Differences in selection drive olfactory receptor genes in different directions in dogs and wolf.

PubMed

Chen, Rui; Irwin, David M; Zhang, Ya-Ping

2012-11-01

The olfactory receptor (OR) gene family is the largest gene family found in mammalian genomes. It is known to evolve through a birth-and-death process. Here, we characterized the sequences of 16 segregating OR pseudogenes in the samples of the wolf and the Chinese village dog (CVD) and compared them with the sequences from dogs of different breeds. Our results show that the segregating OR pseudogenes in breed dogs are under strong purifying selection, while evolving neutrally in the CVD, and show a more complicated pattern in the wolf. In the wolf, we found a trend to remove deleterious polymorphisms and accumulate nondeleterious polymorphisms. On the basis of protein structure of the ORs, we found that the distribution of different types of polymorphisms (synonymous, nonsynonymous, tolerated, and untolerated) varied greatly between the wolf and the breed dogs. In summary, our results suggest that different forms of selection have acted on the segregating OR pseudogenes in the CVD since domestication, breed dogs after breed formation, and ancestral wolf population, which has driven the evolution of these genes in different directions.

Evolution of CCL11: genetic characterization in lagomorphs and evidence of positive and purifying selection in mammals.

PubMed

Neves, Fabiana; Abrantes, Joana; Esteves, Pedro J

2016-07-01

The interactions between chemokines and their receptors are crucial for differentiation and activation of inflammatory cells. CC chemokine ligand 11 (CCL11) binds to CCR3 and to CCR5 that in leporids underwent gene conversion with CCR2. Here, we genetically characterized CCL11 in lagomorphs (leporids and pikas). All lagomorphs have a potentially functional CCL11, and the Pygmy rabbit has a mutation in the stop codon that leads to a longer protein. Other mammals also have mutations at the stop codon that result in proteins with different lengths. By employing maximum likelihood methods, we observed that, in mammals, CCL11 exhibits both signatures of purifying and positive selection. Signatures of purifying selection were detected in sites important for receptor binding and activation. Of the three sites detected as under positive selection, two were located close to the stop codon. Our results suggest that CCL11 is functional in all lagomorphs, and that the signatures of purifying and positive selection in mammalian CCL11 probably reflect the protein's biological roles. © The Author(s) 2016.

Genome-Wide Identification and Evolution Analysis of Trehalose-6-Phosphate Synthase Gene Family in Nelumbo nucifera

PubMed Central

Jin, Qijiang; Hu, Xin; Li, Xin; Wang, Bei; Wang, Yanjie; Jiang, Hongwei; Mattson, Neil; Xu, Yingchun

2016-01-01

Trehalose-6-phosphate synthase (TPS) plays a key role in plant carbohydrate metabolism and the perception of carbohydrate availability. In the present work, the publicly available Nelumbo nucifera (lotus) genome sequence database was analyzed which led to identification of nine lotus TPS genes (NnTPS). It was found that at least two introns are included in the coding sequences of NnTPS genes. When the motif compositions were analyzed we found that NnTPS generally shared the similar motifs, implying that they have similar functions. The dN/dS ratios were always less than 1 for different domains and regions outside domains, suggesting purifying selection on the lotus TPS gene family. The regions outside TPS domain evolved relatively faster than NnTPS domains. A phylogenetic tree was constructed using all predicted coding sequences of lotus TPS genes, together with those from Arabidopsis, poplar, soybean, and rice. The result indicated that those TPS genes could be clearly divided into two main subfamilies (I-II), where each subfamily could be further divided into 2 (I) and 5 (II) subgroups. Analyses of divergence and adaptive evolution show that purifying selection may have been the main force driving evolution of plant TPS genes. Some of the critical sites that contributed to divergence may have been under positive selection. Transcriptome data analysis revealed that most NnTPS genes were predominantly expressed in sink tissues. Expression pattern of NnTPS genes under copper and submergence stress indicated that NNU_014679 and NNU_022788 might play important roles in lotus energy metabolism and participate in stress response. Our results can facilitate further functional studies of TPS genes in lotus. PMID:27746792

Molecular organization and phylogenetic analysis of 5S rDNA in crustaceans of the genus Pollicipes reveal birth-and-death evolution and strong purifying selection.

PubMed

Perina, Alejandra; Seoane, David; González-Tizón, Ana M; Rodríguez-Fariña, Fernanda; Martínez-Lage, Andrés

2011-10-17

The 5S ribosomal DNA (5S rDNA) is organized in tandem arrays with repeat units that consist of a transcribing region (5S) and a variable nontranscribed spacer (NTS), in higher eukaryotes. Until recently the 5S rDNA was thought to be subject to concerted evolution, however, in several taxa, sequence divergence levels between the 5S and the NTS were found higher than expected under this model. So, many studies have shown that birth-and-death processes and selection can drive the evolution of 5S rDNA. In analyses of 5S rDNA evolution is found several 5S rDNA types in the genome, with low levels of nucleotide variation in the 5S and a spacer region highly divergent. Molecular organization and nucleotide sequence of the 5S ribosomal DNA multigene family (5S rDNA) were investigated in three Pollicipes species in an evolutionary context. The nucleotide sequence variation revealed that several 5S rDNA variants occur in Pollicipes genomes. They are clustered in up to seven different types based on differences in their nontranscribed spacers (NTS). Five different units of 5S rDNA were characterized in P. pollicipes and two different units in P. elegans and P. polymerus. Analysis of these sequences showed that identical types were shared among species and that two pseudogenes were present. We predicted the secondary structure and characterized the upstream and downstream conserved elements. Phylogenetic analysis showed an among-species clustering pattern of 5S rDNA types. These results suggest that the evolution of Pollicipes 5S rDNA is driven by birth-and-death processes with strong purifying selection.

Molecular organization and phylogenetic analysis of 5S rDNA in crustaceans of the genus Pollicipes reveal birth-and-death evolution and strong purifying selection

PubMed Central

2011-01-01

Background The 5S ribosomal DNA (5S rDNA) is organized in tandem arrays with repeat units that consist of a transcribing region (5S) and a variable nontranscribed spacer (NTS), in higher eukaryotes. Until recently the 5S rDNA was thought to be subject to concerted evolution, however, in several taxa, sequence divergence levels between the 5S and the NTS were found higher than expected under this model. So, many studies have shown that birth-and-death processes and selection can drive the evolution of 5S rDNA. In analyses of 5S rDNA evolution is found several 5S rDNA types in the genome, with low levels of nucleotide variation in the 5S and a spacer region highly divergent. Molecular organization and nucleotide sequence of the 5S ribosomal DNA multigene family (5S rDNA) were investigated in three Pollicipes species in an evolutionary context. Results The nucleotide sequence variation revealed that several 5S rDNA variants occur in Pollicipes genomes. They are clustered in up to seven different types based on differences in their nontranscribed spacers (NTS). Five different units of 5S rDNA were characterized in P. pollicipes and two different units in P. elegans and P. polymerus. Analysis of these sequences showed that identical types were shared among species and that two pseudogenes were present. We predicted the secondary structure and characterized the upstream and downstream conserved elements. Phylogenetic analysis showed an among-species clustering pattern of 5S rDNA types. Conclusions These results suggest that the evolution of Pollicipes 5S rDNA is driven by birth-and-death processes with strong purifying selection. PMID:22004418

Genome-wide diversity and selective pressure in the human rhinovirus

PubMed Central

Kistler, Amy L; Webster, Dale R; Rouskin, Silvi; Magrini, Vince; Credle, Joel J; Schnurr, David P; Boushey, Homer A; Mardis, Elaine R; Li, Hao; DeRisi, Joseph L

2007-01-01

Background The human rhinoviruses (HRV) are one of the most common and diverse respiratory pathogens of humans. Over 100 distinct HRV serotypes are known, yet only 6 genomes are available. Due to the paucity of HRV genome sequence, little is known about the genetic diversity within HRV or the forces driving this diversity. Previous comparative genome sequence analyses indicate that recombination drives diversification in multiple genera of the picornavirus family, yet it remains unclear if this holds for HRV. Results To resolve this and gain insight into the forces driving diversification in HRV, we generated a representative set of 34 fully sequenced HRVs. Analysis of these genomes shows consistent phylogenies across the genome, conserved non-coding elements, and only limited recombination. However, spikes of genetic diversity at both the nucleotide and amino acid level are detectable within every locus of the genome. Despite this, the HRV genome as a whole is under purifying selective pressure, with islands of diversifying pressure in the VP1, VP2, and VP3 structural genes and two non-structural genes, the 3C protease and 3D polymerase. Mapping diversifying residues in these factors onto available 3-dimensional structures revealed the diversifying capsid residues partition to the external surface of the viral particle in statistically significant proximity to antigenic sites. Diversifying pressure in the pleconaril binding site is confined to a single residue known to confer drug resistance (VP1 191). In contrast, diversifying pressure in the non-structural genes is less clear, mapping both nearby and beyond characterized functional domains of these factors. Conclusion This work provides a foundation for understanding HRV genetic diversity and insight into the underlying biology driving evolution in HRV. It expands our knowledge of the genome sequence space that HRV reference serotypes occupy and how the pattern of genetic diversity across HRV genomes differs from other picornaviruses. It also reveals evidence of diversifying selective pressure in both structural genes known to interact with the host immune system and in domains of unassigned function in the non-structural 3C and 3D genes, raising the possibility that diversification of undiscovered functions in these essential factors may influence HRV fitness and evolution. PMID:17477878

Purification of carbon nanotubes via selective heating

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

Rogers, John A.; Wilson, William L.; Jin, Sung Hun

The present invention provides methods for purifying a layer of carbon nanotubes comprising providing a precursor layer of substantially aligned carbon nanotubes supported by a substrate, wherein the precursor layer comprises a mixture of first carbon nanotubes and second carbon nanotubes; selectively heating the first carbon nanotubes; and separating the first carbon nanotubes from the second carbon nanotubes, thereby generating a purified layer of carbon nanotubes. Devices benefiting from enhanced electrical properties enabled by the purified layer of carbon nanotubes are also described.

Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster

PubMed Central

Schrider, Daniel R.; Houle, David; Lynch, Michael; Hahn, Matthew W.

2013-01-01

Because spontaneous mutation is the source of all genetic diversity, measuring mutation rates can reveal how natural selection drives patterns of variation within and between species. We sequenced eight genomes produced by a mutation-accumulation experiment in Drosophila melanogaster. Our analysis reveals that point mutation and small indel rates vary significantly between the two different genetic backgrounds examined. We also find evidence that ∼2% of mutational events affect multiple closely spaced nucleotides. Unlike previous similar experiments, we were able to estimate genome-wide rates of large deletions and tandem duplications. These results suggest that, at least in inbred lines like those examined here, mutational pressures may result in net growth rather than contraction of the Drosophila genome. By comparing our mutation rate estimates to polymorphism data, we are able to estimate the fraction of new mutations that are eliminated by purifying selection. These results suggest that ∼99% of duplications and deletions are deleterious—making them 10 times more likely to be removed by selection than nonsynonymous mutations. Our results illuminate not only the rates of new small- and large-scale mutations, but also the selective forces that they encounter once they arise. PMID:23733788

Development of Cell-SELEX Technology and Its Application in Cancer Diagnosis and Therapy.

PubMed

Chen, Man; Yu, Yuanyuan; Jiang, Feng; Zhou, Junwei; Li, Yongshu; Liang, Chao; Dang, Lei; Lu, Aiping; Zhang, Ge

2016-12-10

SELEX (systematic evolution of ligands by exponential enrichment) is a process involving the progressive isolation of high selective ssDNA/RNA from a combinatorial single-stranded oligonucleotide library through repeated rounds of binding, partitioning and amplification. SELEX-derived single-stranded DNA/RNA molecules, called aptamers, are selected against a wide range of targets, including purified proteins, live cells, tissues, microorganisms, small molecules and so on. With the development of SELEX technology over the last two decades, various modified SELEX processes have been arisen. A majority of aptamers are selected against purified proteins through traditional SELEX. Unfortunately, more and more evidence showed aptamers selected against purified membrane proteins failed to recognize their targets in live cells. Cell-SELEX could develop aptamers against a particular target cell line to discriminate this cell line from others. Therefore, cell-SELEX has been widely used to select aptamers for the application of both diagnosis and therapy of various diseases, especially for cancer. In this review, the advantages and limitations of cell-SELEX and SELEX against purified protein will be compared. Various modified cell-SELEX techniques will be summarized, and application of cell-SELEX in cancer diagnosis and therapy will be discussed.

Development of Cell-SELEX Technology and Its Application in Cancer Diagnosis and Therapy

PubMed Central

Chen, Man; Yu, Yuanyuan; Jiang, Feng; Zhou, Junwei; Li, Yongshu; Liang, Chao; Dang, Lei; Lu, Aiping; Zhang, Ge

2016-01-01

SELEX (systematic evolution of ligands by exponential enrichment) is a process involving the progressive isolation of high selective ssDNA/RNA from a combinatorial single-stranded oligonucleotide library through repeated rounds of binding, partitioning and amplification. SELEX-derived single-stranded DNA/RNA molecules, called aptamers, are selected against a wide range of targets, including purified proteins, live cells, tissues, microorganisms, small molecules and so on. With the development of SELEX technology over the last two decades, various modified SELEX processes have been arisen. A majority of aptamers are selected against purified proteins through traditional SELEX. Unfortunately, more and more evidence showed aptamers selected against purified membrane proteins failed to recognize their targets in live cells. Cell-SELEX could develop aptamers against a particular target cell line to discriminate this cell line from others. Therefore, cell-SELEX has been widely used to select aptamers for the application of both diagnosis and therapy of various diseases, especially for cancer. In this review, the advantages and limitations of cell-SELEX and SELEX against purified protein will be compared. Various modified cell-SELEX techniques will be summarized, and application of cell-SELEX in cancer diagnosis and therapy will be discussed. PMID:27973403

The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection

PubMed Central

Kong, Yimeng; Pan, Bohu; Chen, Longxian; Wang, Hongbing; Hao, Pei; Li, Xuan

2016-01-01

The hydrolytic deamination of adenosine to inosine (A-to-I editing) in precursor mRNA induces variable gene products at the post-transcription level. How and to what extent A-to-I RNA editing diversifies transcriptome is not fully characterized in the evolution, and very little is known about the selective constraints that drive the evolution of RNA editing events. Here we present a study on A-to-I RNA editing, by generating a global profile of A-to-I editing for a phylogeny of seven Drosophila species, a model system spanning an evolutionary timeframe of approximately 45 million years. Of totally 9281 editing events identified, 5150 (55.5%) are located in the coding sequences (CDS) of 2734 genes. Phylogenetic analysis places these genes into 1,526 homologous families, about 5% of total gene families in the fly lineages. Based on conservation of the editing sites, the editing events in CDS are categorized into three distinct types, representing events on singleton genes (type I), and events not conserved (type II) or conserved (type III) within multi-gene families. While both type I and II events are subject to purifying selection, notably type III events are positively selected, and highly enriched in the components and functions of the nervous system. The tissue profiles are documented for three editing types, and their critical roles are further implicated by their shifting patterns during holometabolous development and in post-mating response. In conclusion, three A-to-I RNA editing types are found to have distinct evolutionary dynamics. It appears that nervous system functions are mainly tested to determine if an A-to-I editing is beneficial for an organism. The coding plasticity enabled by A-to-I editing creates a new class of binary variations, which is a superior alternative to maintain heterozygosity of expressed genes in a diploid mating system. PMID:27467689

The Role of Small RNA-Based Epigenetic Silencing for Purifying Selection on Transposable Elements in Capsella grandiflora

PubMed Central

Horvath, Robert

2017-01-01

Abstract To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifying selection is expected to remove silenced TE insertions near genes more efficiently and prevent their accumulation within a population. To explore how effects of TE silencing on gene regulation shapes purifying selection on TEs, we analyzed whole genome sequencing data from 166 individuals of a large population of the outcrossing species Capsella grandiflora. We found that most TEs are rare, and in chromosome arms, silenced TEs are exposed to stronger purifying selection than those that are not silenced by 24-nucleotide small RNAs, especially with increasing proximity to genes. An age-of-allele test of neutrality on a subset of TEs supports our inference of purifying selection on silenced TEs, suggesting that our results are robust to varying transposition rates. Our results provide new insights into the processes affecting the accumulation of TEs in an outcrossing species and support the view that epigenetic silencing of TEs results in a trade-off between preventing TE proliferation and interference with nearby gene regulation. We also suggest that in the centromeric and pericentromeric regions, the negative aspects of epigenetic TE silencing are missing. PMID:29036316

Landscape genomics: natural selection drives the evolution of mitogenome in penguins.

PubMed

Ramos, Barbara; González-Acuña, Daniel; Loyola, David E; Johnson, Warren E; Parker, Patricia G; Massaro, Melanie; Dantas, Gisele P M; Miranda, Marcelo D; Vianna, Juliana A

2018-01-16

Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica. Signatures of selection of 13 mitochondrial protein-coding genes were evaluated by comparing among species within and among genera (Spheniscus, Pygoscelis, Eudyptula, Eudyptes and Aptenodytes). The genetic data were correlated with environmental data obtained through remote sensing (sea surface temperature [SST], chlorophyll levels [Chl] and a combination of SST and Chl [COM]) through the distribution of these species. We identified the complete mtDNA genomes of several penguin species, including ND6 and 8 tRNAs on the light strand and 12 protein coding genes, 14 tRNAs and two rRNAs positioned on the heavy strand. The highest diversity was found in NADH dehydrogenase genes and the lowest in COX genes. The lowest evolutionary divergence among species was between Humboldt (Spheniscus humboldti) and Galapagos (S. mendiculus) penguins (0.004), while the highest was observed between little penguin (Eudyptula minor) and Adélie penguin (Pygoscelis adeliae) (0.097). We identified a signature of purifying selection (Ka/Ks < 1) across the mitochondrial genome, which is consistent with the hypothesis that purifying selection is constraining mitogenome evolution to maintain Oxidative phosphorylation (OXPHOS) proteins and functionality. Pairwise species maximum-likelihood analyses of selection at codon sites suggest positive selection has occurred on ATP8 (Fixed-Effects Likelihood, FEL) and ND4 (Single Likelihood Ancestral Counting, SLAC) in all penguins. In contrast, COX1 had a signature of strong negative selection. ND4 Ka/Ks ratios were highly correlated with SST (Mantel, p-value: 0.0001; GLM, p-value: 0.00001) and thus may be related to climate adaptation throughout penguin speciation. These results identify mtDNA candidate genes under selection which could be involved in broad-scale adaptations of penguins to their environment. Such knowledge may be particularly useful for developing predictive models of how these species may respond to severe climatic changes in the future.

Production and Evaluation of a Purified Adenovirus Group-Specific (Hexon) Antigen for Use in the Diagnostic Complement Fixation Test

PubMed Central

Dowdle, W. R.; Lambriex, M.; Hierholzer, J. C.

1971-01-01

A simple procedure for the production of large volumes of purified adenovirus group-specific complement-fixing (CF) (hexon) antigen by selective adsorption to and elution from CaHPO4 is described. Results of immunodiffusion tests, electrophoresis, electron microscopy, and tests for hemagglutination and infectivity indicate that the purified antigen consisted of a single virus component (hexon). The purified product contained little host materials. Unlike the crude virus harvest usually employed for serodiagnostic CF tests, the purified antigen demonstrated no anticomplementary activity and did not develop such activity during storage. The purified antigen was equal to or slightly more sensitive than crude virus harvests for serodiagnosis of adenovirus infections. Images PMID:4325021

Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication.

PubMed

Wang, Ming-Shan; Zhang, Rong-Wei; Su, Ling-Yan; Li, Yan; Peng, Min-Sheng; Liu, He-Qun; Zeng, Lin; Irwin, David M; Du, Jiu-Lin; Yao, Yong-Gang; Wu, Dong-Dong; Zhang, Ya-Ping

2016-05-01

As noted by Darwin, chickens have the greatest phenotypic diversity of all birds, but an interesting evolutionary difference between domestic chickens and their wild ancestor, the Red Junglefowl, is their comparatively weaker vision. Existing theories suggest that diminished visual prowess among domestic chickens reflect changes driven by the relaxation of functional constraints on vision, but the evidence identifying the underlying genetic mechanisms responsible for this change has not been definitively characterized. Here, a genome-wide analysis of the domestic chicken and Red Junglefowl genomes showed significant enrichment for positively selected genes involved in the development of vision. There were significant differences between domestic chickens and their wild ancestors regarding the level of mRNA expression for these genes in the retina. Numerous additional genes involved in the development of vision also showed significant differences in mRNA expression between domestic chickens and their wild ancestors, particularly for genes associated with phototransduction and photoreceptor development, such as RHO (rhodopsin), GUCA1A, PDE6B and NR2E3. Finally, we characterized the potential role of the VIT gene in vision, which experienced positive selection and downregulated expression in the retina of the village chicken. Overall, our results suggest that positive selection, rather than relaxation of purifying selection, contributed to the evolution of vision in domestic chickens. The progenitors of domestic chickens harboring weaker vision may have showed a reduced fear response and vigilance, making them easier to be unconsciously selected and/or domesticated.

Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication

PubMed Central

Wang, Ming-Shan; Zhang, Rong-wei; Su, Ling-Yan; Li, Yan; Peng, Min-Sheng; Liu, He-Qun; Zeng, Lin; Irwin, David M; Du, Jiu-Lin; Yao, Yong-Gang; Wu, Dong-Dong; Zhang, Ya-Ping

2016-01-01

As noted by Darwin, chickens have the greatest phenotypic diversity of all birds, but an interesting evolutionary difference between domestic chickens and their wild ancestor, the Red Junglefowl, is their comparatively weaker vision. Existing theories suggest that diminished visual prowess among domestic chickens reflect changes driven by the relaxation of functional constraints on vision, but the evidence identifying the underlying genetic mechanisms responsible for this change has not been definitively characterized. Here, a genome-wide analysis of the domestic chicken and Red Junglefowl genomes showed significant enrichment for positively selected genes involved in the development of vision. There were significant differences between domestic chickens and their wild ancestors regarding the level of mRNA expression for these genes in the retina. Numerous additional genes involved in the development of vision also showed significant differences in mRNA expression between domestic chickens and their wild ancestors, particularly for genes associated with phototransduction and photoreceptor development, such as RHO (rhodopsin), GUCA1A, PDE6B and NR2E3. Finally, we characterized the potential role of the VIT gene in vision, which experienced positive selection and downregulated expression in the retina of the village chicken. Overall, our results suggest that positive selection, rather than relaxation of purifying selection, contributed to the evolution of vision in domestic chickens. The progenitors of domestic chickens harboring weaker vision may have showed a reduced fear response and vigilance, making them easier to be unconsciously selected and/or domesticated. PMID:27033669

Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing.

PubMed

Bataillon, Thomas; Duan, Jinjie; Hvilsom, Christina; Jin, Xin; Li, Yingrui; Skov, Laurits; Glemin, Sylvain; Munch, Kasper; Jiang, Tao; Qian, Yu; Hobolth, Asger; Wang, Jun; Mailund, Thomas; Siegismund, Hans R; Schierup, Mikkel H

2015-03-30

We study genome-wide nucleotide diversity in three subspecies of extant chimpanzees using exome capture. After strict filtering, Single Nucleotide Polymorphisms and indels were called and genotyped for greater than 50% of exons at a mean coverage of 35× per individual. Central chimpanzees (Pan troglodytes troglodytes) are the most polymorphic (nucleotide diversity, θw = 0.0023 per site) followed by Eastern (P. t. schweinfurthii) chimpanzees (θw = 0.0016) and Western (P. t. verus) chimpanzees (θw = 0.0008). A demographic scenario of divergence without gene flow fits the patterns of autosomal synonymous nucleotide diversity well except for a signal of recent gene flow from Western into Eastern chimpanzees. The striking contrast in X-linked versus autosomal polymorphism and divergence previously reported in Central chimpanzees is also found in Eastern and Western chimpanzees. We show that the direction of selection statistic exhibits a strong nonmonotonic relationship with the strength of purifying selection S, making it inappropriate for estimating S. We instead use counts in synonymous versus nonsynonymous frequency classes to infer the distribution of S coefficients acting on nonsynonymous mutations in each subspecies. The strength of purifying selection we infer is congruent with the differences in effective sizes of each subspecies: Central chimpanzees are undergoing the strongest purifying selection followed by Eastern and Western chimpanzees. Coding indels show stronger selection against indels changing the reading frame than observed in human populations. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Plastid–Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae

PubMed Central

Weng, Mao-Lun; Ruhlman, Tracey A.; Jansen, Robert K.

2016-01-01

Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid–nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits. PMID:27190001

Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize.

PubMed

Pophaly, Saurabh D; Tellier, Aurélien

2015-12-01

The maize ancestor experienced a recent whole-genome duplication (WGD) followed by gene erosion which generated two subgenomes, the dominant subgenome (maize1) experiencing fewer deletions than maize2. We take advantage of available extensive polymorphism and gene expression data in maize to study purifying selection and gene expression divergence between WGD retained paralog pairs. We first report a strong correlation in nucleotide diversity between duplicate pairs, except for upstream regions. We then show that maize1 genes are under stronger purifying selection than maize2. WGD retained genes have higher gene dosage and biased Gene Ontologies consistent with previous studies. The relative gene expression of paralogs across tissues demonstrates that 98% of duplicate pairs have either subfunctionalized in a tissuewise manner or have diverged consistently in their expression thereby preventing functional complementation. Tissuewise subfunctionalization seems to be a hallmark of transcription factors, whereas consistent repression occurs for macromolecular complexes. We show that dominant gene expression is a strong determinant of the strength of purifying selection, explaining the inferred stronger negative selection on maize1 genes. We propose a novel expression-based classification of duplicates which is more robust to explain observed polymorphism patterns than the subgenome location. Finally, upstream regions of repressed genes exhibit an enrichment in transposable elements which indicates a possible mechanism for expression divergence. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates

PubMed Central

Roux, Julien; Liu, Jialin; Robinson-Rechavi, Marc

2017-01-01

Abstract The evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied to in situ hybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in nonrenewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation. PMID:28981708

Genomic Heat Shock Element Sequences Drive Cooperative Human Heat Shock Factor 1 DNA Binding and Selectivity*

PubMed Central

Jaeger, Alex M.; Makley, Leah N.; Gestwicki, Jason E.; Thiele, Dennis J.

