quality of sperm preparation medium affects the motility, viability, and DNA integrity of human spermatozoa.

PubMed

Anbari, Fatemeh; Halvaei, Iman; Nabi, Ali; Ghazali, Shahin; Khalili, Mohammad Ali; Johansson, Lars

2016-01-01

The goal was to compare the effects of three different sperm preparation media on sperm motility, viability, and DNA integrity of semen samples from normozoospermic men. A total of 15 normozoospermic males were included in the study. The semen analysis (SA) was performed in accordance with the WHO guidelines (2010). After SA, each sample was divided into three aliquots, and swim-up was performed with three different sperm preparation media (Sperm Preparation Media, Origio, Denmark; Ham's F10, Biochrome, Berlin, Germany; and VitaSperm™, Innovative Biotech, Iran). Sperm motility, viability, and DNA fragmentation were evaluated at 0, 1, 2, and 24 h after swim-up. There were no significant differences, at any time intervals, in the total sperm motility between the different sperm preparation media. However, the rate of progressive motility was significantly higher in spermatozoa prepared using the media from Origio in comparison with VitaSperm™ ( P = 0.03), whereas no significant difference was found against Ham's F10 medium. No significant differences in sperm viability were seen between the media products. However, 1 h after swim-up, the extent of sperm DNA fragmentation was lower in the medium from Origio versus VitaSperm™ ( P = 0.02). The data showed that the quality of medium for preparation of semen samples from normozoospermic men significantly affects the performance of spermatozoa in assisted conception programs.

Direct measurements of the lifetime of medium-heavy hypernuclei

NASA Astrophysics Data System (ADS)

Qiu, X.; Tang, L.; Chen, C.; Margaryan, A.; Wood, S. A.; Achenbach, P.; Ahmidouch, A.; Albayrak, I.; Androic, D.; Asaturyan, A.; Asaturyan, R.; Ates, O.; Badui, R.; Baturin, P.; Boeglin, W.; Bono, J.; Brash, E.; Carter, P.; Chen, X.; Chiba, A.; Christy, M. E.; Dalton, M. M.; Danagoulian, S.; De Leo, R.; Doi, D.; Elaasar, M.; Ent, R.; Fenker, H.; Fujii, Y.; Furic, M.; Gabrielyan, M.; Gan, L.; Garibaldi, F.; Gaskell, D.; Gasparian, A.; Gogami, T.; Hashimoto, O.; Horn, T.; Hu, B.; Hungerford, Ed V.; Jones, M.; Kanda, H.; Kaneta, M.; Kawama, D.; Khanal, H.; Kohl, M.; Liyanage, A.; Luo, W.; Maeda, K.; Markowitz, P.; Marikyan, G.; Maruta, T.; Matsumura, A.; Maxwell, V.; Mkrtchyan, A.; Mkrtchyan, H.; Nagao, S.; Nakamura, S. N.; Narayan, A.; Neville, C.; Niculescu, G.; Niculescu, M. I.; Nunez, A.; Nuruzzaman; Okayasu, Y.; Petkovic, T.; Pochodzalla, J.; Reinhold, J.; Rodriguez, V. M.; Samanta, C.; Sawatzky, B.; Seva, T.; Shichijo, A.; Tadevosyan, V.; Taniya, N.; Tsukada, K.; Veilleux, M.; Vulcan, W.; Wesselmann, F. R.; Yamamoto, T.; Ye, Z.; Yokota, K.; Yuan, L.; Zhamkochyan, S.; Zhu, L.; HKS (JLab E02-017) Collaboration

2018-05-01

The lifetime of a Λ particle embedded in a nucleus (hypernucleus) decreases from that of free Λ decay mainly due to the opening of the ΛN → NN weak decay channel. However, it is generally believed that the lifetime of a hypernucleus attains a constant value (saturation) for medium to heavy hypernuclear masses, yet this hypothesis has been difficult to verify. This paper presents a direct measurement of the lifetime of medium-heavy hypernuclei that were hyper-fragments produced by fission or break-up from heavy hypernuclei initially produced with a 2.34 GeV photon-beam incident on thin Fe, Cu, Ag, and Bi target foils. For each event, fragments were detected in coincident pairs by a low-pressure multi-wire proportional chamber system. The lifetime was extracted from decay time spectrum formed by the difference of the time zeros between the pairs. The measured lifetime from each target is actually a statistical average over a range of mass with mean about 1/2 of the target mass and appears to be a constant of about 200 ps. Although this result cannot exclude unexpected shorter or longer lifetimes for some specific hypernuclei or hypernuclear states, it shows that a systematic decrease in lifetime as hypernuclear mass increases is not a general feature for hypernuclei with mean mass up to A ≈ 130. On the other hand, the success of this experiment and its technique shows that the time delayed fissions observed and used by all the lifetime measurements done so far on heavy hypernuclei could likely have originated from hyper-fragments lighter than the assumed masses.