2014-01-01

The heat shock transcription factor 1 (HSF1) activates expression of a variety of genes involved in cell survival, including protein chaperones, the protein degradation machinery, anti-apoptotic proteins, and transcription factors. Although HSF1 activation has been linked to amelioration of neurodegenerative disease, cancer cells exhibit a dependence on HSF1 for survival. Indeed, HSF1 drives a program of gene expression in cancer cells that is distinct from that activated in response to proteotoxic stress, and HSF1 DNA binding activity is elevated in cycling cells as compared with arrested cells. Active HSF1 homotrimerizes and binds to a DNA sequence consisting of inverted repeats of the pentameric sequence nGAAn, known as heat shock elements (HSEs). Recent comprehensive ChIP-seq experiments demonstrated that the architecture of HSEs is very diverse in the human genome, with deviations from the consensus sequence in the spacing, orientation, and extent of HSE repeats that could influence HSF1 DNA binding efficacy and the kinetics and magnitude of target gene expression. To understand the mechanisms that dictate binding specificity, HSF1 was purified as either a monomer or trimer and used to evaluate DNA-binding site preferences in vitro using fluorescence polarization and thermal denaturation profiling. These results were compared with quantitative chromatin immunoprecipitation assays in vivo. We demonstrate a role for specific orientations of extended HSE sequences in driving preferential HSF1 DNA binding to target loci in vivo. These studies provide a biochemical basis for understanding differential HSF1 target gene recognition and transcription in neurodegenerative disease and in cancer. PMID:25204655

A novel bispecific antibody, S-Fab, induces potent cancer cell killing.

PubMed

Li, Li; He, Ping; Zhou, Changhua; Jing, Li; Dong, Bin; Chen, Siqi; Zhang, Ning; Liu, Yawei; Miao, Ji; Wang, Zhong; Li, Qing

2015-01-01

Bispecific antibodies that engage immune cells to kill cancer cells have been actively studied in cancer immunotherapy. In this study, we present a novel bispecific format, S-Fab, fabricated by linking a single-domain anti-carcinoembryonic antigen VHH to a conventional anti-CD3 Fab. In contrast to most bispecific antibodies, the S-Fab bispecific antibody can be efficiently expressed and purified from bacteria. The purified S-Fab is stable in serum and is able to recruit T cells to drive potent cancer cell killing. In xenograft models, the S-Fab antibody suppresses tumor growth in the presence of human immune cells. Our study suggested that the bispecific S-Fab format can be applied to a wide range of immunotherapies.

Purification and switching protocols for dissipatively stabilized entangled qubit states

NASA Astrophysics Data System (ADS)

Hein, Sven M.; Aron, Camille; Türeci, Hakan E.

2016-06-01

Pure dephasing processes limit the fidelities achievable in driven-dissipative schemes for stabilization of entangled states of qubits. We propose a scheme which, combined with already existing entangling methods, purifies the desired entangled state by driving out of equilibrium auxiliary dissipative cavity modes coupled to the qubits. We lay out the specifics of our scheme and compute its efficiency in the particular context of two superconducting qubits in a cavity-QED architecture, where the strongly coupled auxiliary modes provided by collective cavity excitations can drive and sustain the qubits in maximally entangled Bell states with fidelities reaching 90% for experimentally accessible parameters.

Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish.

PubMed

Pavlova, A; Gan, H M; Lee, Y P; Austin, C M; Gilligan, D M; Lintermans, M; Sunnucks, P

2017-05-01

Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient speciation previously inferred from differentiation in allozymes, microsatellites and mitochondrial control region. The estimated time of lineage divergence suggested an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB, followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence estimates are more recent than previous ones. Our analyses suggested that evolutionary drivers differed between inland MDB and coastal HNB. In the cooler and more climatically variable MDB, mitogenomes evolved under strong purifying selection, whereas in the warmer and more climatically stable HNB, purifying selection was relaxed. Evidence for relaxed selection in the HNB includes elevated transfer RNA and 16S ribosomal RNA polymorphism, presence of potentially mildly deleterious mutations and a codon (ATP6 113 ) displaying signatures of positive selection (ratio of nonsynonymous to synonymous substitution rates (dN/dS) >1, radical change of an amino-acid property and phylogenetic conservation across the Percichthyidae). In addition, the difference could be because of stronger genetic drift in the smaller and historically more subdivided HNB with low per-population effective population sizes.

Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity.

PubMed

Copin, Richard; Wang, Xueying; Louie, Eddie; Escuyer, Vincent; Coscolla, Mireia; Gagneux, Sebastien; Palmer, Guy H; Ernst, Joel D

2016-12-01

Molecular epidemiological assessments, drug treatment optimization, and development of immunological interventions all depend on understanding pathogen adaptation and genetic variation, which differ for specific pathogens. Mycobacterium tuberculosis is an exceptionally successful human pathogen, yet beyond knowledge that this bacterium has low overall genomic variation but acquires drug resistance mutations, little is known of the factors that drive its population genomic characteristics. Here, we compared the genetic diversity of the bacteria that established infection to the bacterial populations obtained from infected tissues during murine M. tuberculosis pulmonary infection and human disseminated M. bovis BCG infection. We found that new mutations accumulate during in vitro culture, but that in vivo, purifying selection against new mutations dominates, indicating that M. tuberculosis follows a dominant lineage model of evolution. Comparing bacterial populations passaged in T cell-deficient and immunocompetent mice, we found that the presence of T cells is associated with an increase in the diversity of the M. tuberculosis genome. Together, our findings put M. tuberculosis genetic evolution in a new perspective and clarify the impact of T cells on sequence diversity of M. tuberculosis.

Natural selection reduced diversity on human y chromosomes.

PubMed

Wilson Sayres, Melissa A; Lohmueller, Kirk E; Nielsen, Rasmus

2014-01-01

The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. While we show that purifying selection removing deleterious mutations can explain the low diversity on the Y chromosome, we cannot exclude the possibility that positive selection acting on beneficial mutations could have also reduced diversity in linked neutral regions, and may have contributed to lowering human Y chromosome diversity. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.

Natural Selection Reduced Diversity on Human Y Chromosomes

PubMed Central

Wilson Sayres, Melissa A.; Lohmueller, Kirk E.; Nielsen, Rasmus

2014-01-01

The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. While we show that purifying selection removing deleterious mutations can explain the low diversity on the Y chromosome, we cannot exclude the possibility that positive selection acting on beneficial mutations could have also reduced diversity in linked neutral regions, and may have contributed to lowering human Y chromosome diversity. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area. PMID:24415951

Induction of Pro-Angiogenic Factors by Pregnancy-Specific Glycoproteins and Studies on Receptor Usage

DTIC Science & Technology

2008-01-01

expression vector. The purified bacoluvirus DNA, containing PSG11, was purified and used to transfect Spodoptera frugiperda (Sf-9) cells (Invitrogen) to...proteins in Spodoptera frugiperda cells using biotin acceptor peptides. Anal Biochem, 1998. 262(2): p. 122-8. 175. Hirt, B., Selective extraction of

Detecting signatures of selection within the Tibetan sheep mitochondrial genome.

PubMed

Niu, Lili; Chen, Xiaoyong; Xiao, Ping; Zhao, Qianjun; Zhou, Jingxuan; Hu, Jiangtao; Sun, Hongxin; Guo, Jiazhong; Li, Li; Wang, Linjie; Zhang, Hongping; Zhong, Tao

2017-11-01

Tibetan sheep, a Chinese indigenous breed, are mainly distributed in plateau and mountain-valley areas at a terrestrial elevation between 2260 and 4100 m. The herd is genetically distinct from the other domestic sheep and undergoes acclimatization to adapt to the hypoxic environment. To date, whether the mitochondrial DNA modification of Tibetan sheep shares the same feature as the other domestic breed remains unknown. In this study, we compared the whole mitogenome sequences from 32 Tibetan sheep, 22 domestic sheep and 24 commercial sheep to identify the selection signatures of hypoxic-tolerant in Tibetan sheep. Nucleotide diversity analysis using the sliding window method showed that the highest level of nucleotide diversity was observed in the control region with a peak value of π = 0.05215, while the lowest π value was detected in the tRNAs region. qPCR results showed that the relative mtDNA copy number in Tibetan sheep was significantly lower than that in Suffolk sheep. None of the mutations in 12S rRNA were fixed in Tibetan sheep, which indicated that there has been less artificial selection in this herd than the other domestic and commercial breeds. Although one site (1277G) might undergo the purifying selection, it was not identified as the breed-specific allele in Tibetan sheep. We proposed that nature selection was the main drive during the domestication of Tibetan sheep and single mutation (or locus) could not reveal the signature of selection as for the high diversity in the mitogenome of Tibetan sheep.

Evolution of substrate specificity in a retained enzyme driven by gene loss

PubMed Central

Juárez-Vázquez, Ana Lilia; Edirisinghe, Janaka N; Verduzco-Castro, Ernesto A; Michalska, Karolina; Wu, Chenggang; Noda-García, Lianet; Babnigg, Gyorgy; Endres, Michael; Medina-Ruíz, Sofía; Santoyo-Flores, Julián; Carrillo-Tripp, Mauricio; Ton-That, Hung; Joachimiak, Andrzej; Henry, Christopher S; Barona-Gómez, Francisco

2017-01-01

The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes. DOI: http://dx.doi.org/10.7554/eLife.22679.001 PMID:28362260

Evolution of Substrate Specificity in A Retained Enzyme Driven by Gene Loss

DOE PAGES

Juarez-Vazquez, Ana L.; Edirisinghe, Janaka N.; Verduzco-Castro, Ernesto A.; ...

2017-03-31

The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. Here, we apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We also observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to amore » monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. These results show how gene loss can drive the evolution of substrate specificity from retained enzymes.« less

Evolution of substrate specificity in a retained enzyme driven by gene loss

DOE PAGES

Juárez-Vázquez, Ana Lilia; Edirisinghe, Janaka N.; Verduzco-Castro, Ernesto A.; ...

2017-03-31

The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence oftrpandhisgenes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficientmore » form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Finally, our results show how gene loss can drive the evolution of substrate specificity from retained enzymes.« less

Evolution of substrate specificity in a retained enzyme driven by gene loss

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

Juárez-Vázquez, Ana Lilia; Edirisinghe, Janaka N.; Verduzco-Castro, Ernesto A.

The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence oftrpandhisgenes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficientmore » form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Finally, our results show how gene loss can drive the evolution of substrate specificity from retained enzymes.« less

Evolution of Substrate Specificity in A Retained Enzyme Driven by Gene Loss

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

Juarez-Vazquez, Ana L.; Edirisinghe, Janaka N.; Verduzco-Castro, Ernesto A.

The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. Here, we apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We also observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to amore » monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. These results show how gene loss can drive the evolution of substrate specificity from retained enzymes.« less

Discovering functional DNA elements using population genomic information: a proof of concept using human mtDNA.

PubMed

Schrider, Daniel R; Kern, Andrew D

2014-06-09

Identifying the complete set of functional elements within the human genome would be a windfall for multiple areas of biological research including medicine, molecular biology, and evolution. Complete knowledge of function would aid in the prioritization of loci when searching for the genetic bases of disease or adaptive phenotypes. Because mutations that disrupt function are disfavored by natural selection, purifying selection leaves a detectable signature within functional elements; accordingly, this signal has been exploited for over a decade through the use of genomic comparisons of distantly related species. While this is so, the functional complement of the genome changes extensively across time and between lineages; therefore, evidence of the current action of purifying selection in humans is essential. Because the removal of deleterious mutations by natural selection also reduces within-species genetic diversity within functional loci, dense population genetic data have the potential to reveal genomic elements that are currently functional. Here, we assess the potential of this approach by examining an ultradeep sample of human mitochondrial genomes (n = 16,411). We show that the high density of polymorphism in this data set precisely delineates regions experiencing purifying selection. Furthermore, we show that the number of segregating alleles at a site is strongly correlated with its divergence across species after accounting for known mutational biases in human mitochondrial DNA (ρ = 0.51; P < 2.2 × 10(-16)). These two measures track one another at a remarkably fine scale across many loci-a correlation that is purely the result of natural selection. Our results demonstrate that genetic variation has the potential to reveal with surprising precision which regions in the genome are currently performing important functions and likely to have deleterious fitness effects when mutated. As more complete human genomes are sequenced, similar power to reveal purifying selection may be achievable in the human nuclear genome. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Plastid-Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae.

PubMed

Weng, Mao-Lun; Ruhlman, Tracey A; Jansen, Robert K

2016-06-27

Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid-nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Coevolution and life cycle specialization of plant cell wall degrading enzymes in a hemibiotrophic pathogen.

PubMed

Brunner, Patrick C; Torriani, Stefano F F; Croll, Daniel; Stukenbrock, Eva H; McDonald, Bruce A

2013-06-01

Zymoseptoria tritici is an important fungal pathogen on wheat that originated in the Fertile Crescent. Its closely related sister species Z. pseudotritici and Z. ardabiliae infect wild grasses in the same region. This recently emerged host-pathogen system provides a rare opportunity to investigate the evolutionary processes shaping the genome of an emerging pathogen. Here, we investigate genetic signatures in plant cell wall degrading enzymes (PCWDEs) that are likely affected by or driving coevolution in plant-pathogen systems. We hypothesize four main evolutionary scenarios and combine comparative genomics, transcriptomics, and selection analyses to assign the majority of PCWDEs in Z. tritici to one of these scenarios. We found widespread differential transcription among different members of the same gene family, challenging the idea of functional redundancy and suggesting instead that specialized enzymatic activity occurs during different stages of the pathogen life cycle. We also find that natural selection has significantly affected at least 19 of the 48 identified PCWDEs. The majority of genes showed signatures of purifying selection, typical for the scenario of conserved substrate optimization. However, six genes showed diversifying selection that could be attributed to either host adaptation or host evasion. This study provides a powerful framework to better understand the roles played by different members of multigene families and to determine which genes are the most appropriate targets for wet laboratory experimentation, for example, to elucidate enzymatic function during relevant phases of a pathogen's life cycle.

Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates.

PubMed

Roux, Julien; Liu, Jialin; Robinson-Rechavi, Marc

2017-11-01

The evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied to in situ hybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in nonrenewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Purified glycosaminoglycans from cooked haddock may enhance Fe uptake via endocytosis in a Caco-2 cell culture model

USDA-ARS?s Scientific Manuscript database

This study aims to understand the enhancing effect of glycosaminoglycans (GAGs), such as chondroitin/dermatan structures, on Fe uptake to Caco-2 cells. High sulfated GAGs were selectively purified from cooked haddock. An in vitro digestion/Caco-2 cell culture model was used to evaluate Fe uptake (ce...

Purified ryanodine receptor from rabbit skeletal muscle is the calcium- release channel of sarcoplasmic reticulum

PubMed Central

1988-01-01

The ryanodine receptor of rabbit skeletal muscle sarcoplasmic reticulum was purified as a single 450,000-dalton polypeptide from CHAPS- solubilized triads using immunoaffinity chromatography. The purified receptor had a [3H]ryanodine-binding capacity (Bmax) of 490 pmol/mg and a binding affinity (Kd) of 7.0 nM. Using planar bilayer recording techniques, we show that the purified receptor forms cationic channels selective for divalent ions. Ryanodine receptor channels were identical to the Ca-release channels described in native sarcoplasmic reticulum using the same techniques. In the present work, four criteria were used to establish this identity: (a) activation of channels by micromolar Ca and millimolar ATP and inhibition by micromolar ruthenium red, (b) a main channel conductance of 110 +/- 10 pS in 54 mM trans Ca, (c) a long- term open state of lower unitary conductance induced by ryanodine concentrations as low as 20 nM, and (d) a permeability ratio PCa/PTris approximately equal to 14. In addition, we show that the purified ryanodine receptor channel displays a saturable conductance in both monovalent and divalent cation solutions (gamma max for K and Ca = 1 nS and 172 pS, respectively). In the absence of Ca, channels had a broad selectivity for monovalent cations, but in the presence of Ca, they were selectively permeable to Ca against K by a permeability ratio PCa/PK approximately equal to 6. Receptor channels displayed several equivalent conductance levels, which suggest an oligomeric pore structure. We conclude that the 450,000-dalton polypeptide ryanodine receptor is the Ca-release channel of the sarcoplasmic reticulum and is the target site of ruthenium red and ryanodine. PMID:2459298

INVESTIGATIONS ON THE ANTIGENICITY OF SNAKE VENOMS

DTIC Science & Technology

The chemical composition of viperotoxin, the neurotoxic protein isolated from the venom of Vipera palestinae has been determined. Viperotoxin is...carboxy-terminal position of the viperotoxin chain. Vipera palestinae hemorrhagin has been purified and isolated. Further tests have established that...active sites, or selective blocking of a part of one active center having two distinct biological activities. Purified neurotoxin of V. palestinae

Methods for purifying carbon materials

DOEpatents

Dailly, Anne [Pasadena, CA; Ahn, Channing [Pasadena, CA; Yazami, Rachid [Los Angeles, CA; Fultz, Brent T [Pasadena, CA

2009-05-26

Methods of purifying samples are provided that are capable of removing carbonaceous and noncarbonaceous impurities from a sample containing a carbon material having a selected structure. Purification methods are provided for removing residual metal catalyst particles enclosed in multilayer carbonaceous impurities in samples generate by catalytic synthesis methods. Purification methods are provided wherein carbonaceous impurities in a sample are at least partially exfoliated, thereby facilitating subsequent removal of carbonaceous and noncarbonaceous impurities from the sample. Methods of purifying carbon nanotube-containing samples are provided wherein an intercalant is added to the sample and subsequently reacted with an exfoliation initiator to achieve exfoliation of carbonaceous impurities.

Certification of caffeine reference material purity by ultraviolet/visible spectrophotometry and high-performance liquid chromatography with diode-array detection as two independent analytical methods.

PubMed

Shehata, A B; Rizk, M S; Rend, E A

2016-10-01

Caffeine reference material certified for purity is produced worldwide, but no research work on the details of the certification process has been published in the literature. In this paper, we report the scientific details of the preparation and certification of pure caffeine reference materials. Caffeine was prepared by extraction from roasted and ground coffee by dichloromethane after heating in deionized water mixed with magnesium oxide. The extract was purified, dried, and bottled in dark glass vials. Stratified random selection was applied to select a number of vials for homogeneity and stability studies, which revealed that the prepared reference material is homogeneous and sufficiently stable. Quantification of caffeine purity % was carried out using a calibrated UV/visible spectrophotometer and a calibrated high-performance liquid chromatography with diode-array detection method. The results obtained from both methods were combined to drive the certified value and its associated uncertainty. The certified value of the reference material purity was found to be 99.86% and its associated uncertainty was ±0.65%, which makes the candidate reference material a very useful calibrant in food and drug chemical analysis. Copyright © 2016. Published by Elsevier B.V.

Conserved noncoding sequences conserve biological networks and influence genome evolution.

PubMed

Xie, Jianbo; Qian, Kecheng; Si, Jingna; Xiao, Liang; Ci, Dong; Zhang, Deqiang

2018-05-01

Comparative genomics approaches have identified numerous conserved cis-regulatory sequences near genes in plant genomes. Despite the identification of these conserved noncoding sequences (CNSs), our knowledge of their functional importance and selection remains limited. Here, we used a combination of DNA methylome analysis, microarray expression analyses, and functional annotation to study these sequences in the model tree Populus trichocarpa. Methylation in CG contexts and non-CG contexts was lower in CNSs, particularly CNSs in the 5'-upstream regions of genes, compared with other sites in the genome. We observed that CNSs are enriched in genes with transcription and binding functions, and this also associated with syntenic genes and those from whole-genome duplications, suggesting that cis-regulatory sequences play a key role in genome evolution. We detected a significant positive correlation between CNS number and protein interactions, suggesting that CNSs may have roles in the evolution and maintenance of biological networks. The divergence of CNSs indicates that duplication-degeneration-complementation drives the subfunctionalization of a proportion of duplicated genes from whole-genome duplication. Furthermore, population genomics confirmed that most CNSs are under strong purifying selection and only a small subset of CNSs shows evidence of adaptive evolution. These findings provide a foundation for future studies exploring these key genomic features in the maintenance of biological networks, local adaptation, and transcription.

Comparative Genomics Provide Insights into Evolution of Trichoderma Nutrition Style

PubMed Central

Xie, Bin-Bin; Qin, Qi-Long; Shi, Mei; Chen, Lei-Lei; Shu, Yan-Li; Luo, Yan; Wang, Xiao-Wei; Rong, Jin-Cheng; Gong, Zhi-Ting; Li, Dan; Sun, Cai-Yun; Liu, Gui-Ming; Dong, Xiao-Wei; Pang, Xiu-Hua; Huang, Feng; Liu, Weifeng; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhang, Yu-Zhong; Song, Xiao-Yan

2014-01-01

Saprotrophy on plant biomass is a recently developed nutrition strategy for Trichoderma. However, the physiology and evolution of this new nutrition strategy is still elusive. We report the deep sequencing and analysis of the genome of Trichoderma longibrachiatum, an efficient cellulase producer. The 31.7-Mb genome, smallest among the sequenced Trichoderma species, encodes fewer nutrition-related genes than saprotrophic T. reesei (Tr), including glycoside hydrolases and nonribosomal peptide synthetase–polyketide synthase. Homology and phylogenetic analyses suggest that a large number of nutrition-related genes, including GH18 chitinases, β-1,3/1,6-glucanases, cellulolytic enzymes, and hemicellulolytic enzymes, were lost in the common ancestor of T. longibrachiatum (Tl) and Tr. dN/dS (ω) calculation indicates that all the nutrition-related genes analyzed are under purifying selection. Cellulolytic enzymes, the key enzymes for saprotrophy on plant biomass, are under stronger purifying selection pressure in Tl and Tr than in mycoparasitic species, suggesting that development of the nutrition strategy of saprotrophy on plant biomass has increased the selection pressure. In addition, aspartic proteases, serine proteases, and metalloproteases are subject to stronger purifying selection pressure in Tl and Tr, suggesting that these enzymes may also play important roles in the nutrition. This study provides insights into the physiology and evolution of the nutrition strategy of Trichoderma. PMID:24482532

Massive expansion and differential evolution of small heat shock proteins with wheat (Triticum aestivum L.) polyploidization.

PubMed

Wang, Xiaoming; Wang, Ruochen; Ma, Chuang; Shi, Xue; Liu, Zhenshan; Wang, Zhonghua; Sun, Qixin; Cao, Jun; Xu, Shengbao

2017-05-31

Wheat (Triticum aestivum), one of the world's most important crops, is facing unprecedented challenges due to global warming. To evaluate the gene resources for heat adaptation in hexaploid wheat, small heat shock proteins (sHSPs), the key plant heat protection genes, were comprehensively analysed in wheat and related species. We found that the sHSPs of hexaploid wheat were massively expanded in A and B subgenomes with intrachromosomal duplications during polyploidization. These expanded sHSPs were under similar purifying selection and kept the expressional patterns with the original copies. Generally, a strong purifying selection acted on the α-crystallin domain (ACD) and theoretically constrain conserved function. Meanwhile, weaker purifying selection and strong positive selection acted on the N-terminal region, which conferred sHSP flexibility, allowing adjustments to a wider range of substrates in response to genomic and environmental changes. Notably, in CI, CV, ER, MI and MII subfamilies, gene duplications, expression variations and functional divergence occurred before wheat polyploidization. Our results indicate the massive expansion of active sHSPs in hexaploid wheat may also provide more raw materials for evolving functional novelties and generating genetic diversity to face future global climate changes, and highlight the expansion of stress response genes with wheat polyploidization.

Comparative genomics provide insights into evolution of trichoderma nutrition style.

PubMed

Xie, Bin-Bin; Qin, Qi-Long; Shi, Mei; Chen, Lei-Lei; Shu, Yan-Li; Luo, Yan; Wang, Xiao-Wei; Rong, Jin-Cheng; Gong, Zhi-Ting; Li, Dan; Sun, Cai-Yun; Liu, Gui-Ming; Dong, Xiao-Wei; Pang, Xiu-Hua; Huang, Feng; Liu, Weifeng; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhang, Yu-Zhong; Song, Xiao-Yan

2014-02-01

Saprotrophy on plant biomass is a recently developed nutrition strategy for Trichoderma. However, the physiology and evolution of this new nutrition strategy is still elusive. We report the deep sequencing and analysis of the genome of Trichoderma longibrachiatum, an efficient cellulase producer. The 31.7-Mb genome, smallest among the sequenced Trichoderma species, encodes fewer nutrition-related genes than saprotrophic T. reesei (Tr), including glycoside hydrolases and nonribosomal peptide synthetase-polyketide synthase. Homology and phylogenetic analyses suggest that a large number of nutrition-related genes, including GH18 chitinases, β-1,3/1,6-glucanases, cellulolytic enzymes, and hemicellulolytic enzymes, were lost in the common ancestor of T. longibrachiatum (Tl) and Tr. dN/dS (ω) calculation indicates that all the nutrition-related genes analyzed are under purifying selection. Cellulolytic enzymes, the key enzymes for saprotrophy on plant biomass, are under stronger purifying selection pressure in Tl and Tr than in mycoparasitic species, suggesting that development of the nutrition strategy of saprotrophy on plant biomass has increased the selection pressure. In addition, aspartic proteases, serine proteases, and metalloproteases are subject to stronger purifying selection pressure in Tl and Tr, suggesting that these enzymes may also play important roles in the nutrition. This study provides insights into the physiology and evolution of the nutrition strategy of Trichoderma.

Duplication and population dynamics shape historic patterns of selection and genetic variation at the major histocompatibility complex in rodents

PubMed Central

Winternitz, Jamie C; Wares, John P

2013-01-01

Genetic variation at the major histocompatibility complex (MHC) is vitally important for wildlife populations to respond to pathogen threats. As natural populations can fluctuate greatly in size, a key issue concerns how population cycles and bottlenecks that could reduce genetic diversity will influence MHC genes. Using 454 sequencing, we characterized genetic diversity at the DRB Class II locus in montane voles (Microtus montanus), a North American rodent that regularly undergoes high-amplitude fluctuations in population size. We tested for evidence of historic balancing selection, recombination, and gene duplication to identify mechanisms maintaining allelic diversity. Counter to our expectations, we found strong evidence of purifying selection acting on the DRB locus in montane voles. We speculate that the interplay between population fluctuations and gene duplication might be responsible for the weak evidence of historic balancing selection and strong evidence of purifying selection detected. To further explore this idea, we conducted a phylogenetically controlled comparative analysis across 16 rodent species with varying demographic histories and MHC duplication events (based on the maximum number of alleles detected per individual). On the basis of phylogenetic generalized linear model-averaging, we found evidence that the estimated number of duplicated loci was positively related to allelic diversity and, surprisingly, to the strength of purifying selection at the DRB locus. Our analyses also revealed that species that had undergone population bottlenecks had lower allelic richness than stable species. This study highlights the need to consider demographic history and genetic structure alongside patterns of natural selection to understand resulting patterns of genetic variation at the MHC. PMID:23789067

Immune Selection In Vitro Reveals Human Immunodeficiency Virus Type 1 Nef Sequence Motifs Important for Its Immune Evasion Function In Vivo

PubMed Central

Lee, Patricia; Ng, Hwee L.; Yang, Otto O.

2012-01-01

Human immunodeficiency virus type 1 (HIV-1) Nef downregulates major histocompatibility complex class I (MHC-I), impairing the clearance of infected cells by CD8+ cytotoxic T lymphocytes (CTLs). While sequence motifs mediating this function have been determined by in vitro mutagenesis studies of laboratory-adapted HIV-1 molecular clones, it is unclear whether the highly variable Nef sequences of primary isolates in vivo rely on the same sequence motifs. To address this issue, nef quasispecies from nine chronically HIV-1-infected persons were examined for sequence evolution and altered MHC-I downregulatory function under Gag-specific CTL immune pressure in vitro. This selection resulted in decreased nef diversity and strong purifying selection. Site-by-site analysis identified 13 codons undergoing purifying selection and 1 undergoing positive selection. Of the former, only 6 have been reported to have roles in Nef function, including 4 associated with MHC-I downregulation. Functional testing of naturally occurring in vivo polymorphisms at the 7 sites with no previously known functional role revealed 3 mutations (A84D, Y135F, and G140R) that ablated MHC-I downregulation and 3 (N52A, S169I, and V180E) that partially impaired MHC-I downregulation. Globally, the CTL pressure in vitro selected functional Nef from the in vivo quasispecies mixtures that predominately lacked MHC-I downregulatory function at the baseline. Overall, these data demonstrate that CTL pressure exerts a strong purifying selective pressure for MHC-I downregulation and identifies novel functional motifs present in Nef sequences in vivo. PMID:22553319

Pseudomonas aeruginosa arylsulfatase: a purified enzyme for the mild hydrolysis of steroid sulfates.

PubMed

Stevenson, Bradley J; Waller, Christopher C; Ma, Paul; Li, Kunkun; Cawley, Adam T; Ollis, David L; McLeod, Malcolm D

2015-10-01

The hydrolysis of sulfate ester conjugates is frequently required prior to analysis for a range of analytical techniques including gas chromatography-mass spectrometry (GC-MS). Sulfate hydrolysis may be achieved with commercial crude arylsulfatase enzyme preparations such as that derived from Helix pomatia but these contain additional enzyme activities such as glucuronidase, oxidase, and reductase that make them unsuitable for many analytical applications. Strong acid can also be used to hydrolyze sulfate esters but this can lead to analyte degradation or increased matrix interference. In this work, the heterologously expressed and purified arylsulfatase from Pseudomonas aeruginosa is shown to promote the mild enzyme-catalyzed hydrolysis of a range of steroid sulfates. The substrate scope of this P. aeruginosa arylsulfatase hydrolysis is compared with commercial crude enzyme preparations such as that derived from H. pomatia. A detailed kinetic comparison is reported for selected examples. Hydrolysis in a urine matrix is demonstrated for dehydroepiandrosterone 3-sulfate and epiandrosterone 3-sulfate. The purified P. aeruginosa arylsulfatase contains only sulfatase activity allowing for the selective hydrolysis of sulfate esters in the presence of glucuronide conjugates as demonstrated in the short three-step chemoenzymatic synthesis of 5α-androstane-3β,17β-diol 17-glucuronide (ADG, 1) from epiandrosterone 3-sulfate. The P. aeruginosa arylsulfatase is readily expressed and purified (0.9 g per L of culture) and thus provides a new and selective method for the hydrolysis of steroid sulfate esters in analytical sample preparation. Copyright © 2015 John Wiley & Sons, Ltd.

Reconstitution and functional comparison of purified GlpF and AqpZ, the glycerol and water channels from Escherichia coli.

PubMed

Borgnia, M J; Agre, P

2001-02-27

A large family of membrane channel proteins selective for transport of water (aquaporins) or water plus glycerol (aquaglyceroporins) has been found in diverse life forms. Escherichia coli has two members of this family-a water channel, AqpZ, and a glycerol facilitator, GlpF. Despite having similar primary amino acid sequences and predicted structures, the oligomeric state and solute selectivity of AqpZ and GlpF are disputed. Here we report biochemical and functional characterizations of affinity-purified GlpF and compare it to AqpZ. Histidine-tagged (His-GlpF) and hemagglutinin-tagged (HA-GlpF) polypeptides encoded by a bicistronic construct were expressed in bacteria. HA-GlpF and His-GlpF appear to form oligomers during Ni-nitrilotriacetate affinity purification. Sucrose gradient sedimentation analyses showed that the oligomeric state of octyl glucoside-solubilized GlpF varies: low ionic strength favors subunit dissociation, whereas Mg(2+) stabilizes tetrameric assembly. Reconstitution of affinity-purified GlpF into proteoliposomes increases glycerol permeability more than 100-fold and water permeability up to 10-fold compared with control liposomes. Glycerol and water permeability of GlpF both occur with low Arrhenius activation energies and are reversibly inhibited by HgCl(2). Our studies demonstrate that, unlike AqpZ, a water-selective stable tetramer, purified GlpF exists in multiple oligomeric forms under nondenaturing conditions and is highly permeable to glycerol but less well permeated by water.

Detection of a lysosomal carboxypeptidase and a lysosomal dipeptidase in highly-purified dipeptidyl aminopeptidase I /cathepsin C/ and the elimination of their activities from preparations used to sequence peptides.

NASA Technical Reports Server (NTRS)

Mcdonald, J. K.; Zeitman, B. B.; Ellis, S.

1972-01-01

Description of the properties of a carboxypeptidase, termed 'catheptic carboxypeptidase C,' and a dipeptidase, termed 'Ser-Met dipeptidase.' Both were found in highly purified DAP I from either beef spleen or rat liver. Methods are described for the removal or selective inactivation of these contaminating enzymes.

Purification of the lactose:H+ carrier of Escherichia coli and characterization of galactoside binding and transport.

PubMed

Wright, J K; Overath, P

1984-02-01

The lactose carrier, a galactoside:H+ symporter in Escherichia coli, has been purified from cytoplasmic membranes by pre-extraction of the membranes with 5-sulfosalicylate, solubilization in dodecyl-O-beta-D-maltoside, Ecteola-column chromatography, and removal of residual impurities by anti-impurity antibodies. Subsequently, the purified carrier was reincorporated into E. coli phospholipid vesicles. Purification was monitored by tracer N-[3H]ethylmaleimide-labeled carrier and by binding of the substrate p-nitrophenyl-alpha-D-galactopyranoside. All purified carrier molecules were active in substrate binding and the purified protein was at least 95% pure by several criteria. Substrate binding to the purified carrier in detergent micelles and in reconstituted proteoliposomes yielded a stoichiometry close to one molecule substrate bound per polypeptide chain. Large unilamellar proteoliposomes (1-5-micron diameter) were prepared from initially small reconstituted vesicles by freeze-thaw cycles and low-speed centrifugation. These proteoliposomes catalyzed facilitated diffusion and active transport in response to artificially imposed electrochemical proton gradients (delta mu H+) or one of its components (delta psi or delta pH). Comparison of the steady-state level of galactoside accumulation and the nominal value of the driving gradients yielded cotransport stoichiometries up to 0.7 proton/galactoside, suggesting that the carrier protein is the only component required for active galactoside transport. The half-saturation constants for active uptake of lactose (KT = 200 microM) or beta-D-galactosyl-1-thio-beta-D-galactoside (KT = 50-80 microM) by the purified carrier were found to be similar to be similar to those measured in cells or cytoplasmic membrane vesicles. The maximum rate for active transport expressed as a turnover number was similar in proteoliposomes and cytoplasmic membrane vesicles (kcat = 3-4 s-1 for lactose) but considerably smaller than in cells (kcat = 40-60 s-1). Possible reasons for this discrepancy are discussed.

Self-Powered Electrostatic Filter with Enhanced Photocatalytic Degradation of Formaldehyde Based on Built-in Triboelectric Nanogenerators.

PubMed

Feng, Yawei; Ling, Lili; Nie, Jinhui; Han, Kai; Chen, Xiangyu; Bian, Zhenfeng; Li, Hexing; Wang, Zhong Lin

2017-12-26

Recently, atmospheric pollution caused by particulate matter or volatile organic compounds (VOCs) has become a serious issue to threaten human health. Consequently, it is highly desirable to develop an efficient purifying technique with simple structure and low cost. In this study, by combining a triboelectric nanogenerator (TENG) and a photocatalysis technique, we demonstrated a concept of a self-powered filtering method for removing pollutants from indoor atmosphere. The photocatalyst P25 or Pt/P25 was embedded on the surface of polymer-coated stainless steel wires, and such steel wires were woven into a filtering network. A strong electric field can be induced on this filtering network by TENG, while both electrostatic adsorption effect and TENG-enhanced photocatalytic effect can be achieved. Rhodamine B (RhB) steam was selected as the pollutant for demonstration. The absorbed RhB on the filter network with TENG in 1 min was almost the same amount of absorption achieved in 15 min without using TENG. Meanwhile, the degradation of RhB was increased over 50% under the drive of TENG. Furthermore, such a device was applied for the degradation of formaldehyde, where degradation efficiency was doubled under the drive of TENG. This work extended the application for the TENG in self-powered electrochemistry, design and concept of which can be possibly applied in the field of haze governance, indoor air cleaning, and photocatalytic pollution removal for environmental protection.

Mitigating Mitochondrial Genome Erosion Without Recombination.

PubMed

Radzvilavicius, Arunas L; Kokko, Hanna; Christie, Joshua R

2017-11-01

Mitochondria are ATP-producing organelles of bacterial ancestry that played a key role in the origin and early evolution of complex eukaryotic cells. Most modern eukaryotes transmit mitochondrial genes uniparentally, often without recombination among genetically divergent organelles. While this asymmetric inheritance maintains the efficacy of purifying selection at the level of the cell, the absence of recombination could also make the genome susceptible to Muller's ratchet. How mitochondria escape this irreversible defect accumulation is a fundamental unsolved question. Occasional paternal leakage could in principle promote recombination, but it would also compromise the purifying selection benefits of uniparental inheritance. We assess this tradeoff using a stochastic population-genetic model. In the absence of recombination, uniparental inheritance of freely-segregating genomes mitigates mutational erosion, while paternal leakage exacerbates the ratchet effect. Mitochondrial fusion-fission cycles ensure independent genome segregation, improving purifying selection. Paternal leakage provides opportunity for recombination to slow down the mutation accumulation, but always at a cost of increased steady-state mutation load. Our findings indicate that random segregation of mitochondrial genomes under uniparental inheritance can effectively combat the mutational meltdown, and that homologous recombination under paternal leakage might not be needed. Copyright © 2017 by the Genetics Society of America.

Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species.

PubMed

Harrisson, K; Pavlova, A; Gan, H M; Lee, Y P; Austin, C M; Sunnucks, P

2016-06-01

Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in genetics-based metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid- to late-Pleistocene divergence of Maccullochella across the GDR (220-710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus.

Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species

PubMed Central

Harrisson, K; Pavlova, A; Gan, H M; Lee, Y P; Austin, C M; Sunnucks, P

2016-01-01

Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in genetics-based metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid- to late-Pleistocene divergence of Maccullochella across the GDR (220–710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus. PMID:26883183

Nucleotide substitutions in dengue virus serotypes from Asian and American countries: insights into intracodon recombination and purifying selection

PubMed Central

2013-01-01

Background Dengue virus (DENV) infection represents a significant public health problem in many subtropical and tropical countries. Although genetically closely related, the four serotypes of DENV differ in antigenicity for which cross protection among serotypes is limited. It is also believed that both multi-serotype infection as well as the evolution of viral antigenicity may have confounding effects in increased dengue epidemics. Numerous studies have been performed that investigated genetic diversity of DENV, but the precise mechanism(s) of dengue virus evolution are not well understood. Results We investigated genome-wide genetic diversity and nucleotide substitution patterns in the four serotypes among samples collected from different countries in Asia and Central and South America and sequenced as part of the Genome Sequencing Center for Infectious Diseases at the Broad Institute. We applied bioinformatics, statistical and coalescent simulation methods to investigate diversity of codon sequences of DENV samples representing the four serotypes. We show that fixation of nucleotide substitutions is more prominent among the inter-continental isolates (Asian and American) of serotypes 1, 2 and 3 compared to serotype 4 isolates (South and Central America) and are distributed in a non-random manner among the genes encoded by the virus. Nearly one third of the negatively selected sites are associated with fixed mutation sites within serotypes. Our results further show that of all the sites showing evidence of recombination, the majority (~84%) correspond to sites under purifying selection in the four serotypes. The analysis further shows that genetic recombination occurs within specific codons, albeit with low frequency (< 5% of all recombination sites) throughout the DENV genome of the four serotypes and reveals significant enrichment (p < 0.05) among sites under purifying selection in the virus. Conclusion The study provides the first evidence for intracodon recombination in DENV and suggests that within codons, genetic recombination has a significant role in maintaining extensive purifying selection of DENV in natural populations. Our study also suggests that fixation of beneficial mutations may lead to virus evolution via translational selection of specific sites in the DENV genome. PMID:23410119

Drugs and driving : a selected bibliography.

DOT National Transportation Integrated Search

1977-01-01

This report presents a selected bibliography on drugs (other than : alcohol alone) and driving. Appendices contain a Topical Index; a : Title Index, an Author Index, and Abstracts of over 600 articles. : Scientific, technical and selected general lit...

Arrayed antibody library technology for therapeutic biologic discovery.

PubMed

Bentley, Cornelia A; Bazirgan, Omar A; Graziano, James J; Holmes, Evan M; Smider, Vaughn V

2013-03-15

Traditional immunization and display antibody discovery methods rely on competitive selection amongst a pool of antibodies to identify a lead. While this approach has led to many successful therapeutic antibodies, targets have been limited to proteins which are easily purified. In addition, selection driven discovery has produced a narrow range of antibody functionalities focused on high affinity antagonism. We review the current progress in developing arrayed protein libraries for screening-based, rather than selection-based, discovery. These single molecule per microtiter well libraries have been screened in multiplex formats against both purified antigens and directly against targets expressed on the cell surface. This facilitates the discovery of antibodies against therapeutically interesting targets (GPCRs, ion channels, and other multispanning membrane proteins) and epitopes that have been considered poorly accessible to conventional discovery methods. Copyright © 2013. Published by Elsevier Inc.

Useful field of view predicts driving in the presence of distracters.

PubMed

Wood, Joanne M; Chaparro, Alex; Lacherez, Philippe; Hickson, Louise

2012-04-01

The Useful Field of View (UFOV) test has been shown to be highly effective in predicting crash risk among older adults. An important question which we examined in this study is whether this association is due to the ability of the UFOV to predict difficulties in attention-demanding driving situations that involve either visual or auditory distracters. Participants included 92 community-living adults (mean age 73.6 ± 5.4 years; range 65-88 years) who completed all three subtests of the UFOV involving assessment of visual processing speed (subtest 1), divided attention (subtest 2), and selective attention (subtest 3); driving safety risk was also classified using the UFOV scoring system. Driving performance was assessed separately on a closed-road circuit while driving under three conditions: no distracters, visual distracters, and auditory distracters. Driving outcome measures included road sign recognition, hazard detection, gap perception, time to complete the course, and performance on the distracter tasks. Those rated as safe on the UFOV (safety rating categories 1 and 2), as well as those responding faster than the recommended cut-off on the selective attention subtest (350 msec), performed significantly better in terms of overall driving performance and also experienced less interference from distracters. Of the three UFOV subtests, the selective attention subtest best predicted overall driving performance in the presence of distracters. Older adults who were rated as higher risk on the UFOV, particularly on the selective attention subtest, demonstrated poorest driving performance in the presence of distracters. This finding suggests that the selective attention subtest of the UFOV may be differentially more effective in predicting driving difficulties in situations of divided attention which are commonly associated with crashes.

High mobility high efficiency organic films based on pure organic materials

DOEpatents

Salzman, Rhonda F [Ann Arbor, MI; Forrest, Stephen R [Ann Arbor, MI

2009-01-27

A method of purifying small molecule organic material, performed as a series of operations beginning with a first sample of the organic small molecule material. The first step is to purify the organic small molecule material by thermal gradient sublimation. The second step is to test the purity of at least one sample from the purified organic small molecule material by spectroscopy. The third step is to repeat the first through third steps on the purified small molecule material if the spectroscopic testing reveals any peaks exceeding a threshold percentage of a magnitude of a characteristic peak of a target organic small molecule. The steps are performed at least twice. The threshold percentage is at most 10%. Preferably the threshold percentage is 5% and more preferably 2%. The threshold percentage may be selected based on the spectra of past samples that achieved target performance characteristics in finished devices.

Photovoltaic performance of TiO2 electrode adsorbed with gardenia yellow purified by nonionic polymeric sorbent in dye-sensitized solar cells.

PubMed

Kwon, Oh Oun; Kim, Eui Jin; Lee, Jae Hyeok; Kim, Tae Young; Park, Kyung Hee; Kim, Sang Yook; Suh, Hwa Jin; Lee, Hyo Jung; Lee, Jae Wook

2015-02-05

To improve the photovoltaic conversion efficiency in dye-sensitized solar cells (DSSCs), TiO2 electrode adsorbed with gardenia yellow purified by nonionic polymeric sorbent was successfully formulated on nanoporous TiO2 surface. Adsorption and desorption properties of crude gardenia yellow solution on a macroporous resin, XAD-1600, were investigated to purify gardenia yellow because of its strong adsorption and desorption abilities as well as high selectivity. To this end, adsorption equilibrium and kinetic data were measured and fitted using adsorption isotherms and kinetic models. Adsorption and desorption breakthrough curves in a column packed with XAD-1600 resin was obtained to optimize the separation process of gardenia yellow. The photovoltaic performance of the photo-electrode adsorbed with the crude and purified gardenia yellow in DSSCs was compared from current-voltage measurements. The results showed that the photovoltaic conversion efficiency was highly dependent on how to separate and purify gardenia yellow as a photosensitizer. Copyright © 2014 Elsevier B.V. All rights reserved.

Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies.

PubMed

Rousselle, Marjolaine; Faivre, Nicolas; Ballenghien, Marion; Galtier, Nicolas; Nabholz, Benoit

2016-10-23

The fixation probability of a recessive beneficial mutation is increased on the X or Z chromosome, relative to autosomes, because recessive alleles carried by X or Z are exposed to selection in the heterogametic sex. This leads to an increased dN/dS ratio on sex chromosomes relative to autosomes, a pattern called the "fast-X" or "fast-Z" effect. Besides positive selection, the strength of genetic drift and the efficacy of purifying selection, which affect the rate of molecular evolution, might differ between sex chromosomes and autosomes. Disentangling the complex effects of these distinct forces requires the genome-wide analysis of polymorphism, divergence and gene expression data in a variety of taxa. Here we study the influence of hemizygosity of the Z chromosome in Maniola jurtina and Pyronia tithonus, two species of butterflies (Lepidoptera, Nymphalidae, Satyrinae). Using transcriptome data, we compare the strength of positive and negative selection between Z and autosomes accounting for sex-specific gene expression. We show that M. jurtina and P. tithonus do not experience a faster, but rather a slightly slower evolutionary rate on the Z than on autosomes. Our analysis failed to detect a significant difference in adaptive evolutionary rate between Z and autosomes, but comparison of male-biased, unbiased and female-biased Z-linked genes revealed an increased efficacy of purifying selection against recessive deleterious mutations in female-biased Z-linked genes. This probably contributes to the lack of fast-Z evolution of satyrines. We suggest that the effect of hemizygosity on the fate of recessive deleterious mutations should be taken into account when interpreting patterns of molecular evolution in sex chromosomes vs. autosomes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Background diet and fat type alters plasma lipoprotein response but not aortic cholesterol accumulation in F1B Golden Syrian hamsters.

PubMed

Dillard, Alice; Matthan, Nirupa R; Spartano, Nicole L; Butkowski, Ann E; Lichtenstein, Alice H

2013-12-01

Dietary modification alters plasma lipoprotein profiles and atherosclerotic lesion progression in humans and some animal models. Variability in response to diet induced atherosclerosis has been reported in hamsters. Assessed was the interaction between background diet composition and dietary fat type on aortic cholesterol accumulation, lipoprotein profiles, hepatic lipids and selected genes. F1B Golden Syrian hamsters (20/group) were fed (12 weeks) semi-purified or non-purified diets containing either 10 % (w/w) coconut oil or safflower oil and 0.15 % (w/w) cholesterol. The non-purified diets relative to semi-purified diets resulted in significantly higher TC (72 % [percent difference] and 38 %, coconut oil and safflower oil, respectively) and nHDL-C (84 and 61 %, coconut oil and safflower oil, respectively), and lower HDL-C (-47 and -45 %, coconut oil and safflower oil, respectively) concentrations. Plasma triacylglycerol concentrations in the hamsters fed the non-purified coconut oil-supplemented diets were three- to fourfold higher than non-purified safflower oil-supplemented, and both semi-purified diets. With the exception of HDL-C, a significant effect of fat type was observed in TC, nHDL-C and triacylglycerol (all P < 0.05) concentrations. Regardless of diet induced differences in lipoprotein profiles, there was no significant effect on aortic cholesterol accumulation. There was an inverse relationship between plasma nHDL-C and triacylglycerol, and hepatic cholesteryl ester content (P < 0.001). Diet induced differences in hepatic gene transcription (LDL receptor, apoB-100, microsomal transfer protein) were not reflected in protein concentrations. Although hamsters fed non-purified and/or saturated fatty acid-supplemented diets had more atherogenic lipoprotein profiles compared to hamsters fed semi-purified and/or polyunsaturated fatty acid-supplemented diets these differences were not reflected in aortic cholesterol accumulation.

CD-ROM Hardware Configurations: Selection and Design.

ERIC Educational Resources Information Center

Jaffe, Lee David; Watkins, Steven G.

1992-01-01

Presents selection and design considerations to help libraries make informed decisions about hardware configurations of CD-ROM systems. Highlights include CD-ROM configurations, including single drive workstations, daisychains, and jukeboxes; network configurations, including remote access; microcomputer features; CD-ROM drive selection; and…

Drive piston assembly for a valve actuator assembly

DOEpatents

Sun, Zongxuan

2010-02-23

A drive piston assembly is provided that is operable to selectively open a poppet valve. The drive piston assembly includes a cartridge defining a generally stepped bore. A drive piston is movable within the generally stepped bore and a boost sleeve is coaxially disposed with respect to the drive piston. A main fluid chamber is at least partially defined by the generally stepped bore, drive piston, and boost sleeve. First and second feedback chambers are at least partially defined by the drive piston and each are disposed at opposite ends of the drive piston. At least one of the drive piston and the boost sleeve is sufficiently configured to move within the generally stepped bore in response to fluid pressure within the main fluid chamber to selectively open the poppet valve. A valve actuator assembly and engine are also provided incorporating the disclosed drive piston assembly.

Electron nanoprobe induced oxidation: A simulation of direct-write purification

DOE PAGES

Fowlkes, J. D.; Geier, B.; Lewis, B. B.; ...

2015-06-01

Electron beam direct-write has recently taken a large step forward with the advent of methods to purify deposits. This development has opened the door for future direct-write device prototyping and editing. In one such approach, an additional beam scanning procedure removes carbonaceous impurities via oxidation from metal–carbon deposits (e.g., PtC 5) in the presence of H 2O or O 2 after deposition. So far, critical aspects of the oxidation reaction remain unclear; experiments reveal clearly that electron stimulated oxidation drives the process yet it is not understood why H 2O purifies by a bottom-up mechanism while O 2 purifies frommore » the top-down. The simulation results presented here suggest that the chemisorption of dissolved O 2 at buried Pt nanoparticle surfaces controls purification in the top-down case while both the high relative solubility coupled with weak physisorption of H 2O explains the bottom-up process. Crucial too is the role that the carbonaceous contaminant itself has on the dissolution and diffusion of O 2 and H 2O. The results pave the way for simulation driven experiments where (1) the transient densification of the deposit can be accounted for in the initial deposit design stage and (2) the deposition and purification steps can be combined.« less

Electron nanoprobe induced oxidation: A simulation of direct-write purification

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

Fowlkes, J. D.; Geier, B.; Lewis, B. B.

Electron beam direct-write has recently taken a large step forward with the advent of methods to purify deposits. This development has opened the door for future direct-write device prototyping and editing. In one such approach, an additional beam scanning procedure removes carbonaceous impurities via oxidation from metal–carbon deposits (e.g., PtC 5) in the presence of H 2O or O 2 after deposition. So far, critical aspects of the oxidation reaction remain unclear; experiments reveal clearly that electron stimulated oxidation drives the process yet it is not understood why H 2O purifies by a bottom-up mechanism while O 2 purifies frommore » the top-down. The simulation results presented here suggest that the chemisorption of dissolved O 2 at buried Pt nanoparticle surfaces controls purification in the top-down case while both the high relative solubility coupled with weak physisorption of H 2O explains the bottom-up process. Crucial too is the role that the carbonaceous contaminant itself has on the dissolution and diffusion of O 2 and H 2O. The results pave the way for simulation driven experiments where (1) the transient densification of the deposit can be accounted for in the initial deposit design stage and (2) the deposition and purification steps can be combined.« less

The stabilisation of purified, reconstituted P-glycoprotein by freeze drying with disaccharides.

PubMed

Heikal, Adam; Box, Karl; Rothnie, Alice; Storm, Janet; Callaghan, Richard; Allen, Marcus

2009-02-01

The drug efflux pump P-glycoprotein (P-gp) (ABCB1) confers multidrug resistance, a major cause of failure in the chemotherapy of tumours, exacerbated by a shortage of potent and selective inhibitors. A high throughput assay using purified P-gp to screen and characterise potential inhibitors would greatly accelerate their development. However, long-term stability of purified reconstituted ABCB1 can only be reliably achieved with storage at -80 degrees C. For example, at 20 degrees C, the activity of ABCB1 was abrogated with a half-life of <1 day. The aim of this investigation was to stabilise purified, reconstituted ABCB1 to enable storage at higher temperatures and thereby enable design of a high throughput assay system. The ABCB1 purification procedure was optimised to allow successful freeze drying by substitution of glycerol with the disaccharides trehalose or maltose. Addition of disaccharides resulted in ATPase activity being retained immediately following lyophilisation with no significant difference between the two disaccharides. However, during storage trehalose preserved ATPase activity for several months regardless of the temperature (e.g. 60% retention at 150 days), whereas ATPase activity in maltose purified P-gp was affected by both storage time and temperature. The data provide an effective mechanism for the production of resilient purified, reconstituted ABCB1.

Dynamic Analysis of Heavy Vehicle Medium Duty Drive Shaft Using Conventional and Composite Material

NASA Astrophysics Data System (ADS)

Kumar, Ashwani; Jain, Rajat; Patil, Pravin P.