Modified human crania from Göbekli Tepe provide evidence for a new form of Neolithic skull cult

PubMed Central

Gresky, Julia; Haelm, Juliane; Clare, Lee

2017-01-01

Archaeological excavations at Göbekli Tepe, a transitional Neolithic site in southeast Turkey, have revealed the earliest megalithic ritual architecture with characteristic T-shaped pillars. Although human burials are still absent from the site, a number of fragmented human bones have been recovered from fill deposits of buildings and from adjacent areas. We focus on three partially preserved human skulls, all of which carry artificial modifications of a type so far unknown from contemporaneous sites and the ethnographic record. As such, modified skull fragments from Göbekli Tepe could indicate a new, previously undocumented variation of skull cult in the Early Neolithic of Anatolia and the Levant. PMID:28782013

Negative Impacts of Human Land Use on Dung Beetle Functional Diversity

PubMed Central

Barragán, Felipe; Moreno, Claudia E.; Escobar, Federico; Halffter, Gonzalo; Navarrete, Dario

2011-01-01

The loss of biodiversity caused by human activity is assumed to alter ecosystem functioning. However our understanding of the magnitude of the effect of these changes on functional diversity and their impact on the dynamics of ecological processes is still limited. We analyzed the functional diversity of copro-necrophagous beetles under different conditions of land use in three Mexican biosphere reserves. In Montes Azules pastures, forest fragments and continuous rainforest were analyzed, in Los Tuxtlas rainforest fragments of different sizes were analyzed and in Barranca de Metztitlán two types of xerophile scrub with different degrees of disturbance from grazing were analyzed. We assigned dung beetle species to functional groups based on food relocation, beetle size, daily activity period and food preferences, and as measures of functional diversity we used estimates based on multivariate methods. In Montes Azules functional richness was lower in the pastures than in continuous rainforest and rainforest fragments, but fragments and continuous forest include functionally redundant species. In small rainforest fragments (<5 ha) in Los Tuxtlas, dung beetle functional richness was lower than in large rainforest fragments (>20 ha). Functional evenness and functional dispersion did not vary among habitat types or fragment size in these reserves. In contrast, in Metztitlán, functional richness and functional dispersion were different among the vegetation types, but differences were not related to the degree of disturbance by grazing. More redundant species were found in submontane than in crassicaule scrub. For the first time, a decrease in the functional diversity in communities of copro-necrophagous beetles resulting from changes in land use is documented, the potential implications for ecosystem functioning are discussed and a series of variables that could improve the evaluation of functional diversity for this biological group is proposed. PMID:21448292

Negative impacts of human land use on dung beetle functional diversity.

PubMed

Barragán, Felipe; Moreno, Claudia E; Escobar, Federico; Halffter, Gonzalo; Navarrete, Dario

2011-03-23

The loss of biodiversity caused by human activity is assumed to alter ecosystem functioning. However our understanding of the magnitude of the effect of these changes on functional diversity and their impact on the dynamics of ecological processes is still limited. We analyzed the functional diversity of copro-necrophagous beetles under different conditions of land use in three Mexican biosphere reserves. In Montes Azules pastures, forest fragments and continuous rainforest were analyzed, in Los Tuxtlas rainforest fragments of different sizes were analyzed and in Barranca de Metztitlán two types of xerophile scrub with different degrees of disturbance from grazing were analyzed. We assigned dung beetle species to functional groups based on food relocation, beetle size, daily activity period and food preferences, and as measures of functional diversity we used estimates based on multivariate methods. In Montes Azules functional richness was lower in the pastures than in continuous rainforest and rainforest fragments, but fragments and continuous forest include functionally redundant species. In small rainforest fragments (<5 ha) in Los Tuxtlas, dung beetle functional richness was lower than in large rainforest fragments (>20 ha). Functional evenness and functional dispersion did not vary among habitat types or fragment size in these reserves. In contrast, in Metztitlán, functional richness and functional dispersion were different among the vegetation types, but differences were not related to the degree of disturbance by grazing. More redundant species were found in submontane than in crassicaule scrub. For the first time, a decrease in the functional diversity in communities of copro-necrophagous beetles resulting from changes in land use is documented, the potential implications for ecosystem functioning are discussed and a series of variables that could improve the evaluation of functional diversity for this biological group is proposed.

Tissue Specific and Hormonal Regulation of Gene Expression

DTIC Science & Technology

1997-08-01

interference assays were performed. These assays identify DNA bases that, when modified, interfere with the binding of the nuclear factor to the hCRH promoter...thymidine residues. The DNA bases that when modified affected the binding of the protein are noted with arrows, and their location in the hCRH...indicated. B. Methylation interference. The fragments were partially methylated using dimethyl sulfate. The DNA bases that when modified affected the

Continuum modeling of catastrophic collisions

NASA Technical Reports Server (NTRS)

Ryan, Eileen V.; Aspaug, Erik; Melosh, H. J.