2016-09-01

The main highlight of this study is structural and modal analysis of single piece drive shaft for selection of material. Drive shaft is used for torque carrying from vehicle transmission to rear wheel differential system. Heavy vehicle medium duty transmission drive shaft was selected as research object. Conventional materials (Steel SM45 C, Stainless Steel) and composite materials (HS carbon epoxy, E Glass Polyester Resin Composite) were selected for the analysis. Single piece composite material drive shaft has advantage over conventional two-piece steel drive shaft. It has higher specific strength, longer life, less weight, high critical speed and higher torque carrying capacity. The main criteria for drive shaft failure are strength and weight. Maximum modal frequency obtained is 919 Hz. Various harmful vibration modes (lateral vibration and torsional vibration) were identified and maximum deflection region was specified. For single-piece drive shaft the natural bending frequency should be higher because it is subjected to torsion and shear stress. Single piece drive shaft was modelled using Solid Edge and Pro-E. Finite Element Analysis was used for structural and modal analysis with actual running boundary condition like frictional support, torque and moment. FEA simulation results were validated with experimental literature results.

Conservation of Transcription Start Sites within Genes across a Bacterial Genus

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

Shao, Wenjun; Price, Morgan N.; Deutschbauer, Adam M.

Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected TSSs. Using high-resolution tiling microarrays and 5'-end RNA sequencing, we identified 2,531 TSSs in S. oneidensis MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved.more » Thirty percent of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated, and they tend to eliminate polar effects, which confirms that they are functional. In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) was significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function.« less

Reactive microglia drive tau pathology and contribute to the spreading of pathological tau in the brain

PubMed Central

Maphis, Nicole; Xu, Guixiang; Kokiko-Cochran, Olga N.; Jiang, Shanya; Cardona, Astrid; Ransohoff, Richard M.; Lamb, Bruce T.

2015-01-01

Pathological aggregation of tau is a hallmark of Alzheimer’s disease and related tauopathies. We have previously shown that the deficiency of the microglial fractalkine receptor (CX3CR1) led to the acceleration of tau pathology and memory impairment in an hTau mouse model of tauopathy. Here, we show that microglia drive tau pathology in a cell-autonomous manner. First, tau hyperphosphorylation and aggregation occur as early as 2 months of age in hTauCx3cr1−/− mice. Second, CD45+ microglial activation correlates with the spatial memory deficit and spread of tau pathology in the anatomically connected regions of the hippocampus. Third, adoptive transfer of purified microglia derived from hTauCx3cr1−/− mice induces tau hyperphosphorylation within the brains of non-transgenic recipient mice. Finally, inclusion of interleukin 1 receptor antagonist (Kineret®) in the adoptive transfer inoculum significantly reduces microglia-induced tau pathology. Together, our results suggest that reactive microglia are sufficient to drive tau pathology and correlate with the spread of pathological tau in the brain. PMID:25833819

Mesenchymal Inflammation Drives Genotoxic Stress in Hematopoietic Stem Cells and Predicts Disease Evolution in Human Pre-leukemia.

PubMed

Zambetti, Noemi A; Ping, Zhen; Chen, Si; Kenswil, Keane J G; Mylona, Maria A; Sanders, Mathijs A; Hoogenboezem, Remco M; Bindels, Eric M J; Adisty, Maria N; Van Strien, Paulina M H; van der Leije, Cindy S; Westers, Theresia M; Cremers, Eline M P; Milanese, Chiara; Mastroberardino, Pier G; van Leeuwen, Johannes P T M; van der Eerden, Bram C J; Touw, Ivo P; Kuijpers, Taco W; Kanaar, Roland; van de Loosdrecht, Arjan A; Vogl, Thomas; Raaijmakers, Marc H G P

2016-11-03

Mesenchymal niche cells may drive tissue failure and malignant transformation in the hematopoietic system, but the underlying molecular mechanisms and relevance to human disease remain poorly defined. Here, we show that perturbation of mesenchymal cells in a mouse model of the pre-leukemic disorder Shwachman-Diamond syndrome (SDS) induces mitochondrial dysfunction, oxidative stress, and activation of DNA damage responses in hematopoietic stem and progenitor cells. Massive parallel RNA sequencing of highly purified mesenchymal cells in the SDS mouse model and a range of human pre-leukemic syndromes identified p53-S100A8/9-TLR inflammatory signaling as a common driving mechanism of genotoxic stress. Transcriptional activation of this signaling axis in the mesenchymal niche predicted leukemic evolution and progression-free survival in myelodysplastic syndrome (MDS), the principal leukemia predisposition syndrome. Collectively, our findings identify mesenchymal niche-induced genotoxic stress in heterotypic stem and progenitor cells through inflammatory signaling as a targetable determinant of disease outcome in human pre-leukemia. Copyright © 2016 Elsevier Inc. All rights reserved.

Electrochemical ion separation in molten salts

DOEpatents

Spoerke, Erik David; Ihlefeld, Jon; Waldrip, Karen; Wheeler, Jill S.; Brown-Shaklee, Harlan James; Small, Leo J.; Wheeler, David R.

2017-12-19

A purification method that uses ion-selective ceramics to electrochemically filter waste products from a molten salt. The electrochemical method uses ion-conducting ceramics that are selective for the molten salt cations desired in the final purified melt, and selective against any contaminant ions. The method can be integrated into a slightly modified version of the electrochemical framework currently used in pyroprocessing of nuclear wastes.

Mutation Accumulation, Soft Selection and the Middle-Class Neighborhood

PubMed Central

Moorad, Jacob A.; Hall, David W.

2009-01-01

The “middle-class neighborhood” is a breeding design intended to allow new mutations to accumulate by lessening the effects of purifying selection through the elimination of among-line fitness variation. We show that this design effectively applies soft selection to the experimental population, potentially causing biased estimates of mutational effects if social effects contribute to fitness. PMID:19448272

Phylogeny and evolution of Newcastle disease virus genotypes isolated in Asia during 2008-2011.

PubMed

Ebrahimi, Mohammad Majid; Shahsavandi, Shahla; Moazenijula, Gholamreza; Shamsara, Mahdi

2012-08-01

The full-length fusion (F) genes of 51 Newcastle disease (ND) strains isolated from chickens in Asia during the period 2008-2011 were genetically analyzed. Phylogenetic analysis showed that genotype VII of NDV still predominant in the domestic poultry of Asia. The sub-genotype VIIb circulated in the Iran and Indian sub-continent countries, whereas VIId sub-genotype existed in Far East countries. The non-synonymous to synonymous substitutions ratio was calculated 0.27 for VIId sub-genotype and 0.51 for VIIb sub-genotype indicates purifying/stabilizing selection which resulted in a low evolution rate in F gene of VIIb sub-genotype. There is evidence of localized positive selection when comparing these sub-genotypes protein sequences. Five codons in F gene of ND viruses had a posterior probability >90% using the Bayesian method, indicating these sites were under positive selection. To identify sites under positive selection; amino acid substitution classified depends on their radicalism and neutrality. The results indicate that although most positions were under purifying selection and can be eliminated, a few positions located in sub-genotype specific regions were subject to positive selection.

New Instrumentation for Phase Partitioning

NASA Technical Reports Server (NTRS)

Harris, J. M.

1985-01-01

Cells and molecules can be purified by partitioning between the two immiscible liquid phases formed by aqueous solutions of poly/ethylene glycol and dextran. Such purification can be more selective, higher yielding, and less destructive to sensitive biological materials than other available techniques. Earth's gravitational field is a hindering factor as it causes sedimentation of particles to be purified and shear-induced particle randomization. The present proposal is directed toward developing new instrumentation for performing phase partitioning both on Earth and in microgravity.

How to maintain chain drives

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

Wright, J.L.

1992-06-18

Properly selected and maintained chain drives can be expected to give thousands of hours of reliable service. Selection is usually done just once. This paper reports on good maintenance which must be done regularly to keep the drive operating. An effective maintenance program for roller chain should include correct type and adequate amounts of lubrication, replacement of worn chains and sprockets, and elimination of drive interferences. It is important to set u a lubrication and inspection/correction schedule to ensure that all required maintenance is carried out.

Development of a 3-step straight-through purification strategy combining membrane adsorbers and resins.

PubMed

Hughson, Michael D; Cruz, Thayana A; Carvalho, Rimenys J; Castilho, Leda R

2017-07-01

The pressures to efficiently produce complex biopharmaceuticals at reduced costs are driving the development of novel techniques, such as in downstream processing with straight-through processing (STP). This method involves directly and sequentially purifying a particular target with minimal holding steps. This work developed and compared six different 3-step STP strategies, combining membrane adsorbers, monoliths, and resins, to purify a large, complex, and labile glycoprotein from Chinese hamster ovary cell culture supernatant. The best performing pathway was cation exchange chromatography to hydrophobic interaction chromatography to affinity chromatography with an overall product recovery of up to 88% across the process and significant clearance of DNA and protein impurities. This work establishes a platform and considerations for the development of STP of biopharmaceutical products and highlights its suitability for integration with single-use technologies and continuous production methods. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:931-940, 2017. © 2017 American Institute of Chemical Engineers.

Purification of Torpedo californica post-synaptic membranes and fractionation of their constituent proteins.

PubMed Central

Elliott, J; Blanchard, S G; Wu, W; Miller, J; Strader, C D; Hartig, P; Moore, H P; Racs, J; Raftery, M A

1980-01-01

A rapid methof for preparation of membrane fractions highly enriched in nicotinic acetylcholine receptor from Torpedo californica electroplax is described. The major step in this purification involves sucrose-density-gradient centrifugation in a reorienting rotor. Further purification of these membranes can be achieved by selective extraction of proteins by use of alkaline pH or by treatment with solutions of lithium di-idosalicylate. The alkali-treated membranes retain functional characteristics of the untreated membranes and in addition contain essentially only the four polypeptides (mol.wts. 40000, 50000, 60000 and 65000) characteristic of the receptor purified by affinity chromatography. Dissolution of the purified membranes or of the alkali-treated purified membranes in sodium cholate solution followed by sucrose-density-gradient centrifugation in the same detergent solution yields solubilized receptor preparations comparable with the most highly purified protein obtained by affinity-chromatographic procedures. Images Fig. 1. Fig. 2. Fig. 3. Fig. 5. Fig. 7. PLATE 1 PMID:7387629

Driving an Active Vibration Balancer to Minimize Vibrations at the Fundamental and Harmonic Frequencies

NASA Technical Reports Server (NTRS)

Holliday, Ezekiel S. (Inventor)

2014-01-01

Vibrations of a principal machine are reduced at the fundamental and harmonic frequencies by driving the drive motor of an active balancer with balancing signals at the fundamental and selected harmonics. Vibrations are sensed to provide a signal representing the mechanical vibrations. A balancing signal generator for the fundamental and for each selected harmonic processes the sensed vibration signal with adaptive filter algorithms of adaptive filters for each frequency to generate a balancing signal for each frequency. Reference inputs for each frequency are applied to the adaptive filter algorithms of each balancing signal generator at the frequency assigned to the generator. The harmonic balancing signals for all of the frequencies are summed and applied to drive the drive motor. The harmonic balancing signals drive the drive motor with a drive voltage component in opposition to the vibration at each frequency.

High-throughput protein concentration and buffer exchange: comparison of ultrafiltration and ammonium sulfate precipitation.

PubMed

Moore, Priscilla A; Kery, Vladimir

2009-01-01

High-throughput protein purification is a complex, multi-step process. There are several technical challenges in the course of this process that are not experienced when purifying a single protein. Among the most challenging are the high-throughput protein concentration and buffer exchange, which are not only labor-intensive but can also result in significant losses of purified proteins. We describe two methods of high-throughput protein concentration and buffer exchange: one using ammonium sulfate precipitation and one using micro-concentrating devices based on membrane ultrafiltration. We evaluated the efficiency of both methods on a set of 18 randomly selected purified proteins from Shewanella oneidensis. While both methods provide similar yield and efficiency, the ammonium sulfate precipitation is much less labor intensive and time consuming than the ultrafiltration.

Basic principles of variable speed drives

NASA Technical Reports Server (NTRS)

Loewenthal, S. H.

1973-01-01

An understanding of the principles which govern variable speed drive operation is discussed for successful drive application. The fundamental factors of torque, speed ratio, and power as they relate to drive selection are discussed. The basic types of variable speed drives, their operating characteristics and their applications are also presented.

Drugs and driving : a selected bibliography : supplement one.

DOT National Transportation Integrated Search

1978-01-01

This report presents a first supplement to Drugs and Driving: A : Selected Bibliography (HS - 802 188), a bibliography of literature : dealing with the relationship between drug use (other than alcohol alone) : and highway safety. This supplement bot...

Method of Controlling Steering of a Ground Vehicle

NASA Technical Reports Server (NTRS)

Guo, Raymond (Inventor); Atluri, Venkata Prasad (Inventor); Bluethmann, William J. (Inventor); Lee, Chunhao J. (Inventor); Vitale, Robert L. (Inventor); Dawson, Andrew D. (Inventor)

2016-01-01

A method of controlling steering of a vehicle through setting wheel angles of a plurality of modular electronic corner assemblies (eModules) is provided. The method includes receiving a driving mode selected from a mode selection menu. A position of a steering input device is determined in a master controller. A velocity of the vehicle is determined, in the master controller, when the determined position of the steering input device is near center. A drive mode request corresponding to the selected driving mode to the plurality of steering controllers is transmitted to the master controller. A required steering angle of each of the plurality of eModules is determined, in the master controller, as a function of the determined position of the steering input device, the determined velocity of the vehicle, and the selected first driving mode. The eModules are set to the respective determined steering angles.

Selection of pecan shell based activated carbons for removal of organic and inorganic impurities from simulated well-water

USDA-ARS?s Scientific Manuscript database

Activated carbons are a byproduct from pyrolysis and have value as a purifying agent. The effectiveness of activated carbons is dependent on feedstock selection and pyrolysis conditions that modify its surface properties. Therefore, pecan shell-based activated carbons (PSACs) were prepared by soakin...

Can Phlorotannins Purified Extracts Constitute a Novel Pharmacological Alternative for Microbial Infections with Associated Inflammatory Conditions?

PubMed Central

Lopes, Graciliana; Sousa, Carla; Silva, Luís R.; Pinto, Eugénia; Andrade, Paula B.; Bernardo, João; Mouga, Teresa; Valentão, Patrícia

2012-01-01

Bacterial and fungal infections and the emerging multidrug resistance are driving interest in fighting these microorganisms with natural products, which have generally been considered complementary to pharmacological therapies. Phlorotannins are polyphenols restricted to brown seaweeds, recognized for their biological capacity. This study represents the first research on the antibacterial, antifungal, anti-inflammatory and antioxidant activity of phlorotannins purified extracts, which were obtained from ten dominant brown seaweeds of the occidental Portuguese coast. Phlorotannins content was determined by the specific dimethoxybenzaldehyde (DMBA) method and a yield between 75 and 969 mg/Kg phloroglucinol units (dry matter) was obtained. Fucus spiralis ranked first, followed by three Cystoseira species. The anti-inflammatory potential of the purified extracts was assessed via inhibitory effect on nitric oxide (NO) production by lipopolysaccharide-stimulated RAW 264.7 macrophage cells, Cystoseira tamariscifolia being the one showing promising activity for the treatment of inflammation. NO scavenging ability was also addressed in cell free systems, F. spiralis being the species with highest capacity. The antimicrobial potential of the extracts was checked against five Gram-positive and four Gram-negative bacteria and three fungi strains, that commonly colonize skin and mucosa and are responsible for food contamination. The different extracts were more effective against Gram-positive bacteria, Staphylococcus epidermidis being the most susceptible species. Concerning antifungal activity, Trichophyton rubrum was the most sensitive species. Although the molecular mechanisms underlying these properties remain poorly understood, the results obtained turn phlorotannins purified extracts a novel and potent pharmacological alternative for the treatment of a wide range of microbial infections, which usually also present an inflammatory component. In addition to the biological properties demonstrated herein, phlorotannins extracts may also be preferred, in order to avoid side effects and allergic reactions commonly associated with synthetic drugs. PMID:22319609

mTOR pathway is activated in endothelial cells from patients with Takayasu arteritis and is modulated by serum immunoglobulin G.

PubMed

Hadjadj, Jérôme; Canaud, Guillaume; Mirault, Tristan; Samson, Maxime; Bruneval, Patrick; Régent, Alexis; Goulvestre, Claire; Witko-Sarsat, Véronique; Costedoat-Chalumeau, Nathalie; Guillevin, Loïc; Mouthon, Luc; Terrier, Benjamin

2018-06-01

Takayasu arteritis (TA) and GCA are large-vessel vasculitides characterized by vascular remodelling involving endothelial cells (ECs) and vascular smooth muscle cells. Mammalian target of rapamycin (mTOR) pathway has been involved in vascular remodelling. We hypothesized that the mTOR pathway was involved in the pathogenesis of large-vessel vasculitis. We used IF analysis on aortic and temporal artery biopsies from patients with TA and GCA to assess the involvement of the mTOR pathway and searched for antibodies targeting ECs in serum by IIF and cellular ELISA. We evaluated in vitro the effect of purified IgG from patients on mTOR pathway activation and cell proliferation. IF analyses on tissues revealed that both mTORC1 and mTORC2 are activated specifically in ECs from TA patients but not in ECs from GCA patients and healthy controls (HCs). Using IIF and ELISA, we observed higher levels of antibodies binding to ECs in TA patients compared with GCA patients and HCs. Using western blot, we demonstrated that purified IgG from TA patients caused mTORC1 activation in ECs, whereas this effect was not observed with purified IgG from GCA patients or HCs. Purified IgG from TA patients induced a significant EC proliferation compared with to GCA and HC IgG, and this effect was decreased after EC exposure with sirolimus, a specific mTOR inhibitor and PI3K inhibitor. Our results suggest that antibodies targeting ECs drive endothelial remodelling in TA through activation of the mTOR pathway, but not in GCA. Inhibition of the mTOR pathway could represent a therapeutic option in TA.

Automated high throughput microscale antibody purification workflows for accelerating antibody discovery

PubMed Central

Luan, Peng; Lee, Sophia; Paluch, Maciej; Kansopon, Joe; Viajar, Sharon; Begum, Zahira; Chiang, Nancy; Nakamura, Gerald; Hass, Philip E.; Wong, Athena W.; Lazar, Greg A.

2018-01-01

ABSTRACT To rapidly find “best-in-class” antibody therapeutics, it has become essential to develop high throughput (HTP) processes that allow rapid assessment of antibodies for functional and molecular properties. Consequently, it is critical to have access to sufficient amounts of high quality antibody, to carry out accurate and quantitative characterization. We have developed automated workflows using liquid handling systems to conduct affinity-based purification either in batch or tip column mode. Here, we demonstrate the capability to purify >2000 antibodies per day from microscale (1 mL) cultures. Our optimized, automated process for human IgG1 purification using MabSelect SuRe resin achieves ∼70% recovery over a wide range of antibody loads, up to 500 µg. This HTP process works well for hybridoma-derived antibodies that can be purified by MabSelect SuRe resin. For rat IgG2a, which is often encountered in hybridoma cultures and is challenging to purify via an HTP process, we established automated purification with GammaBind Plus resin. Using these HTP purification processes, we can efficiently recover sufficient amounts of antibodies from mammalian transient or hybridoma cultures with quality comparable to conventional column purification. PMID:29494273

Variability of selected nutrients and contaminants monitored in rodent diets: A 6-year study

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

Oller, W.L.; Kendall, D.C.; Greenman, D.L.

1989-01-01

The results are given from monitoring a commercial closed-formula cereal-based rodent diet (Purina 5010), two open-formula cereal-based diets (NIH-31 and NIH-07), and one purified diet (AIN-76) for selected nutrients and contaminants. The observed concentrations of nutrients (protein, fat, vitamin A, and thiamine) approximated the manufacturer specifications for closed-formula cereal diet, while the average concentrations of nutrients found in the open-formula cereal diets were well above the nominal concentrations. Nominal concentrations for these open-formula diets tended to be close to the minimum values that were observed. Except for protein levels, greater variation in nutrient concentrations was found in the purified dietmore » than in the cereal diets. Contaminants were generally much lower in the purified diet than in the cereal diets, but the variation of contaminants was about equal in the two types of diets. Open- and closed-formula cereal diets appear to be very similar to each other in the degree of variation of nutrients and contaminants. Cadmium, lead, and selenium are the constituents of greatest concern in assuring the quality of the rodent diets that were evaluated.« less

Effects on driving performance of interacting with an in-vehicle music player: a comparison of three interface layout concepts for information presentation.

PubMed

Mitsopoulos-Rubens, Eve; Trotter, Margaret J; Lenné, Michael G

2011-05-01

Interface design is an important factor in assessing the potential effects on safety of interacting with an in-vehicle information system while driving. In the current study, the layout of information on a visual display was manipulated to explore its effect on driving performance in the context of music selection. The comparative effects of an auditory-verbal (cognitive) task were also explored. The driving performance of 30 participants was assessed under both baseline and dual task conditions using the Lane Change Test. Concurrent completion of the music selection task with driving resulted in significant impairment to lateral driving performance (mean lane deviation and percentage of correct lane changes) relative to the baseline, and significantly greater mean lane deviation relative to the combined driving and the cognitive task condition. The magnitude of these effects on driving performance was independent of layout concept, although significant differences in subjective workload estimates and performance on the music selection task across layout concepts highlights that potential uncertainty regarding design use as conveyed through layout concept could be disadvantageous. The implications of these results for interface design and safety are discussed. Copyright © 2010 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Evolutionary characterization of hemagglutinin gene of H9N2 influenza viruses isolated from Asia.

PubMed

Shahsavandi, Shahla; Salmanian, Ali-Hatef; Ghorashi, Seyed Ali; Masoudi, Shahin; Ebrahimi, Mohammad Majid

2012-08-01

The full length hemagglutinin (HA) genes of 287 H9N2 AI strains isolated from chickens in Asia during the period 1994-2009 were genetically analyzed. Phylogenetic analysis showed that G1-like viruses circulated in the Middle East and Indian sub-continent countries, whereas other sublineages existed in Far East countries. It also revealed G1-like viruses with an average 96.7% identity clustered into two subgroups largely based on their time of isolation. The Ka/Ks ratio was calculated 0.34 for subgroup 1 and 0.57 for subgroup 2 indicates purifying/stabilizing selection, but despite this there is evidence of localized positive selection when comparing the subgroups 1 and 2 protein sequences. Five sites in HA H9N2 viruses had a posterior probability >0.5 using the Bayesian method, indicating these sites were under positive selection. These sites were found to be associated with the globular head region of HA. To identify sites under positive selection; amino acid substitution classified depends on their radicalism and neutrality. The results indicate that, although most positions in HAs were under purifying selection and can be eliminated, a few positions located in the antigenic regions and receptor binding sites were subject to positive selection. Copyright © 2011 Elsevier Ltd. All rights reserved.

Selection of Therapeutic H5N1 Monoclonal Antibodies Following IgVH Repertoire Analysis in Mice

PubMed Central

Gray, Sean A.; Moore, Margaret; VandenEkart, Emily J.; Roque, Richard P.; Bowen, Richard A.; Van Hoeven, Neal; Wiley, Steven R.; Clegg, Christopher H.

2016-01-01

The rapid rate of influenza virus mutation drives the emergence of new strains that inflict serious seasonal epidemics and less frequent, but more deadly, pandemics. While vaccination provides the best protection against influenza, its utility is often diminished by the unpredictability of new pathogenic strains. Consequently, efforts are underway to identify new antiviral drugs and monoclonal antibodies that can be used to treat recently infected individuals and prevent disease in vulnerable populations. Next Generation Sequencing (NGS) and the analysis of antibody gene repertoires is a valuable tool for Ab discovery. Here, we describe a technology platform for isolating therapeutic monoclonal antibodies (MAbs) by analyzing the IgVH repertoires of mice immunized with recombinant H5N1 hemagglutinin (rH5). As an initial proof of concept, 35 IgVH genes selected using a CDRH3 search algorithm, co-expressed in a murine IgG2a expression vector with a panel of germline murine kappa genes, and culture supernatants screened for antigen binding. Seventeen of the 35 IgVH MAbs (49%) bound rH5VN1203 in preliminary screens and 8 of 9 purified MAbs inhibited 3 heterosubtypic strains of H5N1 virus when assayed by HI, and 2 MAbs demonstrated prophylactic and therapeutic activity in virus-challenged mice. This is the first example in which an NGS discovery platform has been used to isolate anti-influenza MAbs with relevant therapeutic activity. PMID:27109194

Process for removal of water and silicon mu-oxides from chlorosilanes

DOEpatents

Tom, Glenn M.; McManus, James V.

1992-03-10

A scavenger composition having utility for removal of water and silicon mu-oxide impurities from chlorosilanes, such scavenger composition comprising: (a) a support; and (b) associated with the support, one or more compound(s) selected from the group consisting of compounds of the formula: R.sub.a-x MCl.sub.x wherein: M is a metal selected from the group consisting of the monovalent metals lithium, sodium, and potassium; the divalent metals magnesium, strontium, barium, and calcium; and the trivalent metal aluminum; R is alkyl; a is a number equal to the valency of metal M; and x is a number having a value of from 0 to a, inclusive; and wherein said compound(s) of the formula R.sub.a-x MCl.sub.x have been activated for impurity-removal service by a reaction scheme selected from those of the group consisting of: (i) reaction of such compound(s) with hydrogen chloride to form a first reaction product therefrom, followed by reaction of the first reaction product with a chlorosilane of the formula: SiH.sub.4-y Cl.sub.y, wherein y is a number having a value of from 1 to 3, inclusive; and (ii) reaction of such compound(s) with a chlorosilane of the formula: SiH.sub.4-y Cl.sub.y wherein y is a number having a value of 1 to 3, inclusive. A corresponding method of making the scavenger composition, and of purifying a chlorosilane which contains oxygen and silicon mu-oxide impurities, likewise are disclosed, together with a purifier apparatus, in which a bed of the scavenger composition is disposed. The composition, purification process, and purifier apparatus of the invention have utility in purifying gaseous chlorosilanes which are employed in the semiconductor industry as silicon source reagents for forming epitaxial silicon layers.

Composition, process, and apparatus, for removal of water and silicon mu-oxides from chlorosilanes

DOEpatents

Tom, Glenn M.; McManus, James V.

1991-10-15

A scavenger composition having utility for removal of water and silicon mu-oxide impurities from chlorosilanes, such scavenger composition comprising: (a) a support; and (b) associated with the support, one or more compound(s) selected from the group consisting of compounds of the formula: R.sub.a-x MCl.sub.x wherein: M is a metal selected from the group consisting of the monovalent metals lithium, sodium, and potassium; the divalent metals magnesium, strontium, barium, and calcium; and the trivalent metal aluminum; R is alkyl; a is a number equal to the valency of metal M; and x is a number having a value from 0 to a, inclusive; and wherein said compound(s) of the formula R.sub.a-x MCl.sub.x have been activated for impurity-removal service by a reaction scheme selected from those of the group consisting of: (i) reaction of such compound(s) with hydrogen chloride to form a first reaction product therefrom, followed by reaction of the first reaction product with a chlorosilane of the formula: SiH.sub.4"y Cl.sub.y, wherein y is a number having a value of from 1 to 3, inclusive; and (ii) reaction of such compound(s) with a chlorosilane of the formula: SiH.sub.4-y Cl.sub.y wherein y is a number having a value of 1 to 3, inclusive. A corresponding method of making the scavenger composition, and of purifying a chlorosilane which contains oxygen and silicon mu-oxide impurities, likewise are disclosed, together with a purifier apparatus, in which a bed of the scavenger composition is disposed. The composition, purification process, and purifier apparatus of the invention have utility in purifying gaseous chlorosilanes which are employed in the semiconductor industry as silicon source reagents for forming epitaxial silicon layers.