1991-01-01

A two dimensional hydrocode based on 2-D SALE was modified to include strength effects and fragmentation equations for fracture resulting from tensile stress in one dimension. Output from this code includes a complete fragmentation summary for each cell of the modeled object: fragment size (mass) distribution, vector velocities of particles, peak values of pressure and tensile stress, and peak strain rates associated with fragmentation. Contour plots showing pressure and temperature at given times within the object are also produced. By invoking axial symmetry, three dimensional events can be modeled such as zero impact parameter collisions between asteroids. The code was tested against the one dimensional model and the analytical solution for a linearly increasing tensile stress under constant strain rate.

Numerical artifacts in the Generalized Porous Medium Equation: Why harmonic averaging itself is not to blame

NASA Astrophysics Data System (ADS)

Maddix, Danielle C.; Sampaio, Luiz; Gerritsen, Margot

2018-05-01

The degenerate parabolic Generalized Porous Medium Equation (GPME) poses numerical challenges due to self-sharpening and its sharp corner solutions. For these problems, we show results for two subclasses of the GPME with differentiable k (p) with respect to p, namely the Porous Medium Equation (PME) and the superslow diffusion equation. Spurious temporal oscillations, and nonphysical locking and lagging have been reported in the literature. These issues have been attributed to harmonic averaging of the coefficient k (p) for small p, and arithmetic averaging has been suggested as an alternative. We show that harmonic averaging is not solely responsible and that an improved discretization can mitigate these issues. Here, we investigate the causes of these numerical artifacts using modified equation analysis. The modified equation framework can be used for any type of discretization. We show results for the second order finite volume method. The observed problems with harmonic averaging can be traced to two leading error terms in its modified equation. This is also illustrated numerically through a Modified Harmonic Method (MHM) that can locally modify the critical terms to remove the aforementioned numerical artifacts.

Apical-to-basolateral transepithelial transport of cow's milk caseins by intestinal Caco-2 cell monolayers: MS-based quantitation of cellularly degraded α- and β-casein fragments.

PubMed

Sakurai, Nao; Nishio, Shunsuke; Akiyama, Yuka; Miyata, Shinji; Oshima, Kenzi; Nadano, Daita; Matsuda, Tsukasa

2018-02-27

Casein is the major milk protein to nourish infants but, in certain population, it causes cow's milk allergy, indicating the uptake of antigenic casein and their peptides through the intestinal epithelium. Using human intestinal Caco-2 cell monolayers, the apical-to-basal transepithelial transport of casein was investigated. Confocal microscopy using component-specific antibodies showed that αs1-casein antigens became detectable as punctate signals at the apical-side cytoplasm and reached to the cytoplasm at a tight-junction level within a few hours. Such intracellular casein signals were more remarkable than those of the other antigens, β-lactoglobulin and ovalbumin, colocalized in part with an early endosome marker protein, EEA1, and decreased in the presence of cytochalasin D or sodium azide and also at lowered temperature at 4 °C. LC-MS analysis of the protein fraction in the basal-side medium identified the αs1-casein fragment including the N-terminal region and the αs2-casein fragment containing the central part of polypeptide at 100∼1000 fmol per well levels. Moreover, β-casein C-terminal overlapping peptides were identified in the peptide fraction below 10 kDa of the basal medium. These results suggest that caseins are partially degraded by cellular proteases and/or peptidases and immunologically active casein fragments are transported to basal side of the cell monolayers.

Mass spectrometric characterization of circulating and functional antigens derived from piperacillin in patients with cystic fibrosis1

PubMed Central

Whitaker, Paul; Meng, Xiaoli; Lavergne, Sidonie N.; El-Ghaiesh, Sabah; Monshi, Manal; Earnshaw, Caroline; Peckham, Daniel; Gooi, Jimmy; Conway, Steve; Pirmohamed, Munir; Jenkins, Rosalind E.; Naisbitt, Dean J.; Park, B. Kevin