Purified phenolics from hydrothermal treatments of biomass: ability to protect sunflower bulk oil and model food emulsions from oxidation.

PubMed

Conde, Enma; Moure, Andrés; Domínguez, Herminia; Gordon, Michael H; Parajó, Juan Carlos

2011-09-14

The phenolic fractions released during hydrothermal treatment of selected feedstocks (corn cobs, eucalypt wood chips, almond shells, chestnut burs, and white grape pomace) were selectively recovered by extraction with ethyl acetate and washed with ethanol/water solutions. The crude extracts were purified by a relatively simple adsorption technique using a commercial polymeric, nonionic resin. Utilization of 96% ethanol as eluting agent resulted in 47.0-72.6% phenolic desorption, yielding refined products containing 49-60% w/w phenolics (corresponding to 30-58% enrichment with respect to the crude extracts). The refined extracts produced from grape pomace and from chestnut burs were suitable for protecting bulk oil and oil-in-water and water-in-oil emulsions. A synergistic action with bovine serum albumin in the emulsions was observed.

Bovicin HC5 inhibits wasteful amino acid degradation by mixed ruminal bacteria in vitro.

PubMed

Lima, Janaína R; Ribon, Andréa de O Barros; Russell, James B; Mantovani, Hilário C

2009-03-01

Streptococcus bovis HC5 produces a broad spectrum lantibiotic (bovicin HC5) that inhibits pure cultures of hyper ammonia-producing bacteria (HAB). Experiments were preformed to see if: (1) S. bovis HC5 cells could inhibit the deamination of amino acids by mixed ruminal bacteria taken directly from a cow, (2) semi-purified bovicin was as effective as S. bovis HC5 cells, and 3) semi-purified and the feed additive monensin were affecting the same types of ammonia-producing ruminal bacteria. Because purified and semi-purified bovicin HC5 was as effective as S. bovis HC5 cells, it appeared that bovicin HC5 was penetrating the cell membranes of HAB before it could be degraded by peptidases and proteinases. Mixed ruminal bacteria that were successively transferred and enriched nine times with trypticase did not become significantly more resistant to either bovicin HC5 (50 AU mL(-1)) or monensin (5 microM), and amplified rDNA restriction analysis indicated that bovicin HC5 and monensin appeared to be selecting against the same types of bacteria.

Purifying Selection Maintains Dosage-Sensitive Genes during Degeneration of the Threespine Stickleback Y Chromosome

PubMed Central

White, Michael A.; Kitano, Jun; Peichel, Catherine L.

2015-01-01

Sex chromosomes are subject to unique evolutionary forces that cause suppression of recombination, leading to sequence degeneration and the formation of heteromorphic chromosome pairs (i.e., XY or ZW). Although progress has been made in characterizing the outcomes of these evolutionary processes on vertebrate sex chromosomes, it is still unclear how recombination suppression and sequence divergence typically occur and how gene dosage imbalances are resolved in the heterogametic sex. The threespine stickleback fish (Gasterosteus aculeatus) is a powerful model system to explore vertebrate sex chromosome evolution, as it possesses an XY sex chromosome pair at relatively early stages of differentiation. Using a combination of whole-genome and transcriptome sequencing, we characterized sequence evolution and gene expression across the sex chromosomes. We uncovered two distinct evolutionary strata that correspond with known structural rearrangements on the Y chromosome. In the oldest stratum, only a handful of genes remain, and these genes are under strong purifying selection. By comparing sex-linked gene expression with expression of autosomal orthologs in an outgroup, we show that dosage compensation has not evolved in threespine sticklebacks through upregulation of the X chromosome in males. Instead, in the oldest stratum, the genes that still possess a Y chromosome allele are enriched for genes predicted to be dosage sensitive in mammals and yeast. Our results suggest that dosage imbalances may have been avoided at haploinsufficient genes by retaining function of the Y chromosome allele through strong purifying selection. PMID:25818858

Predicting Motor Vehicle Collisions in a Driving Simulator in Young Adults Using the Useful Field of View Assessment.

PubMed

McManus, Benjamin; Cox, Molly K; Vance, David E; Stavrinos, Despina

2015-01-01

Being involved in motor vehicle collisions is the leading cause of death in 1- to 34-year-olds, and risk is particularly high in young adults. The Useful Field of View (UFOV) task, a cognitive measure of processing speed, divided attention, and selective attention, has been shown to be predictive of motor vehicle collisions in older adults, but its use as a predictor of driving performance in a young adult population has not been investigated. The present study examined whether UFOV was a predictive measure of motor vehicle collisions in a driving simulator in a young adult population. The 3-subtest version of UFOV (lower scores measured in milliseconds indicate better performance) was administered to 60 college students. Participants also completed an 11-mile simulated drive to provide driving performance metrics. Findings suggested that subtests 1 and 2 suffered from a ceiling effect. UFOV subtest 3 significantly predicted collisions in the simulated drive. Each 30 ms slower on the subtest was associated with nearly a 10% increase in the risk of a simulated collision. Post hoc analyses revealed a small partially mediating effect of subtest 3 on the relationship between driving experience and collisions. The selective attention component of UFOV subtest 3 may be a predictive measure of crash involvement in a young adult population. Improvements in selective attention may be the underlying mechanism in how driving experience improves driving performance.

Cellular immune response in MDR-TB patients to different protein expression of MDR and susceptible Mycobacterium tuberculosis: Rv0147, a novel MDR-TB biomarker.

PubMed

Hadizadeh Tasbiti, Alireza; Yari, Shamsi; Siadat, Seyed Davar; Tabarsi, Payam; Saeedfar, Kayvan; Yari, Fatemeh

2018-02-01

Tuberculosis (TB) is a crucial public health problem with prevalence of multidrug resistant (MDR) rising. An accurate TB biomarker is urgently needed to monitor the response to treatment in patients with MDR tuberculosis. To analyze interaction between selected MDR-TB purified protein and immune cells, dendritic cells from MDR-TB patients and healthy subjects were stimulated by 55KDa protein fractions (Rv0147). The purified proteins identified by proteomic techniques (two-dimensional gel electrophoresis, mass spectrometry) and peptide sequences are known to bind a MHC class I alleles which are extracted from the Immune Epitope Database and Analysis Resource database ( www.iedb.org ). T cells were isolated from PBMC by negative selection and cells were cultured in RPMI-1640 at 37 °C and 5% CO 2 . Cell culture was assayed for cytokine IL-10 and INF-γ by ELISA. We found that INF-γ production was significantly (335 ± 35.5 pg/ml, P ˂ 0.05) upregulated after protein candidate (Rv0147) stimulation by dendritic cells from MDR-TB patients, whereas IL-10 production was greatly reduced compared with production in healthy subjects (212 ± 9.94 pg/ml, P ˂ 0.05). In fact, the purified protein, Rv0147, stimulated dendritic cells from MDR-TB patients, failed to produce IL-10 and directly stimulates INF-γ production by T cells. These results suggest that the purified protein, Rv0147, may stimulate Th1 type protective cytokine response in MDR-TB patients but not in normal subjects. The production of INF-γ but not IL-10 in the presence of purified protein, Rv0147, may be shifted to Th1 responses in MDR-TB patients and supports its potential as protein vaccine candidates against TB.

Biopotency of serine protease inhibitors from cowpea (Vigna unguiculata) seeds on digestive proteases and the development of Spodoptera littoralis (Boisduval).

PubMed

Abd El-latif, Ashraf Oukasha

2015-05-01

Serine protease inhibitors (PIs) have been described in many plant species and are universal throughout the plant kingdom, where trypsin inhibitors is the most common type. In the present study, trypsin and chymotrypsin inhibitory activity was detected in the seed flour extracts of 13 selected cultivars/accessions of cowpea. Two cowpea cultivars, Cream7 and Buff, were found to have higher trypsin and chymotrypsin inhibitory potential compared to other tested cultivars for which they have been selected for further purification studies using ammonium sulfate fractionation and DEAE-Sephadex A-25 column. Cream7-purified proteins showed two bands on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) corresponding to molecular mass of 17.10 and 14.90 kDa, while the purified protein from Buff cultivar showed a single band corresponding mass of 16.50 kDa. The purified inhibitors were stable at temperature below 60°C and were active at wide range of pH from 2 to 12. The kinetic analysis revealed noncompetitive type of inhibition for both inhibitors against both enzymes. The inhibitor constant (Ki ) values suggested high affinity between inhibitors and enzymes. Purified inhibitors were found to have deep and negative effects on the mean larval weight, larval mortality, pupation, and mean pupal weight of Spodoptera littoralis, where Buff PI was more effective than Cream7 PI. It may be concluded that cowpea PI gene(s) could be potential insect control protein for future studies in developing insect-resistant transgenic plants. © 2014 Wiley Periodicals, Inc.

Mutants of feline immunodeficiency virus resistant to 2',3'-dideoxy-2',3'-didehydrothymidine.

PubMed Central

Zhu, Y Q; Remington, K M; North, T W

1996-01-01

We selected mutants of feline immunodeficiency virus (FIV) that are resistant to 2',3'-dideoxy-2',3'-didehydrothymidine (d4T). Two mutants were selected in cultured cells with a stepwise increase in d4T concentration, resulting in mutants able to replicate in 100 microM d4T. These mutants were three- to sixfold more resistant to d4T than wild-type FIV. They were also cross-resistant to 3'-azido-3'-deoxythymidine (AZT), 3'-fluoro-2',3'-dideoxythymidine, 2',3'-dideoxycytidine, 2',3'-dideoxyinosine, and 9-(2-phosphonylmethoxyethyl)adenine, and they were highly resistant to phosphonoformic acid (PFA). Plaque-purified mutants were isolated from each of the mutant populations. The mutant phenotype was stable, because both of the plaque-purified mutants remained d4T resistant even after three passages in the absence of d4T. One of the plaque-purified mutants, designated D4R-3c, was further characterized. Compared with wild-type reverse transcriptase (RT), RT purified from D4R-3c was 3-fold resistant to inhibition by the 5'-triphosphate of d4T, 10-fold resistant to inhibition by the 5'-triphosphate of AZT, and 6-fold resistant to PFA. D4R-3c had a single point mutation in the RT-encoding region of the pol gene at position 2474, resulting in a Val to Ile mutation at codon 47 of the FIV RT. The role of this mutation in d4T resistance was confirmed by site-directed mutagenesis. PMID:8878567

Purification of diverse hemoglobins by metal salt precipitation.

PubMed

Zimmerman, Devon; Dienes, Jack; Abdulmalik, Osheiza; Elmer, Jacob J

2016-09-01

Although donated blood is the preferred material for transfusion, its limited availability and stringent storage requirements have motivated the development of blood substitutes. The giant extracellular hemoglobin (aka erythrocruorin) of the earthworm Lumbricus terrestris (LtEc) has shown promise as a blood substitute, but an efficient purification method for LtEc must be developed to meet the potential large demand for blood substitutes. In this work, an optimized purification process that uses divalent and trivalent metal salts to selectively precipitate human, earthworm, and bloodworm hemoglobin (HbA, LtEc, and GdHb, respectively) from crude solutions was developed. Although several metal ions were able to selectively precipitate LtEc, Zn(2+) and Ni(2+) provided the lowest heme oxidation and highest overall yield of LtEc. In contrast, Zn(2+) was the only metal ion that completely precipitated HbA and GdHb. Polyacrylamide gel electrophoresis (PAGE) analysis shows that metal precipitation removes several impurities to provide highly pure hemoglobin samples. Heme oxidation levels were relatively low for Zn(2+)-purified HbA and LtEc (2.4±1.3% and 5.3±2.1%, respectively), but slightly higher for Ni(2+)-purified LtEc (8.4±1.2%). The oxygen affinity and cooperativity of the precipitated samples are also identical to samples purified with tangential flow filtration (TFF) alone, indicating the metal precipitation does not significantly affect the function of the hemoglobins. Overall, these results show that hemoglobins from several different species can be highly purified using a combination of metal (Zn(2+)) precipitation and tangential flow filtration. Copyright © 2015 Elsevier Inc. All rights reserved.

Differential Contributions of Selective Attention and Sensory Integration to Driving Performance in Healthy Aging and Alzheimer's Disease.

PubMed

Venkatesan, Umesh M; Festa, Elena K; Ott, Brian R; Heindel, William C

2018-05-01

Patients with Alzheimer's disease (AD) demonstrate deficits in cross-cortical feature binding distinct from age-related changes in selective attention. This may have consequences for driving performance given its demands on multisensory integration. We examined the relationship of visuospatial search and binding to driving in patients with early AD and elderly controls (EC). Participants (42 AD; 37 EC) completed search tasks requiring either luminance-motion (L-M) or color-motion (C-M) binding, analogs of within and across visual processing stream binding, respectively. Standardized road test (RIRT) and naturalistic driving data (CDAS) were collected alongside clinical screening measures. Patients performed worse than controls on most cognitive and driving indices. Visual search and clinical measures were differentially related to driving behavior across groups. L-M search and Trail Making Test (TMT-B) were associated with RIRT performance in controls, while C-M binding, TMT-B errors, and Clock Drawing correlated with CDAS performance in patients. After controlling for demographic and clinical predictors, L-M reaction time significantly predicted RIRT performance in controls. In patients, C-M binding made significant contributions to CDAS above and beyond demographic and clinical predictors. RIRT and C-M binding measures accounted for 51% of variance in CDAS performance in patients. Whereas selective attention is associated with driving behavior in EC, cross-cortical binding appears most sensitive to driving in AD. This latter relationship may emerge only in naturalistic settings, which better reflect patients' driving behavior. Visual integration may offer distinct insights into driving behavior, and thus has important implications for assessing driving competency in early AD. (JINS, 2018, 24, 486-497).

Are selective serotonin reuptake inhibitors safe for drivers? What is the evidence?

PubMed

Ravera, Silvia; Ramaekers, Johannes G; de Jong-van den Berg, Lolkje T W; de Gier, Johan J

2012-05-01

Selective serotonin reuptake inhibitors (SSRIs) are widely used medications to treat several psychiatric diseases and, above all, depression. They seem to be as effective as older antidepressants but have a different adverse effect profile. Despite their favorable safety profile, little is known about their influence on traffic safety. To conduct a literature review to summarize the current evidence on the role of SSRIs in traffic safety, particularly concerning undesirable effects that could potentially impair fitness to drive, experimental and pharmacoepidemiologic studies on driving impairment, 2 existing categorization systems for driving-impairing medications, and the European legislative procedures for assessing fitness to drive before issuing a driver's license and driving under the influence of medicines. The article search was performed in the following electronic databases: MEDLINE, PsycINFO, ScienceDirect, and SafetyLit. The English-language scientific literature was searched using key words such as SSRIs and psychomotor performance, car crash or traffic accident, and adverse effects. For inclusion in this review, papers had to be full-text articles, refer to possible driving-related adverse effects, and be experimental or pharmacoepidemiologic studies on SSRIs and traffic accident risks. No restrictions concerning publication year were applied. Ten articles were selected as background information on driving-related adverse effects, and 15 articles were selected regarding experimental and pharmacoepidemiologic work. Regarding SSRI adverse effects, the most reported undesirable effects referring to driving impairment were anxiety, agitation, sleep disturbances, headache, increased risk of suicidal behavior, and deliberate self-harm. Regarding the remaining issues addressed in this article, inconsistencies were found between the outcomes of the selected experimental and epidemiologic studies and between the 2 existing categorization systems under evaluation. Some pitfalls of the current legislative scenario were identified as well. Based on the current evidence, it was concluded that more experimental and epidemiologic research is needed to elucidate the relationship between SSRI use and traffic safety. Furthermore, a revision of the existing categorization systems and harmonized European legislation in the field of medication use and driving were highly recommended. Copyright © 2012 Elsevier HS Journals, Inc. All rights reserved.

What Determines Limb Selection for Reaching?

ERIC Educational Resources Information Center

Helbig, Casi Rabb; Gabbard, Carl

2004-01-01

While motor dominance appears to drive limb selection for reaching movements at the midline and ipsilateral (dominant) side, this study examined the possible determinants associated with what drives the programming of movements in response to stimuli presented in contralateral space. Experiment 1 distinguished between object proximity and a…

Insights into recent and ancient trends in the co-evolution of Earth and life as revealed by microbial genomics

NASA Astrophysics Data System (ADS)

Anderson, R. E.; Huber, J. A.; Parsons, C.; Stüeken, E.

2017-12-01

Since the origin of life over 4 billion years ago, life has fundamentally altered the habitability of Earth. Similarly, the environment molds the evolutionary trajectory of life itself through natural selection. Microbial genomes retain a "memory" of the co-evolution of life and Earth and can be analyzed to better understand trends and events in both the recent and distant past. To examine evolutionary trends in the more recent past, we have used metagenomics analyses to investigate which environmental factors play the strongest role in driving the evolution of microbes in deep-sea hydrothermal vents, which are thought to have been important habitats in the earliest stages of life's evolution. We have shown that microbial populations in a deep, basalt-hosted system appear to be under stronger purifying selection than populations inhabiting a cooler serpentinizing system less than 20 km away, suggesting that environmental context and geochemistry have an important impact on evolutionary rates and trends. We also found evidence that viruses play an important role in driving evolution in these habitats. Changing environmental conditions may also effect long-term evolutionary trends in Earth's distant past, as revealed by comparative genomics. By reconciling phylogenetic trees for microbial species with trees of metabolic genes, we can determine approximately when crucial metabolic genes began to spread across the tree of life through horizontal gene transfer. Using these methods, we conducted an analysis of the relative timing of the spread of genes related to the nitrogen cycle. Our results indicate that the rate of horizontal gene transfer for important genes related to denitrification increased after the Great Oxidation Event, concurrent with geochemical evidence for increasing availability of nitrate, suggesting that the oxygenation of the atmosphere and surface ocean may have been an important determining factor for the spread of denitrification genes across the tree of life. In contrast, genes related to nitrogen fixation display much more consistent rates of horizontal gene transfer throughout Earth's history. Studies that couple genomics approaches with geochemistry have the potential to reveal insights into the co-evolution of life and Earth both in the recent and distant past.

Strong Purifying Selection at Synonymous Sites in D. melanogaster

PubMed Central

Lawrie, David S.; Messer, Philipp W.; Hershberg, Ruth; Petrov, Dmitri A.

2013-01-01

Synonymous sites are generally assumed to be subject to weak selective constraint. For this reason, they are often neglected as a possible source of important functional variation. We use site frequency spectra from deep population sequencing data to show that, contrary to this expectation, 22% of four-fold synonymous (4D) sites in Drosophila melanogaster evolve under very strong selective constraint while few, if any, appear to be under weak constraint. Linking polymorphism with divergence data, we further find that the fraction of synonymous sites exposed to strong purifying selection is higher for those positions that show slower evolution on the Drosophila phylogeny. The function underlying the inferred strong constraint appears to be separate from splicing enhancers, nucleosome positioning, and the translational optimization generating canonical codon bias. The fraction of synonymous sites under strong constraint within a gene correlates well with gene expression, particularly in the mid-late embryo, pupae, and adult developmental stages. Genes enriched in strongly constrained synonymous sites tend to be particularly functionally important and are often involved in key developmental pathways. Given that the observed widespread constraint acting on synonymous sites is likely not limited to Drosophila, the role of synonymous sites in genetic disease and adaptation should be reevaluated. PMID:23737754

Evolution of the Male-Determining Gene SRY Within the Cat Family Felidae

PubMed Central

King, V.; Goodfellow, P. N.; Wilkerson, A. J. Pearks; Johnson, W. E.; O'Brien, S. J.; Pecon-Slattery, J.

2007-01-01

In most placental mammals, SRY is a single-copy gene located on the Y chromosome and is the trigger for male sex determination during embryonic development. Here, we present comparative genomic analyses of SRY (705 bp) along with the adjacent noncoding 5′ flank (997 bp) and 3′ flank (948 bp) in 36 species of the cat family Felidae. Phylogenetic analyses indicate that the noncoding genomic flanks and SRY closely track species divergence. However, several inconsistencies are observed in SRY. Overall, the gene exhibits purifying selection to maintain function (ω = 0.815) yet SRY is under positive selection in two of the eight felid lineages. SRY has low numbers of nucleotide substitutions, yet most encode amino acid changes between species, and four different species have significantly altered SRY due to insertion/deletions. Moreover, fixation of nonsynonymous substitutions between sister taxa is not consistent and may occur rapidly, as in the case of domestic cat, or not at all over long periods of time, as observed within the Panthera lineage. The former resembles positive selection during speciation, and the latter purifying selection to maintain function. Thus, SRY evolution in cats likely reflects the different phylogeographic histories, selection pressures, and patterns of speciation in modern felids. PMID:17277366

Positive selection in the SLC11A1 gene in the family Equidae.

PubMed

Bayerova, Zuzana; Janova, Eva; Matiasovic, Jan; Orlando, Ludovic; Horin, Petr

2016-05-01

Immunity-related genes are a suitable model for studying effects of selection at the genomic level. Some of them are highly conserved due to functional constraints and purifying selection, while others are variable and change quickly to cope with the variation of pathogens. The SLC11A1 gene encodes a transporter protein mediating antimicrobial activity of macrophages. Little is known about the patterns of selection shaping this gene during evolution. Although it is a typical evolutionarily conserved gene, functionally important polymorphisms associated with various diseases were identified in humans and other species. We analyzed the genomic organization, genetic variation, and evolution of the SLC11A1 gene in the family Equidae to identify patterns of selection within this important gene. Nucleotide SLC11A1 sequences were shown to be highly conserved in ten equid species, with more than 97 % sequence identity across the family. Single nucleotide polymorphisms (SNPs) were found in the coding and noncoding regions of the gene. Seven codon sites were identified to be under strong purifying selection. Codons located in three regions, including the glycosylated extracellular loop, were shown to be under diversifying selection. A 3-bp indel resulting in a deletion of the amino acid 321 in the predicted protein was observed in all horses, while it has been maintained in all other equid species. This codon comprised in an N-glycosylation site was found to be under positive selection. Interspecific variation in the presence of predicted N-glycosylation sites was observed.

Quantification of quercetin glycosides in 6 onion cultivars and comparisons of hydrolysis-HPLC and spectrophotometric methods in measuring total quercetin concentrations.

PubMed

Yoo, Kil Sun; Lee, Eun Jin; Patil, Bhimanagouda S

2010-03-01

This study was performed to purify and quantify quercetin glycosides (QG) and aglycone (free) quercetin (Q) in 6 selected onion cultivars and to compare analytical approaches based on high-performance liquid chromatography (HPLC) and spectrophotometry for the quantification of total quercetin (TQ) concentrations. Individual mono- and di-glycoside Q compounds were purified using a semipreparative HPLC and identified by comparing spectral data and by confirming corresponding peaks of QG and Q after incomplete enzyme-hydrolysis. Purified QG were quantified as Q by enzyme-hydrolysis/HPLC. TQ concentrations obtained from 20 onion bulbs with enzyme-hydrolysis/HPLC, no-hydrolysis/HPLC, and a spectrophotometric method without prior hydrolysis were significantly correlated (r(2)= 0.99) and were about 15% higher, identical, or 10% less than those concentrations by a standard acid-hydrolysis/HPLC method, respectively. During enzyme-hydrolysis of onion extracts, progressive reduction of the QG and formation of the corresponding mono-glycosides and Q were monitored using an analytical HPLC. TQ ranged from 83 to 330 microg/g F.W. in 6 selected cultivars of long-day or short-day onions. Q3,4'G and Q4'G were the 2 major compounds and comprised approximately between 94% and 97% of TQ in onions.

Anticancer activity of bacteriophage T4 and its mutant HAP1 in mouse experimental tumour models.

PubMed

Dabrowska, Krystyna; Opolski, Adam; Wietrzyk, Joanna; Switala-Jelen, Kinga; Godlewska, Joanna; Boratynski, Janusz; Syper, Danuta; Weber-Dabrowska, Beata; Gorski, Andrzej

2004-01-01

Previously, we have shown the ability of the bacteriophage T4 and its substrain HAP1 (selected for a higher affinity to melanoma cells) to reveal antimetastatic activity in a mouse melanoma model. Here, we investigated the potential phage anticancer activity in primary tumour models. Mice were inoculated subcutaneously with B16 or LLC cells (collected from in vitro culture). Bacteriophages T4 and HAP1 were injected intraperitoneally daily (8 x 10(8)pfu/mouse, except the experiment concerning the dose-dependence). Treatment with purified preparations of bacteriophage T4 resulted in significant reduction of tumour size, the effect being dose-dependent. HAP1 was more effective than T4 and its activity was also dose-dependent. Parallel experiments with non-purified bacteriophage lysates resulted in significant stimulation of tumour growth. These data suggest that purified bacteriophages may inhibit tumour growth, a phenomenon with potentially important clinical implications in oncology.

[Study on extraction and purification technology of Hubei ophiopogon saponins].

PubMed

Lin, Yun-Han; Li, Chong-Ming; Li, Xiao-Dong; Xiang, Yang; Zhang, Ya-Qin; Zhang, Xiao-Cun; Liu, Xia

2013-05-01

To explore the extraction and purification technology of total saponins from the effective parts of Liriope spicata. Orthogonal design was used. Macroporous resin was selected to separate and purify total saponin from the effective parts of Liriope spicata. The process validation was conducted. The total saponins was determined by Ultraviolet Spectrophotometry. The optimal extraction conditions were as follows: 10 times the amount of ethanol (70%) for each occasion and hot reflux (3 x 2 h). Total saponins was purified by D101 macroporous resin. The concentration of eluting ethanol was 50% - 70%. Ethanol (70%) was selected as the best eluent. The result of process validation was consistent with the study. The process is simple and stable enough to significantly improve the extraction rate of the effective parts. The study can provide reference for the research and production of effective parts of traditional Chinese medicine such as Liriope spicata.

Host-Parasite Interactions and Purifying Selection in a Microsporidian Parasite of Honey Bees

PubMed Central

Huang, Qiang; Chen, Yan Ping; Wang, Rui Wu; Cheng, Shang; Evans, Jay D.

2016-01-01

To clarify the mechanisms of Nosema ceranae parasitism, we deep-sequenced both honey bee host and parasite mRNAs throughout a complete 6-day infection cycle. By time-series analysis, 1122 parasite genes were significantly differently expressed during the reproduction cycle, clustering into 4 expression patterns. We found reactive mitochondrial oxygen species modulator 1 of the host to be significantly down regulated during the entire infection period. Our data support the hypothesis that apoptosis of honey bee cells was suppressed during infection. We further analyzed genome-wide genetic diversity of this parasite by comparing samples collected from the same site in 2007 and 2013. The number of SNP positions per gene and the proportion of non-synonymous substitutions per gene were significantly reduced over this time period, suggesting purifying selection on the parasite genome and supporting the hypothesis that a subset of N. ceranae strains might be dominating infection. PMID:26840596

Host-Parasite Interactions and Purifying Selection in a Microsporidian Parasite of Honey Bees.

PubMed

Huang, Qiang; Chen, Yan Ping; Wang, Rui Wu; Cheng, Shang; Evans, Jay D

2016-01-01

To clarify the mechanisms of Nosema ceranae parasitism, we deep-sequenced both honey bee host and parasite mRNAs throughout a complete 6-day infection cycle. By time-series analysis, 1122 parasite genes were significantly differently expressed during the reproduction cycle, clustering into 4 expression patterns. We found reactive mitochondrial oxygen species modulator 1 of the host to be significantly down regulated during the entire infection period. Our data support the hypothesis that apoptosis of honey bee cells was suppressed during infection. We further analyzed genome-wide genetic diversity of this parasite by comparing samples collected from the same site in 2007 and 2013. The number of SNP positions per gene and the proportion of non-synonymous substitutions per gene were significantly reduced over this time period, suggesting purifying selection on the parasite genome and supporting the hypothesis that a subset of N. ceranae strains might be dominating infection.

Role of laccase from Coriolus versicolor MTCC-138 in selective oxidation of aromatic methyl group.

PubMed

Chaurasia, Pankaj Kumar; Singh, Sunil Kumar; Bharati, Shashi Lata

2014-01-01

Now a day, laccases are the most promising enzymes in the area of biotechnology and synthesis. One of the best applications of laccases is the selective oxidation of aromatic methyl group to aldehyde group. Such transformations are valuable because it is difficult to stop the reaction at aldehyde stage. Chemical methods used for such biotransformations areexpensive and give poor yields. But, the laccase-catalyzed biotransformations of such type are non-expensive and yield is excellent. Authors have used crude laccase obtained from the liquid culture growth medium of fungal strain Coriolus versicolor MTCC-138 for the biotransformations of toluene, 3-nitrotoluene, and 4-chlorotoluene to benzaldehyde, 3-nitrobenzaldehyde, and 4-chlorobenzaldehyde, respectively, instead of purified laccase because purification process requires much time and cost. This communication reports that crude laccase can also be used in the place of purified laccase as effective biocatalyst.

UNC Collaboratory Project: Overview

DTIC Science & Technology

1990-11-01

technical, and other expository documents. Crucial to our success has been the selection of driving problems whose solutions have been of significance not...systems, and with the growing necessity for "team science", we believe the time is right to select a new driving problem -- support for multiple...the WE computer system. The WE system includes sensors imbedded within it that record each users’ action These records include each menu selection

Evaluation of Kentucky's "You Drink and Drive. You Lose" campaign.

DOT National Transportation Integrated Search

2002-10-01

Kentucky was selected within the Southeast Region of the United States by the National Highway Traffic Safety Administration to conduct a comprehensive impaired driving campaign entitled "You Drink & Drive. You Lose". The campaign was conducted aroun...

Effects of Simulated Hypogravity and Diet on Estrous Cycling in Rats

NASA Technical Reports Server (NTRS)

Tou, Janet C.; Grindeland, Richard E.; Baer, Lisa A.; Wade, Charles E.

2003-01-01

Environmental factors can disrupt ovulatory cycles. The study objective was to determine the effect of diet and simulated hypogravity on rat estrous cycles. Age 50 d Sprague-Dawley rats were randomly assigned to he fed either a purified or chow diet. Only normal cycling rats were used. Experimental rats (n=9-10/group) were kept as ambulatory controls (AC) or subjected to 40 d simulated hypogravity using a disuse atrophy hindlimb suspension (HLS) model. There was no effect on estrous cycles of AC fed either diet. At day 18, HLS rats fed either diet, had lengthened estrous cycles due to prolonged diestrus. HLS rats fed purified diet also had reduced time in estrus. Plasma estradiol was reduced in HLS rats fed purified diet but there was no effect on progesterone. This may have occurred because blood was collected from rats in estrus. Urinary progesterone collected during initial HLS was elevated in rats fed purified diet. In AC, corticosterone was elevated in chow vs purified diet fed rats. Differences were particularly striking following the application of a stressor with HLS/chow-fed rats displaying an enhanced stress response. Results emphasize the importance of diet selection when measuring endocrine-sensitive endpoints. HLS is a useful model for investigating the effects of environment on reproduction and providing insight about the impact extreme environment such as spaceflight on female reproductive health.

CenH3 evolution reflects meiotic symmetry as predicted by the centromere drive model

PubMed Central

Zedek, František; Bureš, Petr

2016-01-01

The centromere drive model explaining rapid evolution of eukaryotic centromeres predicts higher frequency of positive selection acting on centromeric histone H3 (CenH3) in clades with asymmetric meiosis compared to the clades with only symmetric meiosis. However, despite the impression one might get from the literature, this key prediction of the centromere drive model has not only never been confirmed, but it has never been tested, because all the previous studies dealt only with the presence or absence instead of the frequency of positive selection. To provide evidence for or against different frequencies of positively selected CenH3 in asymmetrics and symmetrics, we have inferred the selective pressures acting on CenH3 in seventeen eukaryotic clades, including plants, animals, fungi, ciliates and apicomplexa, using codon-substitution models, and compared the inferred frequencies between asymmetrics and symmetrics in a quantitative manner. We have found that CenH3 has been evolving adaptively much more frequently in clades with asymmetric meiosis compared with clades displaying only symmetric meiosis which confirms the prediction of centromere drive model. Our findings indicate that the evolution of asymmetric meiosis required CenH3 to evolve adaptively more often to counterbalance the negative consequences of centromere drive. PMID:27629066

Characterizing on-road driving performance in individuals with traumatic brain injury who pass or fail an on-road driving assessment.

PubMed

Stolwyk, Renerus J; Charlton, Judith L; Ross, Pamela E; Bédard, Michel; Marshall, Shawn; Gagnon, Sylvain; Gooden, James R; Ponsford, Jennie L

2018-01-15

To characterise on-road driving performance in individuals with traumatic brain injury who fail on-road driving assessment, compared with both those who pass assessment and healthy controls, and the injury and cognitive factors associated with driving performance. Cross-sectional. Forty eight participants with traumatic brain injury (Age M = 40.50 SD = 14.62, 77% male, post-traumatic amnesia days M = 28.74 SD =27.68) and 48 healthy matched controls completed a standardised on-road driving assessment in addition to cognitive measures. Individuals with traumatic brain injury who passed on-road driving assessment performed no differently from controls while individuals with traumatic brain injury who failed the assessment demonstrated significantly worse driving performance relative to controls across a range of driving manoeuvres and error types including observation of on-road environment, speed control, gap selection, lane position, following distance and basic car control. Longer time post-injury and reduced visual perception were both significantly correlated with reduced driving skills. This exploratory study indicated that drivers with traumatic brain injury who failed on-road assessment demonstrated a heterogeneous pattern of impaired driving manoeuvres, characterised by skill deficits across both operational (e.g., basic car control and lane position) and tactical domains (e.g., following distance, gap selection, and observation) of driving. These preliminary findings can be used for implementation of future driving assessments and rehabilitation programs. Implications for rehabilitation Clinicians should be aware that the majority of individuals with traumatic brain injury were deemed fit to resume driving following formal on-road assessment, despite having moderate to very severe traumatic brain injuries. Drivers with traumatic brain injury who failed an on-road assessment demonstrated a heterogeneous pattern of impaired skills including errors with observation, speed regulation, gap selection, and vehicle control and accordingly had difficulty executing a diverse range of common driving manoeuvres. Comprehensive, formal on-road assessments, incorporating a range of skills, and manoeuvres, are needed to evaluate readiness to return to driving following traumatic brain injury. Individually tailored driver rehabilitation programs need to address these heterogeneous skill deficits to best support individuals to make a successful return to driving post-traumatic brain injury.

Selection and characterization of a mutant of feline immunodeficiency virus resistant to 2',3'-dideoxycytidine.

PubMed Central

Medlin, H K; Zhu, Y Q; Remington, K M; Phillips, T R; North, T W

1996-01-01

We have selected and plaque purified a mutant of feline immunodeficiency virus (FIV) that is resistant to 2',3'-dideoxycytidine (ddC). This mutant was selected in cultured cells in the continuous presence of 25 microM ddC. The mutant, designated DCR-5c, was fourfold resistant to ddC, threefold resistant to 2',3'-dideoxyinosine, and more than fourfold resistant to phosphonoformic acid. DCR-5c displayed little or no resistance to (-)-beta-2',3'-dideoxy-3'-thiacytidine, 3'-azido-3'-deoxythymidine, or 9-(2-phosphonylmethoxyethyl) adenine. Reverse transcriptase purified from DCR-5c was less susceptible to inhibition by ddCTP, phosphonoformic acid, ddATP, or azido-dTTP than the wild-type FIV reverse transcriptase. Sequence analysis of DCR-5c revealed a single base change (G to C at nucleotide 2342) in the reverse transcriptase-encoding region of FIV. This mutation results in substitution of His for Asp at codon 3 of FIV reverse transcriptase. The role of this mutation in ddC resistance was confirmed by site-directed mutagenesis. PMID:8849258

Absence of positive selection on CenH3 in Luzula suggests that holokinetic chromosomes may suppress centromere drive.

PubMed

Zedek, František; Bureš, Petr

2016-12-01

The centromere drive theory explains diversity of eukaryotic centromeres as a consequence of the recurrent conflict between centromeric repeats and centromeric histone H3 (CenH3), in which selfish centromeres exploit meiotic asymmetry and CenH3 evolves adaptively to counterbalance deleterious consequences of driving centromeres. Accordingly, adaptively evolving CenH3 has so far been observed only in eukaryotes with asymmetric meiosis. However, if such evolution is a consequence of centromere drive, it should depend not only on meiotic asymmetry but also on monocentric or holokinetic chromosomal structure. Selective pressures acting on CenH3 have never been investigated in organisms with holokinetic meiosis despite the fact that holokinetic chromosomes have been hypothesized to suppress centromere drive. Therefore, the present study evaluates selective pressures acting on the CenH3 gene in holokinetic organisms for the first time, specifically in the representatives of the plant genus Luzula (Juncaceae), in which the kinetochore formation is not co-localized with any type of centromeric repeat. PCR, cloning and sequencing, and database searches were used to obtain coding CenH3 sequences from Luzula species. Codon substitution models were employed to infer selective regimes acting on CenH3 in Luzula KEY RESULTS: In addition to the two previously published CenH3 sequences from L. nivea, 16 new CenH3 sequences have been isolated from 12 Luzula species. Two CenH3 isoforms in Luzula that originated by a duplication event prior to the divergence of analysed species were found. No signs of positive selection acting on CenH3 in Luzula were detected. Instead, evidence was found that selection on CenH3 of Luzula might have been relaxed. The results indicate that holokinetism itself may suppress centromere drive and, therefore, holokinetic chromosomes might have evolved as a defence against centromere drive. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Observation of hohlraum-wall motion with spectrally selective x-ray imaging at the National Ignition Facility

NASA Astrophysics Data System (ADS)

Izumi, N.; Meezan, N. B.; Divol, L.; Hall, G. N.; Barrios, M. A.; Jones, O.; Landen, O. L.; Kroll, J. J.; Vonhof, S. A.; Nikroo, A.; Jaquez, J.; Bailey, C. G.; Hardy, C. M.; Ehrlich, R. B.; Town, R. P. J.; Bradley, D. K.; Hinkel, D. E.; Moody, J. D.

2016-11-01

The high fuel capsule compression required for indirect drive inertial confinement fusion requires careful control of the X-ray drive symmetry throughout the laser pulse. When the outer cone beams strike the hohlraum wall, the plasma ablated off the hohlraum wall expands into the hohlraum and can alter both the outer and inner cone beam propagations and hence the X-ray drive symmetry especially at the final stage of the drive pulse. To quantitatively understand the wall motion, we developed a new experimental technique which visualizes the expansion and stagnation of the hohlraum wall plasma. Details of the experiment and the technique of spectrally selective x-ray imaging are discussed.

Observation of hohlraum-wall motion with spectrally selective x-ray imaging at the National Ignition Facility.

PubMed

Izumi, N; Meezan, N B; Divol, L; Hall, G N; Barrios, M A; Jones, O; Landen, O L; Kroll, J J; Vonhof, S A; Nikroo, A; Jaquez, J; Bailey, C G; Hardy, C M; Ehrlich, R B; Town, R P J; Bradley, D K; Hinkel, D E; Moody, J D

2016-11-01

The high fuel capsule compression required for indirect drive inertial confinement fusion requires careful control of the X-ray drive symmetry throughout the laser pulse. When the outer cone beams strike the hohlraum wall, the plasma ablated off the hohlraum wall expands into the hohlraum and can alter both the outer and inner cone beam propagations and hence the X-ray drive symmetry especially at the final stage of the drive pulse. To quantitatively understand the wall motion, we developed a new experimental technique which visualizes the expansion and stagnation of the hohlraum wall plasma. Details of the experiment and the technique of spectrally selective x-ray imaging are discussed.

Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs.

PubMed

Gonen, Serap; Jenko, Janez; Gorjanc, Gregor; Mileham, Alan J; Whitelaw, C Bruce A; Hickey, John M

2017-01-04

This paper uses simulation to explore how gene drives can increase genetic gain in livestock breeding programs. Gene drives are naturally occurring phenomena that cause a mutation on one chromosome to copy itself onto its homologous chromosome. We simulated nine different breeding and editing scenarios with a common overall structure. Each scenario began with 21 generations of selection, followed by 20 generations of selection based on true breeding values where the breeder used selection alone, selection in combination with genome editing, or selection with genome editing and gene drives. In the scenarios that used gene drives, we varied the probability of successfully incorporating the gene drive. For each scenario, we evaluated genetic gain, genetic variance [Formula: see text], rate of change in inbreeding ([Formula: see text]), number of distinct quantitative trait nucleotides (QTN) edited, rate of increase in favourable allele frequencies of edited QTN and the time to fix favourable alleles. Gene drives enhanced the benefits of genome editing in seven ways: (1) they amplified the increase in genetic gain brought about by genome editing; (2) they amplified the rate of increase in the frequency of favourable alleles and reduced the time it took to fix them; (3) they enabled more rapid targeting of QTN with lesser effect for genome editing; (4) they distributed fixed editing resources across a larger number of distinct QTN across generations; (5) they focussed editing on a smaller number of QTN within a given generation; (6) they reduced the level of inbreeding when editing a subset of the sires; and (7) they increased the efficiency of converting genetic variation into genetic gain. Genome editing in livestock breeding results in short-, medium- and long-term increases in genetic gain. The increase in genetic gain occurs because editing increases the frequency of favourable alleles in the population. Gene drives accelerate the increase in allele frequency caused by editing, which results in even higher genetic gain over a shorter period of time with no impact on inbreeding.

Method for refining contaminated iridium

DOEpatents

Heshmatpour, B.; Heestand, R.L.

1982-08-31

Contaminated iridium is refined by alloying it with an alloying agent selected from the group consisting of manganese and an alloy of manganese and copper, and then dissolving the alloying agent from the formed alloy to provide a purified iridium powder.

Sexual selection drives speciation in an Amazonian frog

USGS Publications Warehouse

Boul, K.E.; Funk, W.C.; Darst, C.R.; Cannatella, D.C.; Ryan, M.J.

2007-01-01

One proposed mechanism of speciation is divergent sexual selection, whereby divergence in female preferences and male signals results in behavioural isolation. Despite the appeal of this hypothesis, evidence for it remains inconclusive. Here, we present several lines of evidence that sexual selection is driving behavioural isolation and speciation among populations of an Amazonian frog (Physalaemus petersi). First, sexual selection has promoted divergence in male mating calls and female preferences for calls between neighbouring populations, resulting in strong behavioural isolation. Second, phylogenetic analysis indicates that populations have become fixed for alternative call types several times throughout the species' range, and coalescent analysis rejects genetic drift as a cause for this pattern, suggesting that this divergence is due to selection. Finally, gene flow estimated with microsatellite loci is an average of 30 times lower between populations with different call types than between populations separated by a similar geographical distance with the same call type, demonstrating genetic divergence and incipient speciation. Taken together, these data provide strong evidence that sexual selection is driving behavioural isolation and speciation, supporting sexual selection as a cause for speciation in the wild. ?? 2006 The Royal Society.

Detection and avoidance of a carnivore odor by prey

PubMed Central

Ferrero, David M.; Lemon, Jamie K.; Fluegge, Daniela; Pashkovski, Stan L.; Korzan, Wayne J.; Datta, Sandeep Robert; Spehr, Marc; Fendt, Markus; Liberles, Stephen D.

2011-01-01

Predator–prey relationships provide a classic paradigm for the study of innate animal behavior. Odors from carnivores elicit stereotyped fear and avoidance responses in rodents, although sensory mechanisms involved are largely unknown. Here, we identified a chemical produced by predators that activates a mouse olfactory receptor and produces an innate behavioral response. We purified this predator cue from bobcat urine and identified it to be a biogenic amine, 2-phenylethylamine. Quantitative HPLC analysis across 38 mammalian species indicates enriched 2-phenylethylamine production by numerous carnivores, with some producing >3,000-fold more than herbivores examined. Calcium imaging of neuronal responses in mouse olfactory tissue slices identified dispersed carnivore odor-selective sensory neurons that also responded to 2-phenylethylamine. Two prey species, rat and mouse, avoid a 2-phenylethylamine odor source, and loss-of-function studies involving enzymatic depletion of 2-phenylethylamine from a carnivore odor indicate it to be required for full avoidance behavior. Thus, rodent olfactory sensory neurons and chemosensory receptors have the capacity for recognizing interspecies odors. One such cue, carnivore-derived 2-phenylethylamine, is a key component of a predator odor blend that triggers hard-wired aversion circuits in the rodent brain. These data show how a single, volatile chemical detected in the environment can drive an elaborate danger-associated behavioral response in mammals. PMID:21690383

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation.

PubMed

Yang, Zhenzhen; Zhang, Yeting; Wafula, Eric K; Honaas, Loren A; Ralph, Paula E; Jones, Sam; Clarke, Christopher R; Liu, Siming; Su, Chun; Zhang, Huiting; Altman, Naomi S; Schuster, Stephan C; Timko, Michael P; Yoder, John I; Westwood, James H; dePamphilis, Claude W

2016-10-24

Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to be much less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-living Lindenbergia Following initial phylogenetic detection and an extensive validation procedure, 52 high-confidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence. Analyses of intron sequences in putative donor and recipient lineages provide evidence for integration of genomic fragments far more often than retro-processed RNA sequences. Purifying selection predominates in functionally transferred sequences, with a small fraction of adaptively evolving sites. HGT-acquired genes are preferentially expressed in the haustorium-the organ of parasitic plants-and are strongly biased in predicted gene functions, suggesting that expression products of horizontally acquired genes are contributing to the unique adaptive feeding structure of parasitic plants.

Probing intracellular motor protein activity using an inducible cargo trafficking assay.

PubMed

Kapitein, Lukas C; Schlager, Max A; van der Zwan, Wouter A; Wulf, Phebe S; Keijzer, Nanda; Hoogenraad, Casper C

2010-10-06

Although purified cytoskeletal motor proteins have been studied extensively with the use of in vitro approaches, a generic approach to selectively probe actin and microtubule-based motor protein activity inside living cells is lacking. To examine specific motor activity inside living cells, we utilized the FKBP-rapalog-FRB heterodimerization system to develop an in vivo peroxisomal trafficking assay that allows inducible recruitment of exogenous and endogenous kinesin, dynein, and myosin motors to drive specific cargo transport. We demonstrate that cargo rapidly redistributes with distinct dynamics for each respective motor, and that combined (antagonistic) actions of more complex motor combinations can also be probed. Of importance, robust cargo redistribution is readily achieved by one type of motor protein and does not require the presence of opposite-polarity motors. Simultaneous live-cell imaging of microtubules and kinesin or dynein-propelled peroxisomes, combined with high-resolution particle tracking, revealed that peroxisomes frequently pause at microtubule intersections. Titration and washout experiments furthermore revealed that motor recruitment by rapalog-induced heterodimerization is dose-dependent but irreversible. Our assay directly demonstrates that robust cargo motility does not require the presence of opposite-polarity motors, and can therefore be used to characterize the motile properties of specific types of motor proteins. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Plant P450s as versatile drivers for evolution of species-specific chemical diversity

PubMed Central

Hamberger, Björn; Bak, Søren

2013-01-01

The irreversible nature of reactions catalysed by P450s makes these enzymes landmarks in the evolution of plant metabolic pathways. Founding members of P450 families are often associated with general (i.e. primary) metabolic pathways, restricted to single copy or very few representatives, indicative of purifying selection. Recruitment of those and subsequent blooms into multi-member gene families generates genetic raw material for functional diversification, which is an inherent characteristic of specialized (i.e. secondary) metabolism. However, a growing number of highly specialized P450s from not only the CYP71 clan indicate substantial contribution of convergent and divergent evolution to the observed general and specialized metabolite diversity. We will discuss examples of how the genetic and functional diversification of plant P450s drives chemical diversity in light of plant evolution. Even though it is difficult to predict the function or substrate of a P450 based on sequence similarity, grouping with a family or subfamily in phylogenetic trees can indicate association with metabolism of particular classes of compounds. Examples will be given that focus on multi-member gene families of P450s involved in the metabolic routes of four classes of specialized metabolites: cyanogenic glucosides, glucosinolates, mono- to triterpenoids and phenylpropanoids. PMID:23297350

Extreme primary and secondary protein structure variability in the chimeric male-transmitted cytochrome c oxidase subunit II protein in freshwater mussels: Evidence for an elevated amino acid substitution rate in the face of domain-specific purifying selection

PubMed Central

2008-01-01

Background Freshwater unionoidean bivalves, and species representing two marine bivalve orders (Mytiloida and Veneroida), exhibit a mode of mtDNA inheritance involving distinct maternal (F) and paternal (M) transmission routes concomitant with highly divergent gender-associated mtDNA genomes. Additionally, male unionoidean bivalves have a ~550 bp 3' coding extension to the cox2 gene (Mcox2e), that is apparently absent from all other metazoan taxa. Results Our molecular sequence analyses of MCOX2e indicate that both the primary and secondary structures of the MCOX2e region are evolving much faster than other regions of the F and M COX2-COX1 gene junction. The near N-terminus ~2/3 of the MCOX2e region contains an interspecifically variable number of predicted transmembrane helices (TMH) and interhelical loops (IHL) whereas the C-terminus ~1/3 is relatively conserved and hydrophilic while containing conserved functional motifs. MCOX2e displays an overall pattern of purifying selection that leads to the preservation of TMH/IHL and C-terminus tail sub-regions. However, 14 amino acid positions in the MCOX2e TMH/IHL sub-region might be targeted by diversifying selection, each representing a site where there exists interspecific variation for the constituent amino acids residing in a TMH or IHL. Conclusion Our results indicate that Mcox2e is unique to unionoidean bivalves, likely the result of a single insertion event that took place over 65 MYA and that MCOX2e is functional. The predicted TMH number, length and position variability likely stems from substitution-based processes rather than the typically implicated insertion/deletion events. MCOX2e has relatively high rates of primary and secondary structure evolution, with some amino acid residues potentially subjected to site-specific positive selection, yet an overall pattern of purifying selection leading to the preservation of the TMH/IHL and hydrophilic C-terminus tail subregions. The more conserved C-terminus tail (relative to the TMH/IHL sub-region of MCOX2e) is likely biologically active because it contains functional motifs. The rapid evolution of primary and secondary structure in MCOX2e, combined with the action of both positive and purifying selection, provide supporting evidence for the hypothesis that MCOX2e has a novel reproductive function within unionoidean bivalves. All tolled, our data indicate that unionoidean bivalve MCOX2 is the first reported chimeric animal mtDNA-encoded protein. PMID:18513440

CONTROL ROD DRIVE MECHANISM FOR A NUCLEAR REACTOR

DOEpatents

Hawke, B.C.; Liederbach, F.J.; Lones, W.

1963-05-14

A lead-screw-type control rod drive featuring an electric motor and a fluid motor arranged to provide a selectably alternative driving means is described. The electric motor serves to drive the control rod slowly during normal operation, while the fluid motor, assisted by an automatic declutching of the electric motor, affords high-speed rod insertion during a scram. (AEC)

Genome-wide identification of the MADS-box transcription factor family in pear (Pyrus bretschneideri) reveals evolution and functional divergence.

PubMed

Wang, Runze; Ming, Meiling; Li, Jiaming; Shi, Dongqing; Qiao, Xin; Li, Leiting; Zhang, Shaoling; Wu, Jun

2017-01-01

MADS-box transcription factors play significant roles in plant developmental processes such as floral organ conformation, flowering time, and fruit development. Pear ( Pyrus ), as the third-most crucial temperate fruit crop, has been fully sequenced. However, there is limited information about the MADS family and its functional divergence in pear. In this study, a total of 95 MADS-box genes were identified in the pear genome, and classified into two types by phylogenetic analysis. Type I MADS-box genes were divided into three subfamilies and type II genes into 14 subfamilies. Synteny analysis suggested that whole-genome duplications have played key roles in the expansion of the MADS family, followed by rearrangement events. Purifying selection was the primary force driving MADS-box gene evolution in pear, and one gene pairs presented three codon sites under positive selection. Full-scale expression information for PbrMADS genes in vegetative and reproductive organs was provided and proved by transcriptional and reverse transcription PCR analysis. Furthermore, the PbrMADS11(12) gene, together with partners PbMYB10 and PbbHLH3 was confirmed to activate the promoters of the structural genes in anthocyanin pathway of red pear through dual luciferase assay. In addition, the PbrMADS11 and PbrMADS12 were deduced involving in the regulation of anthocyanin synthesis response to light and temperature changes. These results provide a solid foundation for future functional analysis of PbrMADS genes in different biological processes, especially of pigmentation in pear.