2011-01-01

A mechanistic understanding of the relationship between the chemistry of drug antigen formation and immune function is lacking. Thus, mass spectrometric methods were employed to detect and fully characterize circulating antigens derived from piperacillin in patients undergoing therapy and the nature of the drug derived-epitopes on protein which can function as an antigen to stimulate T-cells. Albumin modification with piperacillin in vitro resulted in the formation of two distinct haptens, one formed directly from piperacillin and a second in which the dioxopiperazine ring had undergone hydrolysis. Modification was time- and concentration-dependent, with selective modification of Lys541 observed at low concentrations, whereas at higher concentrations up to 13/59 lysine residues were modified, four of which (Lys190, 195, 432 and 541) were detected in patients’ plasma. Piperacillin-specific T-lymphocyte responses (proliferation, cytokines and granzyme-B release) were detected ex vivo with cells from hypersensitive patients, and analysis of incubation medium showed that modification of the same lysine residues in albumin occurred in situ. The antigenicity of piperacillin-modified albumin was confirmed by stimulation of T-cells with characterized synthetic conjugates. Analysis of minimally-modified T-cell stimulatory albumin conjugates revealed peptide sequences incorporating Lys190, 432 and 541 as principal functional epitopes for T-cells. This study has characterized the multiple haptenic structures on albumin in patients, and showed that they constitute functional antigenic determinants for T-cells. PMID:21606251

Many-body physics in two-component Bose–Einstein condensates in a cavity: fragmented superradiance and polarization

NASA Astrophysics Data System (ADS)

Lode, Axel U. J.; Diorico, Fritz S.; Wu, RuGway; Molignini, Paolo; Papariello, Luca; Lin, Rui; Lévêque, Camille; Exl, Lukas; Tsatsos, Marios C.; Chitra, R.; Mauser, Norbert J.

2018-05-01

We consider laser-pumped one-dimensional two-component bosons in a parabolic trap embedded in a high-finesse optical cavity. Above a threshold pump power, the photons that populate the cavity modify the effective atom trap and mediate a coupling between the two components of the Bose–Einstein condensate. We calculate the ground state of the laser-pumped system and find different stages of self-organization depending on the power of the laser. The modified potential and the laser-mediated coupling between the atomic components give rise to rich many-body physics: an increase of the pump power triggers a self-organization of the atoms while an even larger pump power causes correlations between the self-organized atoms—the BEC becomes fragmented and the reduced density matrix acquires multiple macroscopic eigenvalues. In this fragmented superradiant state, the atoms can no longer be described as two-level systems and the mapping of the system to the Dicke model breaks down.

Using hadron-in-jet data in a global analysis of D* fragmentation functions

NASA Astrophysics Data System (ADS)

Anderle, Daniele P.; Kaufmann, Tom; Stratmann, Marco; Ringer, Felix; Vitev, Ivan

2017-08-01

We present a novel global QCD analysis of charged D*-meson fragmentation functions at next-to-leading order accuracy. This is achieved by making use of the available data for single-inclusive D*-meson production in electron-positron annihilation, hadron-hadron collisions, and, for the first time, in-jet fragmentation in proton-proton scattering. It is shown how to include all relevant processes efficiently and without approximations within the Mellin moment technique, specifically for the in-jet fragmentation cross section. The presented technical framework is generic and can be straightforwardly applied to future analyses of fragmentation functions for other hadron species, as soon as more in-jet fragmentation data become available. We choose to work within the zero mass variable flavor number scheme which is applicable for sufficiently high energies and transverse momenta. The obtained optimum set of parton-to-D* fragmentation functions is accompanied by Hessian uncertainty sets which allow one to propagate hadronization uncertainties to other processes of interest.

Analytical solution for tension-saturated and unsaturated flow from wicking porous pipes in subsurface irrigation: The Kornev-Philip legacies revisited

NASA Astrophysics Data System (ADS)

Kacimov, A. R.; Obnosov, Yu. V.

2017-03-01

The Russian engineer Kornev in his 1935 book raised perspectives of subsurface "negative pressure" irrigation, which have been overlooked in modern soil science. Kornev's autoirrigation utilizes wicking of a vacuumed water from a porous pipe into a dry adjacent soil. We link Kornev's technology with a slightly modified Philip (1984)'s analytical solutions for unsaturated flow from a 2-D cylindrical pipe in an infinite domain. Two Darcian flows are considered and connected through continuity of pressure along the pipe-soil contact. The first fragment is a thin porous pipe wall in which water seeps at tension saturation; the hydraulic head is a harmonic function varying purely radially across the wall. The Thiem solution in this fragment gives the boundary condition for azimuthally varying suction pressure in the second fragment, ambient soil, making the exterior of the pipe. The constant head, rather than Philip's isobaricity boundary condition, along the external wall slightly modifies Philip's formulae for the Kirchhoff potential and pressure head in the soil fragment. Flow characteristics (magnitudes of the Darcian velocity, total flow rate, and flow net) are explicitly expressed through series of Macdonald's functions. For a given pipe's external diameter, wall thickness, position of the pipe above a free water datum in the supply tank, saturated conductivities of the wall and soil, and soil's sorptive number, a nonlinear equation with respect to the total discharge from the pipe is obtained and solved by a computer algebra routine. Efficiency of irrigation is evaluated by computation of the moisture content within selected zones surrounding the porous pipe.