Genome-wide identification of the MADS-box transcription factor family in pear (Pyrus bretschneideri) reveals evolution and functional divergence

PubMed Central

Li, Jiaming; Shi, Dongqing; Qiao, Xin; Li, Leiting; Zhang, Shaoling

2017-01-01

MADS-box transcription factors play significant roles in plant developmental processes such as floral organ conformation, flowering time, and fruit development. Pear (Pyrus), as the third-most crucial temperate fruit crop, has been fully sequenced. However, there is limited information about the MADS family and its functional divergence in pear. In this study, a total of 95 MADS-box genes were identified in the pear genome, and classified into two types by phylogenetic analysis. Type I MADS-box genes were divided into three subfamilies and type II genes into 14 subfamilies. Synteny analysis suggested that whole-genome duplications have played key roles in the expansion of the MADS family, followed by rearrangement events. Purifying selection was the primary force driving MADS-box gene evolution in pear, and one gene pairs presented three codon sites under positive selection. Full-scale expression information for PbrMADS genes in vegetative and reproductive organs was provided and proved by transcriptional and reverse transcription PCR analysis. Furthermore, the PbrMADS11(12) gene, together with partners PbMYB10 and PbbHLH3 was confirmed to activate the promoters of the structural genes in anthocyanin pathway of red pear through dual luciferase assay. In addition, the PbrMADS11 and PbrMADS12 were deduced involving in the regulation of anthocyanin synthesis response to light and temperature changes. These results provide a solid foundation for future functional analysis of PbrMADS genes in different biological processes, especially of pigmentation in pear. PMID:28924499

Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements

PubMed Central

Szitenberg, Amir; Cha, Soyeon; Opperman, Charles H.; Bird, David M.; Blaxter, Mark L.; Lunt, David H.

2016-01-01

Abstract Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host’s genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways have been suggested to account for the disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power, however, because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long-term effects on TE evolution. Here, we test the long-term determinants of TE evolution by comparing 42 nematode genomes spanning over 500 million years of diversification. This analysis includes numerous transitions between life history states, and RNAi pathways, and evaluates if these forces are sufficiently persistent to affect the long-term evolution of TE loads in eukaryotic genomes. Although we demonstrate statistical power to detect selection, we find no evidence that variation in these factors influence genomic TE loads across extended periods of time. In contrast, the effects of genetic drift appear to persist and control TE variation among species. We suggest that variation in the tested factors are largely inconsequential to the large differences in TE content observed between genomes, and only by these large-scale comparisons can we distinguish long-term and persistent effects from transient or random changes. PMID:27566762

Apparatus for purifying arsine, phosphine, ammonia, and inert gases to remove Lewis acid and oxidant impurities therefrom

DOEpatents

Tom, Glenn M.; Brown, Duncan W.

1991-01-08

An apparatus for purifying a gaseous mixture comprising arsine, phosphine, ammonia, and/or inert gases, to remove Lewis acid and/or oxidant impurities therefrom, comprising a vessel containing a bed of a scavenger, the scavenger including a support having associated therewith an anion which is effective to remove such impurities, such anion being selected from one or more members of the group consisting of: (i) carbanions whose corresponding protonated compounds have a pK.sub.a value of from about 22 to about 36; and (ii) anions formed by reaction of such carbanions with the primary component of the mixture.

Ozone removal capability of a welding fume respirator containing activated charcoal.

PubMed

Johnston, A R; Dyrud, J F; Shih, Y T

1989-09-01

Development of air purifying respirators for protection against ozone has been slowed by concerns about oxidation of charcoal and other available sorbents. The suitability of a charcoal sorbent for low concentrations of ozone was evaluated as a part of the development of a half-mask air purifying respirator designed for welding fumes and ozone. Testing of the respirator confirmed that charcoal can be a suitable sorbent for low levels of ozone. Where the respirator is properly selected, fit tested, and worn, respirator use against welding fumes and ozone at concentrations not exceeding 10 times the permissible exposure limit had been recommended.

Selection of Human Antibody Fragments which Bind Novel Breast Tumor Antigens

DTIC Science & Technology

1996-09-01

OmniGene cycler. The products were gel C6.5 must occur rarely in the repertoire, since none purified, isolated from the gel using DEAE membranes, of 92...C6VHCDR3A, C6VHCDR3B, C6VHCDR3C, and minute) using a Hybaid OmniGene cycler. To introduce C6VHCDR3D. a Notl restriction site at the 3’ end of the scFv gene...34C for 20 30 sec, 55 *C for 30 sec and 72°C for 30 sec) using a Hybaid OmniGene cycler. The products were gel purified, isolated from the gel using

Effect of promoter driving selectable marker on corn transformation.

PubMed

Prakash, N Shiva; Prasad, V; Chidambram, Thillai P; Cherian, Shoba; Jayaprakash, T L; Dasgupta, Santanu; Wang, Qi; Mann, Michael T; Spencer, T Michael; Boddupalli, Raghava S

2008-08-01

Identification of an appropriate selection agent and its corresponding selectable marker gene is one of the first steps in establishing a transformation protocol for a given plant species. As the promoter controls expression level of the genes, the promoter driving the selectable marker gene can affect transformation. However, investigations into the direct effect of promoters driving selectable marker on transformation are lacking in the literature though many reports of relative strengths of promoters driving reporter genes like GUS or CAT or GFP are available. In the present study, we have compared rice Actin1 and CaMV.35S (commonly used promoters in monocotyledonous plant transformation) promoters driving nptII for their effectiveness in paromomycin selection of transgenic corn events. To enable statistically meaningful analysis of the results, a large sample size of nearly 5,000 immature embryos (explants) was employed producing approximately 1,250 independent events from each of the two constructs in four independent experiments. The rate of appearance of resistant calli and percentage of resistant calli recovered was higher with P-Os.Actin1/nptII/nos3' as compared to P-CaMV.35S/nptII/nos3' in all four experiments. There was no appreciable difference either in the frequency of plant regeneration or in the morphological characteristics of plants recovered from the two constructs. Although the escape rate trended lower with P-Os.Actin1 as compared to P-CaMV.35S, the recovery of low copy events was significantly higher with P-CaMV.35S. The higher transformation frequency with P-Os.Actin1 could be related to the strength of this promoter as compared to P-CaMV.35S in the explants and/or calli. Based on these results, we infer that the promoter driving the selectable marker is an important factor to be considered while establishing a high throughput transformation protocol as it could not only influence the transformation frequency but also the copy number of the transgene in the recovered transgenics.

Technical adequacy of bisulfite sequencing and pyrosequencing for detection of mitochondrial DNA methylation: Sources and avoidance of false-positive detection.

PubMed

Owa, Chie; Poulin, Matthew; Yan, Liying; Shioda, Toshi

2018-01-01

The existence of cytosine methylation in mammalian mitochondrial DNA (mtDNA) is a controversial subject. Because detection of DNA methylation depends on resistance of 5'-modified cytosines to bisulfite-catalyzed conversion to uracil, examined parameters that affect technical adequacy of mtDNA methylation analysis. Negative control amplicons (NCAs) devoid of cytosine methylation were amplified to cover the entire human or mouse mtDNA by long-range PCR. When the pyrosequencing template amplicons were gel-purified after bisulfite conversion, bisulfite pyrosequencing of NCAs did not detect significant levels of bisulfite-resistant cytosines (brCs) at ND1 (7 CpG sites) or CYTB (8 CpG sites) genes (CI95 = 0%-0.94%); without gel-purification, significant false-positive brCs were detected from NCAs (CI95 = 4.2%-6.8%). Bisulfite pyrosequencing of highly purified, linearized mtDNA isolated from human iPS cells or mouse liver detected significant brCs (~30%) in human ND1 gene when the sequencing primer was not selective in bisulfite-converted and unconverted templates. However, repeated experiments using a sequencing primer selective in bisulfite-converted templates almost completely (< 0.8%) suppressed brC detection, supporting the false-positive nature of brCs detected using the non-selective primer. Bisulfite-seq deep sequencing of linearized, gel-purified human mtDNA detected 9.4%-14.8% brCs for 9 CpG sites in ND1 gene. However, because all these brCs were associated with adjacent non-CpG brCs showing the same degrees of bisulfite resistance, DNA methylation in this mtDNA-encoded gene was not confirmed. Without linearization, data generated by bisulfite pyrosequencing or deep sequencing of purified mtDNA templates did not pass the quality control criteria. Shotgun bisulfite sequencing of human mtDNA detected extremely low levels of CpG methylation (<0.65%) over non-CpG methylation (<0.55%). Taken together, our study demonstrates that adequacy of mtDNA methylation analysis using methods dependent on bisulfite conversion needs to be established for each experiment, taking effects of incomplete bisulfite conversion and template impurity or topology into consideration.

Observation of hohlraum-wall motion with spectrally selective x-ray imaging at the National Ignition Facility

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

Izumi, N., E-mail: izumi2@llnl.gov; Meezan, N. B.; Divol, L.

The high fuel capsule compression required for indirect drive inertial confinement fusion requires careful control of the X-ray drive symmetry throughout the laser pulse. When the outer cone beams strike the hohlraum wall, the plasma ablated off the hohlraum wall expands into the hohlraum and can alter both the outer and inner cone beam propagations and hence the X-ray drive symmetry especially at the final stage of the drive pulse. To quantitatively understand the wall motion, we developed a new experimental technique which visualizes the expansion and stagnation of the hohlraum wall plasma. Details of the experiment and the techniquemore » of spectrally selective x-ray imaging are discussed.« less

Meiotic drive influences the outcome of sexually antagonistic selection at a linked locus.

PubMed

Patten, M M

2014-11-01

Most meiotic drivers, such as the t-haplotype in Mus and the segregation distorter (SD) in Drosophila, act in a sex-specific manner, gaining a transmission advantage through one sex although suffering only the fitness costs associated with the driver in the other. Their inheritance is thus more likely through one of the two sexes, a property they share with sexually antagonistic alleles. Previous theory has shown that pairs of linked loci segregating for sexually antagonistic alleles are more likely to remain polymorphic and that linkage disequilibrium accrues between them. I probe this similarity between drive and sexual antagonism and examine the evolution of chromosomes experiencing these selection pressures simultaneously. Reminiscent of previous theory, I find that: the opportunity for polymorphism increases for a sexually antagonistic locus that is physically linked to a driving locus; the opportunity for polymorphism at a driving locus also increases when linked to a sexually antagonistic locus; and stable linkage disequilibrium accompanies any polymorphic equilibrium. Additionally, I find that drive at a linked locus favours the fixation of sexually antagonistic alleles that benefit the sex in which drive occurs. Further, I show that under certain conditions reduced recombination between these two loci is selectively favoured. These theoretical results provide clear, testable predictions about the nature of sexually antagonistic variation on driving chromosomes and have implications for the evolution of genomic architecture. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Assessment of hemolytic activity, enzyme production and bacteriocin characterization of Bacillus subtilis LR1 isolated from the gastrointestinal tract of fish.

PubMed

Banerjee, Goutam; Nandi, Ankita; Ray, Arun Kumar

2017-01-01

In the present investigation, probiotic potential (antagonistic activity, enzyme production, hemolytic activity, biosafety, antibiotic sensitivity and bile tolerance level) of Bacillus subtilis LR1 was evaluated. Bacteriocin produced by the bacterial strain B. subtilis LR1 isolated from the gastrointestinal tract of Labeo rohita was purified and characterized. The molecular weight of the purified bacteriocin was ~50 kDa in 12 % Native PAGE and showed inhibitory activity against four fish pathogens such as Bacillus mycoides, Aeromonas salmonicida, Pseudomonas fluorescens and Aeromonas hydrophila. The purified bacteriocin was maximally active at temperature 40 °C and pH 7.0, while none of the tested surfactants affect the bacteriocin activity. Extracellular enzyme activity of the selected bacterial strain was also evaluated. Amylase activity was estimated to be highest (38.23 ± 1.15 µg of maltose liberated mg -1  protein ml -1 of culture filtrate) followed by cellulase and protease activity. The selected bacterium was sensitive to most of the antibiotics used in this experiment, can tolerate 0.25 % bile salt and non-hemolytic in nature. Finally, the efficiency of the proposed probiotic candidate was evaluated in in vivo condition. It was detected that the bacterial strain can effectively reduce bacterial pathogenicity in Indian major carps.

Development of a Novel Human scFv Against EGFR L2 Domain by Phage Display Technology.

PubMed

Rahbarnia, Leila; Farajnia, Safar; Babaei, Hossein; Majidi, Jafar; Veisi, Kamal; Khosroshahi, Shiva Ahdi; Tanomand, Asghar

2017-01-01

Epidermal growth factor receptor (EGFR) as a transmembrane tyrosine kinase receptor frequently overexpresses in tumors with epithelial origin. The L2 domain from extracellular part of EGFR is involved in ligand binding and the blockage of this domain prevents activation of related signaling pathways. This study was aimed to develop a novel human scFv against EGFR L2 domain as a promising target for cancer therapy. The L2 recombinant protein was purified and used for panning a human scFv phage library (Tomlinson I). In this study, a novel screening strategy was applied to select clones with high binding and enrichment of rare specific phage clones of the L2 protein. After five biopanning rounds several specific clones were isolated which among them one phage clone with high binding was purified for further analysis. The specific interaction of selected clone against target antigen was confirmed by ELISA and western blotting. Immunofluorescence staining showed that purified scFv binds to A431 cells surface, displaying EGFR surface receptor. In the present study, we isolated for the first time a novel human scFv against EGFR L2 domain. This study can be the groundwork for developing more effective diagnostic and therapeutic agents against EGFR overexpressing cancers using this novel human anti-L2 ScFv. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Molecular population genetics of the insulin/TOR signal transduction pathway: a network-level analysis in Drosophila melanogaster.

PubMed

Alvarez-Ponce, David; Guirao-Rico, Sara; Orengo, Dorcas J; Segarra, Carmen; Rozas, Julio; Aguadé, Montserrat

2012-01-01

The IT-insulin/target of rapamycin (TOR)-signal transduction pathway is a relatively well-characterized pathway that plays a central role in fundamental biological processes. Network-level analyses of DNA divergence in Drosophila and vertebrates have revealed a clear gradient in the levels of purifying selection along this pathway, with the downstream genes being the most constrained. Remarkably, this feature does not result from factors known to affect selective constraint such as gene expression, codon bias, protein length, and connectivity. The present work aims to establish whether the selective constraint gradient detected along the IT pathway at the between-species level can also be observed at a shorter time scale. With this purpose, we have surveyed DNA polymorphism in Drosophila melanogaster and divergence from D. simulans along the IT pathway. Our network-level analysis shows that DNA polymorphism exhibits the same polarity in the strength of purifying selection as previously detected at the divergence level. This equivalent feature detected both within species and between closely and distantly related species points to the action of a general mechanism, whose action is neither organism specific nor evolutionary time dependent. The detected polarity would be, therefore, intrinsic to the IT pathway architecture and function.

Efficient production of artificially designed gelatins with a Bacillus brevis system.

PubMed

Kajino, T; Takahashi, H; Hirai, M; Yamada, Y

2000-01-01

Artificially designed gelatins comprising tandemly repeated 30-amino-acid peptide units derived from human alphaI collagen were successfully produced with a Bacillus brevis system. The DNA encoding the peptide unit was synthesized by taking into consideration the codon usage of the host cells, but no clones having a tandemly repeated gene were obtained through the above-mentioned strategy. Minirepeat genes could be selected in vivo from a mixture of every possible sequence encoding an artificial gelatin by randomly ligating the mixed sequence unit and transforming it into Escherichia coli. Larger repeat genes constructed by connecting minirepeat genes obtained by in vivo selection were also stable in the expression host cells. Gelatins derived from the eight-unit and six-unit repeat genes were extracellularly produced at the level of 0.5 g/liter and easily purified by ammonium sulfate fractionation and anion-exchange chromatography. The purified artificial gelatins had the predicted N-terminal sequences and amino acid compositions and a solgel property similar to that of the native gelatin. These results suggest that the selection of a repeat unit sequence stable in an expression host is a shortcut for the efficient production of repetitive proteins and that it can conveniently be achieved by the in vivo selection method. This study revealed the possible industrial application of artificially designed repetitive proteins.

Cell selection and characterization of a novel human endothelial cell specific nanobody.

PubMed

Ahmadvand, Davoud; Rasaee, Mohammad J; Rahbarizadeh, Fatemeh; Kontermann, Roland E; Sheikholislami, Farzaneh

2009-05-01

Antibody-based targeting of angiogenesis and vascular targeting therapy of cancer are extremely attractive conceptually and open new important diagnostic and therapeutic opportunities. Compelling evidence suggests that CD105 represents an ideal target for anti-angiogenic therapy and its presence in solid tumor vasculature has prognostic value. Camelids produce functional antibodies devoid of light chains and constant heavy chain domain (CH1). Nanobodies, the antigen-binding fragments of such heavy chain antibodies, are therefore comprised in one single domain. The aim of this study was to explore the possibilities of using anti-endoglin nanobody as an angiogenesis inhibitor. The anti-CD105 nanobody (AR-86a) was isolated from immune library by selections on purified antigens and target cells. Immunocytochemistry and FACS analysis showed that the purified nanobody reacted specifically with human umbilical vein endothelial cells (HUVECs) but not with other cell lines such as MDA-MB-453, Mel III, T-47D, MCF-7, AGO and HT 29. Further, selected nanobody potently inhibited proliferation of human endothelial cells and formation of capillary-like structures. This selected high affinity anti-endoglin nanobody may offer high specificity towards tumors with reduced side effects, and may be less likely to elicit drug resistance compared to conventional therapy.

Parent-progeny sequencing indicates higher mutation rates in heterozygotes.

PubMed

Yang, Sihai; Wang, Long; Huang, Ju; Zhang, Xiaohui; Yuan, Yang; Chen, Jian-Qun; Hurst, Laurence D; Tian, Dacheng

2015-07-23

Mutation rates vary within genomes, but the causes of this remain unclear. As many prior inferences rely on methods that assume an absence of selection, potentially leading to artefactual results, we call mutation events directly using a parent-offspring sequencing strategy focusing on Arabidopsis and using rice and honey bee for replication. Here we show that mutation rates are higher in heterozygotes and in proximity to crossover events. A correlation between recombination rate and intraspecific diversity is in part owing to a higher mutation rate in domains of high recombination/diversity. Implicating diversity per se as a cause, we find an ∼3.5-fold higher mutation rate in heterozygotes than in homozygotes, with mutations occurring in closer proximity to heterozygous sites than expected by chance. In a genome that is a patchwork of heterozygous and homozygous domains, mutations occur disproportionately more often in the heterozygous domains. If segregating mutations predispose to a higher local mutation rate, clusters of genes dominantly under purifying selection (more commonly homozygous) and under balancing selection (more commonly heterozygous), might have low and high mutation rates, respectively. Our results are consistent with this, there being a ten times higher mutation rate in pathogen resistance genes, expected to be under positive or balancing selection. Consequently, we do not necessarily need to evoke extremely weak selection on the mutation rate to explain why mutational hot and cold spots might correspond to regions under positive/balancing and purifying selection, respectively.

Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga)

PubMed Central

Price, Trevor D.

2015-01-01

Low rates of sequence evolution associated with purifying selection can be interrupted by episodic changes in selective regimes. Visual pigments are a unique system in which we can investigate the functional consequences of genetic changes, therefore connecting genotype to phenotype in the context of natural and sexual selection pressures. We study the RH2 and RH1 visual pigments (opsins) across 22 bird species belonging to two ecologically convergent clades, the New World warblers (Parulidae) and Old World warblers (Phylloscopidae), and evaluate rates of evolution in these clades along with data from 21 additional species. We demonstrate generally slow evolution of these opsins: both Rh1 and Rh2 are highly conserved across Old World and New World warblers. However, Rh2 underwent a burst of evolution within the New World genus Setophaga, where it accumulated substitutions at 6 amino acid sites across the species we studied. Evolutionary analyses revealed a significant increase in dN/dS in Setophaga, implying relatively strong selective pressures to overcome long-standing purifying selection. We studied the effects of each substitution on spectral tuning and found they do not cause large spectral shifts. Thus substitutions may reflect other aspects of opsin function, such as those affecting photosensitivity and/or dark-light adaptation. Although it is unclear what these alterations mean for color perception, we suggest that rapid evolution is linked to sexual selection, given the exceptional plumage colour diversification in Setophaga. PMID:25827331

Influence of driving cycles on exhaust emissions and fuel consumption of gasoline passenger car in Bangkok.

PubMed

Nutramon, Tamsanya; Supachart, Chungpaibulpatana

2009-01-01

The influence of different driving cycles on their exhaust emissions and fuel consumption rate of gasoline passenger car was investigated in Bangkok based on the actual measurements obtained from a test vehicle driving on a standard chassis dynamometer. A newly established Bangkok driving cycle (BDC) and the European driving cycle (EDC) which is presently adopted as the legislative cycle for testing automobiles registered in Thailand were used. The newly developed BDC is constructed using the driving characteristic data obtained from the real on-road driving tests along selected traffic routes. A method for selecting appropriate road routes for real driving tests is also introduced. Variations of keyed driving parameters of BDC with different driving cycles were discussed. The results showed that the HC and CO emission factors of BDC are almost two and four times greater than those of EDC, respectively. Although the difference in the NOx emission factor is small, the value from BDC is still greater than that of EDC by 10%. Under BDC, the test vehicle consumes fuel about 25% more than it does under EDC. All these differences are mainly attributed to the greater proportion of idle periods and higher fluctuations of vehicle speed in the BDC cycle. This result indicated that the exhausted emissions and fuel consumption of vehicles obtained from tests under the legislative modal-type driving cycle (EDC) are significantly different from those actually produced under real traffic conditions especially during peak periods.

MC1R diversity in Northern Island Melanesia has not been constrained by strong purifying selection and cannot explain pigmentation phenotype variation in the region.

PubMed

Norton, Heather L; Werren, Elizabeth; Friedlaender, Jonathan

2015-10-19

Variation in human skin pigmentation evolved in response to the selective pressure of ultra-violet radiation (UVR). Selection to maintain darker skin in high UVR environments is expected to constrain pigmentation phenotype and variation in pigmentation loci. Consistent with this hypothesis, the gene MC1R exhibits reduced diversity in African populations from high UVR regions compared to low-UVR non-African populations. However, MC1R diversity in non-African populations that have evolved under high-UVR conditions is not well characterized. In order to test the hypothesis that MC1R variation has been constrained in Melanesians the coding region of the MC1R gene was sequenced in 188 individuals from Northern Island Melanesia. The role of purifying selection was assessed using a modified McDonald Kreitman's test. Pairwise FST was calculated between Melanesian populations and populations from the 1000 Genomes Project. The SNP rs2228479 was genotyped in a larger sample (n = 635) of Melanesians and tested for associations with skin and hair pigmentation. We observe three nonsynonymous and two synonymous mutations. A modified McDonald Kreitman's test failed to detect a significant signal of purifying selection. Pairwise FST values calculated between the four islands sampled here indicate little regional substructure in MC1R. When compared to African, European, East and South Asian populations, Melanesians do not exhibit reduced population divergence (measured as FST) or a high proportion of haplotype sharing with Africans, as one might expect if ancestral haplotypes were conserved across high UVR populations in and out of Africa. The only common nonsynonymous polymorphism observed, rs2228479, is not significantly associated with skin or hair pigmentation in a larger sample of Melanesians. The pattern of sequence diversity here does not support a model of strong selective constraint on MC1R in Northern Island Melanesia This absence of strong constraint, as well as the recent population history of the region, may explain the observed frequencies of the derived rs2228479 allele. These results emphasize the complex genetic architecture of pigmentation phenotypes, which are controlled by multiple, possibly interacting loci. They also highlight the role that population history can play in influencing phenotypic diversity in the absence of strong natural selection.

Air actuated clutch for four wheel drive vehicles

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

Clohessy, K.E.

1986-12-09

A control system is described for selectively engaging and disengaging a vehicle wheel and a vehicle drive mechanism comprising; a spindle having inside and outside rotative support surfaces, the spindle adapted to be mounted to a vehicle frame, an axle portion rotatably supported on the inside support surface, and drive means for selectively and rotatively driving the axle portion relative to the spindle; a wheel hub assembly adapted to carry a vehicle wheel, the hub assembly rotatively supported on the outside support surface of the spindle; a sealed expansion chamber defined in part by the spindle, the axle portion, themore » hub assembly and a movable wall carried by the hub assembly, venting means venting the outer side of the movable wall to atmospheric pressure, the clutch ring engaged by the movable wall for movement of the clutch ring with movement of the movable wall as induced by a pressure difference generated within the chamber, and pressurizing means for selectively pressurizing and depressurizing the expansion chamber to thereby selectively shift the clutch ring between the positions of interlocking the axle portion and hub assembly and unlocking the axle portion and hub assembly.« less

Human scFv antibodies (Afribumabs) against Africanized bee venom: Advances in melittin recognition.

PubMed

Pessenda, Gabriela; Silva, Luciano C; Campos, Lucas B; Pacello, Elenice M; Pucca, Manuela B; Martinez, Edson Z; Barbosa, José E

2016-03-15

Africanized Apis mellifera bees, also known as killer bees, have an exceptional defensive instinct, characterized by mass attacks that may cause envenomation or death. From the years 2000-2013, 77,066 bee accidents occurred in Brazil. Bee venom comprises several substances, including melittin and phospholipase A2 (PLA2). Due to the lack of antivenom for bee envenomation, this study aimed to produce human monoclonal antibody fragments (single chain fragment variable; scFv), by using phage display technology. These fragments targeted melittin and PLA2, the two major components of bee venom, to minimize their toxic effects in cases of mass envenomation. Two phage antibody selections were performed using purified melittin. As the commercial melittin is contaminated with PLA2, phages specific to PLA2 were also obtained during one of the selections. Specific clones for melittin and PLA2 were selected for the production of soluble scFvs, named here Afribumabs: prefix: afrib- (from Africanized bee); stem/suffix: -umab (fully human antibody). Afribumabs 1 and 2 were tested in in vitro and in vivo assays to assess their ability to inhibit the toxic actions of purified melittin, PLA2, and crude bee venom. Afribumabs reduced hemolysis caused by purified melittin and PLA2 and by crude venom in vitro and reduced edema formation in the paws of mice and prolonged the survival of venom-injected animals in vivo. These results demonstrate that Afribumabs may contribute to the production of the first non-heterologous antivenom treatment against bee envenomation. Such a treatment may overcome some of the difficulties associated with conventional immunotherapy techniques. Copyright © 2016 Elsevier Ltd. All rights reserved.

Expression and purification of recombinant human serum albumin from selectively terminable transgenic rice.

PubMed

Zhang, Qing; Yu, Hui; Zhang, Feng-zhen; Shen, Zhi-cheng

2013-10-01

Human serum albumin (HSA) is widely utilized for medical purposes and biochemical research. Transgenic rice has proved to be an attractive bioreactor for mass production of recombinant HSA (rHSA). However, transgene spread is a major environmental and food safety concern for transgenic rice expressing proteins of medical value. This study aimed to develop a selectively terminable transgenic rice line expressing HSA in rice seeds, and a simple process for recovery and purification of rHSA for economical manufacture. An HSA expression cassette was inserted into a T-DNA vector encoding an RNA interference (RNAi) cassette suppressing the CYP81A6 gene. This gene detoxifies the herbicide bentazon and is linked to the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) cassette which confers glyphosate tolerance. ANX Sepharose Fast Flow (ANX FF) anion exchange chromatography coupled with Butyl Sepharose High Performance (Butyl HP) hydrophobic interaction chromatography was used to purify rHSA. A transgenic rice line, HSA-84, was obtained with stable expression of rHSA of up to 0.72% of the total dry weight of the dehusked rice seeds. This line also demonstrated high sensitivity to bentazon, and thus could be killed selectively by a spray of bentazon. A two-step chromatography purification scheme was established to purify the rHSA from rice seeds to a purity of 99% with a recovery of 62.4%. Results from mass spectrometry and N-terminus sequencing suggested that the purified rHSA was identical to natural plasma-derived HSA. This study provides an alternative strategy for large-scale production of HSA with a built-in transgene safety control mechanism.

Solubilization conditions for bovine heart mitochondrial membranes allow selective purification of large quantities of respiratory complexes I, III, and V.

PubMed

Shimada, Satoru; Maeda, Shintaro; Hikita, Masahide; Mieda-Higa, Kaoru; Uene, Shigefumi; Nariai, Yukiko; Shinzawa-Itoh, Kyoko

2018-04-24

Ascertaining the structure and functions of mitochondrial respiratory chain complexes is essential to understanding the biological mechanisms of energy conversion; therefore, numerous studies have examined these complexes. A fundamental part of that research involves devising a method for purifying samples with good reproducibility; the samples obtained need to be stable and their constituents need to retain the same structure and functions they possess when in mitochondrial membranes. Submitochondrial bovine heart particles were isolated using differential centrifugation to adjust to a membrane concentration of 46.0% (w/v) or 31.5% (w/v) based on weight. After 0.7% (w/v) deoxycholic acid, 0.4% (w/v) decyl maltoside, and 7.2% (w/v) potassium chloride were added to the mitochondrial membranes, those membranes were solubilized. At a membrane concentration of 46%, complex V was selectively solubilized, whereas at a concentration of 31.5% (w/v), complexes I and III were solubilized. Two steps-sucrose density gradient centrifugation and anion-exchange chromatography on a POROS HQ 20 μm column-enabled selective purification of samples that retained their structure and functions. These two steps enabled complexes I, III, and V to be purified in two days with a high yield. Complexes I, III, and V were stabilized with n-decyl-β-D-maltoside. A total of 200 mg-300 mg of those complexes from one bovine heart (1.1 kg muscle) was purified with good reproducibility, and the complexes retained the same functions they possessed while in mitochondrial membranes. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Expression and purification of native and functional influenza A virus matrix 2 proton selective ion channel.

PubMed

Desuzinges Mandon, Elodie; Traversier, Aurélien; Champagne, Anne; Benier, Lorraine; Audebert, Stéphane; Balme, Sébastien; Dejean, Emmanuel; Rosa Calatrava, Manuel; Jawhari, Anass

2017-03-01

Influenza A virus displays one of the highest infection rates of all human viruses and therefore represents a severe human health threat associated with an important economical challenge. Influenza matrix protein 2 (M2) is a membrane protein of the viral envelope that forms a proton selective ion channel. Here we report the expression and native isolation of full length active M2 without mutations or fusions. The ability of the influenza virus to efficiently infect MDCK cells was used to express native M2 protein. Using a Calixarene detergents/surfactants based approach; we were able to solubilize most of M2 from the plasma membrane and purify it. The tetrameric form of native M2 was maintained during the protein preparation. Mass spectrometry shows that M2 was phosphorylated in its cytoplasmic tail (serine 64) and newly identifies an acetylation of the highly conserved Lysine 60. ELISA shows that solubilized and purified M2 was specifically recognized by M2 antibody MAB65 and was able to displace the antibody from M2 MDCK membranes. Using a bilayer voltage clamp measurement assay, we demonstrate a pH dependent proton selective ion channel activity. The addition of the M2 ion channel blocker amantadine allows a total inhibition of the channel activity, illustrating therefore the specificity of purified M2 activity. Taken together, this work shows the production and isolation of a tetrameric and functional native M2 ion channel that will pave the way to structural and functional characterization of native M2, conformational antibody development, small molecules compounds screening towards vaccine treatment. Copyright © 2016 Elsevier Inc. All rights reserved.

Characterization of polysaccharides with marked inhibitory effect on lipid accumulation in Pleurotus eryngii.

PubMed

Chen, Jingjing; Yong, Yangyang; Xing, Meichun; Gu, Yifan; Zhang, Zhao; Zhang, Shizhu; Lu, Ling

2013-09-12

Mushrooms have a great potential for the production of useful bioactive metabolites. To explore the bioactive compounds from edible mushrooms for interfering with the development of macrophage-derived foam cells, which is recognized as the hallmark of early atherosclerosis, eight types of mushrooms polysaccharides had been selected to be tested. Consequently, different mushrooms polysaccharides displayed diverse component profiles. Of polysaccharides that we tested, the Pleurotus eryngii polysaccharide had the strongest inhibitory effect on lipid accumulation. Furthermore, through fractionation of DEAE-52 and Sephadex G-100, the polysaccharide from P. eryngii had been successfully purified and identified. By the analysis of IR, GC, and HPLC, the purified polysaccharide was estimated to be 30-38 kDa for the average molecular weight with the monosaccharide composition mainly composed of D-types of mannose, glucose and galactose. Findings presented in this report firstly provide direct evidence, which links the purified polysaccharide moiety with the biological function in foam-cell model. Copyright © 2013 Elsevier Ltd. All rights reserved.

Human proinsulin C-peptide from a precursor overexpressed in Pichia pastoris.

PubMed

Huang, Yang-Bin; Li, Jiang; Gao, Xin; Sun, Jiu-Ru; Lu, Yi; Feng, Tao; Fei, Jian; Cui, Da-Fu; Xia, Qi-Chang; Ren, Jun; Zhang, You-Shang

2006-08-01

In this article we report the production of human proinsulin C-peptide with 31 amino acid residues from a precursor overexpressed in Pichia pastoris. A C-peptide precursor expression plasmid containing nine C-peptide genes in tandem was constructed and used to transform P. pastoris. Transformants with a high copy number of the C-peptide precursor gene integrated into the chromosome of P. pastoris were selected. In high-density fermentation in a 300 liter fermentor using a simple culture medium composed mainly of salt and methanol, the C-peptide precursor was overexpressed to a level of 2.28 g per liter. A simple procedure was established to purify the expression product from the culture medium. The purified C-peptide precursor was converted into C-peptide by trypsin and carboxypeptidase B joint digestion. The yield of C-peptide with a purity of 96% was 730 mg per liter of culture. The purified C-peptide was characterized by mass spectrometry, N- and C-terminal amino acid sequencing, and sodium dodecylsulfate-polyacrylamide gel electrophoresis.

Efficient syntheses of polyamine and polyamine amide voltage-sensitive calcium channel blockers: FTX-3.3 and sFTX-3.3.

PubMed

Moya, E; Blagbrough, I S

1996-02-01

Efficient syntheses of FTX-3.3 and sFTX-3.3, voltage-sensitive calcium channel blockers are described. These modified polyamines were prepared from selectively protected polyamines and purified on a practical scale.

Size-selective separation of polydisperse gold nanoparticles in supercritical ethane.

PubMed

Williams, Dylan P; Satherley, John

2009-04-09

The aim of this study was to use supercritical ethane to selectively disperse alkanethiol-stabilized gold nanoparticles of one size from a polydisperse sample in order to recover a monodisperse fraction of the nanoparticles. A disperse sample of metal nanoparticles with diameters in the range of 1-5 nm was prepared using established techniques then further purified by Soxhlet extraction. The purified sample was subjected to supercritical ethane at a temperature of 318 K in the pressure range 50-276 bar. Particles were characterized by UV-vis absorption spectroscopy, TEM, and MALDI-TOF mass spectroscopy. The results show that with increasing pressure the dispersibility of the nanoparticles increases, this effect is most pronounced for smaller nanoparticles. At the highest pressure investigated a sample of the particles was effectively stripped of all the smaller particles leaving a monodisperse sample. The relationship between dispersibility and supercritical fluid density for two different size samples of alkanethiol-stabilized gold nanoparticles was considered using the Chrastil chemical equilibrium model.

Determination of zearalenone and its metabolites in endometrial cancer by coupled separation techniques.

PubMed

Gadzała-Kopciuch, Renata; Cendrowski, Krzysztof; Cesarz, Anna; Kiełbasa, Paweł; Buszewski, Bogusław

2011-10-01

This study presents a selective method of isolation of zearalenone (ZON) and its metabolite, α-zearalenol (α-ZOL), in neoplastically changed human tissue by accelerated solvent and ultrasonic extractions using a mixture of acetonitrile/water (84/16% v/v) as the extraction solvent. Extraction effectiveness was determined through the selection of parameters (composition of the solvent mixture, temperature, pressure, number of cycles) with tissue contamination at the level of nanograms per gram. The produced acetonitrile/water extracts were purified, and analytes were enriched in columns packed with homemade molecularly imprinted polymers. Purified extracts were determined by liquid chromatography (LC) coupled with different detection systems (diode array detection--DAD and mass spectrometry--MS) involving the Ascentis RP-Amide as a stationary phase and gradient elution. The combination of UE-MISPE-LC (ultrasonic extraction--molecularly imprinted solid-phase extraction--liquid chromatography) produced high (R≈95-98%) and repeatable (RSD<3%) recovery values for ZON and α-ZOL. © The Author(s) 2011. This article is published with open access at Springerlink.com

Commercial Milk Enzyme-Linked Immunosorbent Assay (ELISA) Kit Reactivities to Purified Milk Proteins and Milk-Derived Ingredients.

PubMed

Ivens, Katherine O; Baumert, Joseph L; Taylor, Steve L

2016-07-01

Numerous commercial enzyme-linked immunosorbent assay (ELISA) kits exist to quantitatively detect bovine milk residues in foods. Milk contains many proteins that can serve as ELISA targets including caseins (α-, β-, or κ-casein) and whey proteins (α-lactalbumin or β-lactoglobulin). Nine commercially-available milk ELISA kits were selected to compare the specificity and sensitivity with 5 purified milk proteins and 3 milk-derived ingredients. All of the milk kits were capable of quantifying nonfat dry milk (NFDM), but did not necessarily detect all individual protein fractions. While milk-derived ingredients were detected by the kits, their quantitation may be inaccurate due to the use of different calibrators, reference materials, and antibodies in kit development. The establishment of a standard reference material for the calibration of milk ELISA kits is increasingly important. The appropriate selection and understanding of milk ELISA kits for food analysis is critical to accurate quantification of milk residues and informed risk management decisions. © 2016 Institute of Food Technologists®

Crude and purified proteasome activity assays are affected by type of microplate.

PubMed

Cui, Ziyou; Gilda, Jennifer E; Gomes, Aldrin V

2014-02-01

Measurement of proteasome activity is fast becoming a commonly used assay in many laboratories. The most common method to measure proteasome activity involves measuring the release of fluorescent tags from peptide substrates in black microplates. Comparisons of black plates used for measuring fluorescence with different properties show that the microplate properties significantly affect the measured activities of the proteasome. The microplate that gave the highest reading of trypsin-like activity of the purified 20S proteasome gave the lowest reading of chymotrypsin-like activity of the 20S proteasome. Plates with medium binding surfaces from two different companies showed an approximately 2-fold difference in caspase-like activity for purified 20S proteasomes. Even standard curves generated using free 7-amino-4-methylcoumarin (AMC) were affected by the microplate used. As such, significantly different proteasome activities, as measured in nmol AMC released/mg/min, were obtained for purified 20S proteasomes as well as crude heart and liver samples when using different microplates. The naturally occurring molecule betulinic acid activated the chymotrypsin-like proteasome activity in three different plates but did not affect the proteasome activity in the nonbinding surface microplate. These findings suggest that the type of proteasome activity being measured and sample type are important when selecting a microplate. Copyright © 2013 Elsevier Inc. All rights reserved.

Growth inhibitory and proapoptotic effects of l-asparaginase from Fusarium culmorum ASP-87 on human leukemia cells (Jurkat).

PubMed

Meghavarnam, Anil K; Salah, Maryam; Sreepriya, Meenakshisundaram; Janakiraman, Savitha

2017-06-01

The objective of this study was to evaluate the anticancer properties of l-asparaginase purified from fungal isolate Fusarium culmorum ASP-87 against human T-cell leukemia cell line (Jurkat). The growth inhibitory and proapoptotic effects of purified l-asparaginase on Jurkat cell lines were investigated by determining its influence on cell viability, colony formation, DNA fragmentation, and cell cycle progression. The results revealed that purified l-asparaginase showed significant decrease in cell survival with IC 50 value of 90 μg/mL (9 IU/mL). The enzyme inhibited colony formation and showed characteristic laddering pattern on agarose gel thereby confirming the induction of apoptosis. Further, cell cycle analysis revealed that the enzyme induced apoptotic cell death by arresting the growth of cells at G 2 -M phase. However, the enzyme did not elicit any toxic effects on human erythrocytes. l-asparaginase purified from F. culmorum ASP-87 showed significant and selective cytotoxic and apoptotic effects on human T-cell leukemic cells in dose-dependent manner. Results of the study give leads for the anticancer effects of fungal l-asparaginase and its potential usefulness in the chemotherapy of leukemia. © 2016 Société Française de Pharmacologie et de Thérapeutique.

[Cloning, expression and identification of functional fragment rC3B of human complement C3 in E. Coli].

PubMed

Gan, Hui; Zhou, Yong; Sun, Ping; Zhu, Xiao-Xia; Wang, Quan-Li; Zhan, Lin-Sheng

2007-08-01

This study was purposed to verify the binding part of human complement C3 to complement receptor III (CRIII) in monocytes, the peptide rC3B, including the binding-site, was expressed, purified and identified. rC3B, the binding part of human complement C3 to CRIII, was selected by computer-aided modeling and summarizing researches published. Then, rC3B gene fragment was amplified by PCR, and cloned into prokaryotic vector pQE30a. The fusion protein rC3B was expressed in E.coli M15 and purified by Ni(2+)-chelating affinity chromatography. The activity of rC3B was identified by Western blot and adherence assay with monocytes. The results showed that rC3B fragment was obtained, and a prokaryotic expression vector pQE30-rC3B was constructed. rC3B was efficiently expressed and purified. In Western blot, the target protein showed the activity of binding with C3 antibody, while the purified protein showed the activity of adherence with monocytes. It is concluded that the recombinant C3B was obtained and identified, and this study lay the basis for the further functional analysis of C3.

Photocatalytic air purifiers for indoor air: European standard and pilot room experiments.

PubMed

Costarramone, N; Cantau, C; Desauziers, V; Pécheyran, C; Pigot, T; Lacombe, S

2017-05-01

At the European level (CEN/TC386), some efforts are currently devoted to new standards for comparing the efficiency of commercial photocatalytic material/devices in various application fields. Concerning prototype or commercial indoor photocatalytic air purifiers designed for volatile organic compounds (VOC) abatement, the methodology is based on a laboratory airtight chamber. The photocatalytic function is demonstrated by the mineralization of a mixture of five VOCs. Experimental data were obtained for four selected commercial devices and three commercial materials: drop of VOC concentration, but also identification of secondary species (with special attention to formaldehyde), mineralization rates, and Clean Air Delivery Rate (CADR). With two efficient air purifiers, these laboratory experiments were compared to the results in two experimental rooms (35-40 m 3 ) where air pollution was introduced through wooden floor and furniture. The systems' ageing was also studied. The safety of the commercial products was also assessed by the determination of nanoparticle release. Standardized tests are useful to rank photocatalytic air purifiers and passive materials and to discard inefficient ones. A good correlation between the standard experiments and the experimental room experiments was found, even if in the latter case, the concentration of lower weight VOCs drops less quickly than that of heavier VOCs.

Overproduction and partial purification of the Norrie disease gene product, norrin, from a recombinant baculovirus.

PubMed

Shastry, Barkur S; Trese, Michael T

2003-12-05

Abnormal vascularization of the peripheral retina and retinal detachment are common clinical characteristics of Norrie disease (ND), familial exudative vitreoretinopathy, Coats' disease, and retinopathy of prematurity. Although little is known about the molecular basis of these diseases, studies have shown that all of these diseases are associated with mutations in the ND gene. In spite of this, little is known about norrin, its molecular mechanism of action, and its functional relationship with the development of abnormal retinal vasculature. To obtain a large quantity of norrin for structural and functional studies, we have overproduced it in insect cells. For this purpose, a cDNA fragment (869 bp) was isolated from a human retinal cDNA library by amplification and was cloned into an expression vector. The purified plasmid was co-transfected with wild-type linearized Bac-N-Blue DNA into S. frugiperda Sf21 insect cells. The recombinant virus plaques were purified and clones were selected based on the level of recombinant protein expressed in Sf21 cells infected with a purified recombinant virus. From these, a high-titer stock was generated and subsequently used to prepare a fused protein on a large scale. The protein was partially purified by the process of immobilized metal affinity chromatography and the use of ion exchange chromatography

The risk of a safety-critical event associated with mobile device use in specific driving contexts.

PubMed

Fitch, Gregory M; Hanowski, Richard J; Guo, Feng

2015-01-01

We explored drivers' mobile device use and its associated risk of a safety-critical event (SCE) in specific driving contexts. Our premise was that the SCE risk associated with mobile device use increases when the driving task becomes demanding. Data from naturalistic driving studies involving commercial motor vehicle drivers and light vehicle drivers were partitioned into subsets representative of specific driving contexts. The subsets were generated using data set attributes that included level of service and relation to junction. These attributes were selected based on exogenous factors known to alter driving task demands. The subsets were analyzed using a case-cohort approach, which was selected to complement previous investigations of mobile device SCE risk using naturalistic driving data. Both commercial motor vehicle and light vehicle drivers varied as to how much they conversed on a mobile device but did not vary their engagement in visual-manual subtasks. Furthermore, commercial motor vehicle drivers conversed less frequently as the driving task demands increased, whereas light vehicle drivers did not. The risk of an SCE associated with mobile device use was dependent on the subtask performed and the driving context. Only visual-manual subtasks were associated with an increased SCE risk, whereas conversing was associated with a decreased risk in some driving contexts. Drivers' engagement in mobile device subtasks varies by driving context. The SCE risk associated with mobile device use is dependent on the types of subtasks performed and the driving context. The findings of this exploratory study can be applied to the design of driver-vehicle interfaces that mitigate distraction by preventing visual-manual subtasks while driving.

Relating surfactant properties to activity and solubilization of the human adenosine a3 receptor.

PubMed

Berger, Bryan W; García, Roxana Y; Lenhoff, Abraham M; Kaler, Eric W; Robinson, Clifford R

2005-07-01

The effects of various surfactants on the activity and stability of the human adenosine A3 receptor (A3) were investigated. The receptor was expressed using stably transfected HEK293 cells at a concentration of 44 pmol functional receptor per milligram membrane protein and purified using over 50 different nonionic surfactants. A strong correlation was observed between a surfactant's ability to remove A3 from the membrane and the ability of the surfactant to remove A3 selectively relative to other membrane proteins. The activity of A3 once purified also correlates well with the selectivity of the surfactant used. The effects of varying the surfactant were much stronger than those achieved by including A3 ligands in the purification scheme. Notably, all surfactants that gave high efficiency, selectivity and activity fall within a narrow range of hydrophile-lipophile balance values. This effect may reflect the ability of the surfactant to pack effectively at the hydrophobic transmembrane interface. These findings emphasize the importance of identifying appropriate surfactants for a particular membrane protein, and offer promise for the development of rapid, efficient, and systematic methods to facilitate membrane protein purification.

High level of microsynteny and purifying selection affect the evolution of WRKY family in Gramineae.

PubMed

Jin, Jing; Kong, Jingjing; Qiu, Jianle; Zhu, Huasheng; Peng, Yuancheng; Jiang, Haiyang

2016-01-01

The WRKY gene family, which encodes proteins in the regulation processes of diverse developmental stages, is one of the largest families of transcription factors in higher plants. In this study, by searching for interspecies gene colinearity (microsynteny) and dating the age distributions of duplicated genes, we found 35 chromosomal segments of subgroup I genes of WRKY family (WRKY I) in four Gramineae species (Brachypodium, rice, sorghum, and maize) formed eight orthologous groups. After a stepwise gene-by-gene reciprocal comparison of all the protein sequences in the WRKY I gene flanking areas, highly conserved regions of microsynteny were found in the four Gramineae species. Most gene pairs showed conserved orientation within syntenic genome regions. Furthermore, tandem duplication events played the leading role in gene expansion. Eventually, environmental selection pressure analysis indicated strong purifying selection for the WRKY I genes in Gramineae, which may have been followed by gene loss and rearrangement. The results presented in this study provide basic information of Gramineae WRKY I genes and form the foundation for future functional studies of these genes. High level of microsynteny in the four grass species provides further evidence that a large-scale genome duplication event predated speciation.

Structure and evolution analysis of pollen receptor-like kinase in Zea mays and Arabidopsis thaliana.

PubMed

Wang, Dongxu; Wang, He; Irfan, Muhammad; Fan, Mingxia; Lin, Feng

2014-08-01

Receptor-like kinase (RLKs) is an important member in protein kinase family which is widely involved in plant growth, development and defense responses. It is significant to analyze the kinase structure and evolution of pollen RLKs in order to study their mechanisms. In our study, 64 and 73 putative pollen RLKs were chosen from maize and Arabidopsis. Phylogenetic analysis showed that the pollen RLKs were conservative and might had existed before divergence between monocot and dicot which were mainly concentrated in RLCK-VII and LRR-III two subfamilies. Chromosomal localization and gene duplication analysis showed the expansion of pollen RLKs were mainly caused by segmental duplication. By calculating Ka/Ks value of extracellular domain, intracellular domain and kinase domain in pollen RLKs, we found that the pollen RLKs duplicated genes had mainly experienced the purifying selection, while maize might have experienced weaker purifying selection. Meanwhile, extracellular domain might have experienced stronger diversifying selection than intracellular domain in both species. Estimation of duplication time showed that the duplication events of Arabidopsis have occurred approximately between 18 and 69 million years ago, compared to 0.67-170 million years ago of maize. Copyright © 2014 Elsevier Ltd. All rights reserved.

Calcium Channels: Structure and Function (Annals of the New York Academy of Sciences. Volume 560)

DTIC Science & Technology

1989-06-26

many protease inhibitors were used , we believe that proteolysis was a problem. We therefore modified our purification protocol and have obtained a...recover activity by selective combination of fractions were unsuccessful. Chemical Cross-Linking of [ 25 Jo-CgTX Cross-linking of w-CgTX derivatives using ... using the planar bilayer recording technique and by comparing ligand-dependent gating, ionic selectivity , and pharmacology of purified ryanodine

Detection of driver engagement in secondary tasks from observed naturalistic driving behavior.

PubMed

Ye, Mengqiu; Osman, Osama A; Ishak, Sherif; Hashemi, Bita

2017-09-01

Distracted driving has long been acknowledged as one of the leading causes of death or injury in roadway crashes. The focus of past research has been mainly on the impact of different causes of distraction on driving behavior. However, only a few studies attempted to address how some driving behavior attributes could be linked to the cause of distraction. In essence, this study takes advantage of the rich SHRP 2 Naturalistic Driving Study (NDS) database to develop a model for detecting the likelihood of a driver's involvement in secondary tasks from distinctive attributes of driving behavior. Five performance attributes, namely speed, longitudinal acceleration, lateral acceleration, yaw rate, and throttle position were used to describe the driving behavior. A model was developed for each of three selected secondary tasks: calling, texting, and passenger interaction. The models were developed using a supervised feed-forward Artificial Neural Network (ANN) architecture to account for the effect of inherent nonlinearity in the relationships between driving behavior and secondary tasks. The results show that the developed ANN models were able to detect the drivers' involvement in calling, texting, and passenger interaction with an overall accuracy of 99.5%, 98.1%, and 99.8%, respectively. These results show that the selected driving performance attributes were effective in detecting the associated secondary tasks with driving behavior. The results are very promising and the developed models could potentially be applied in crash investigations to resolve legal disputes in traffic accidents. Copyright © 2017 Elsevier Ltd. All rights reserved.

Designing a System for Computer-Assisted Instruction in Road Education: A First Evaluation.

ERIC Educational Resources Information Center

Garcia-Ros, Rafael; Montoro, Luis; Valero, Pedro; Bayarri, Salvador; Martinez, Tomas

1999-01-01

Describes SIVAS, a computer-based system for driver education based on visual simulation that was developed in Spain to support theoretical concepts about driving in driving schools. Explains how teachers can select pre-built scenarios related to driving lessons in order to make up a lecture. (Author/LRW)

Mobility systems activity for lunar rovers at MSFC

NASA Technical Reports Server (NTRS)

Jones, C. S., Jr.; Nola, F. J.

1971-01-01

The Apollo Lunar Roving Vehicle (LRV) mobility system is described. Special emphasis is given to the redundancy aspects and to the selection of the drive motors. A summary chart of the performance on the lunar surface during the Apollo 15 flight is included. An appendix gives details on some development work on high efficiency drive systems and compares these systems to the selected system.

Guidelines for developing a high-visibility enforcement campaign to reduce unsafe driving behaviors among drivers of passenger and commercial motor vehicles : a Selective Traffic Enforcement Program (STEP) based on the Ticketing Aggressive Cars and Trucks (TACT) pilot project

DOT National Transportation Integrated Search

2007-10-01

The goal of Selective Traffic Enforcement Programs (STEPs) is to induce motorists to drive safely. To achieve this goal, the STEP model combines intensive enforcement of a specific traffic safety law with extensive communication, education, and outre...

Selective Activation of Transcription by a Novel CCAAT Binding Factor

NASA Astrophysics Data System (ADS)

Maity, Sankar N.; Golumbek, Paul T.; Karsenty, Gerard; de Crombrugghe, Benoit

1988-07-01

A novel CCAAT binding factor (CBF) composed of two different subunits has been extensively purified from rat liver. Both subunits are needed for specific binding to DNA. Addition of this purified protein to nuclear extracts of NIH 3T3 fibroblasts stimulates transcription from several promoters including the α 2(I) collagen, the α 1(I) collagen, the Rous sarcoma virus long terminal repeat (RSV-LTR), and the adenovirus major late promoter. Point mutations in the CCAAT motif that show either no binding or a decreased binding of CBF likewise abolish or reduce activation of transcription by CBF. Activation of transcription requires, therefore, the specific binding of CBF to its recognition sites.

Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance.

PubMed

Morales, Hernán E; Pavlova, Alexandra; Joseph, Leo; Sunnucks, Paul

2015-06-01

Diversifying selection on metabolic pathways can reduce intraspecific gene flow and promote population divergence. An opportunity to explore this arises from mitonuclear discordance observed in an Australian bird Eopsaltria australis. Across >1500 km, nuclear differentiation is low and latitudinally structured by isolation by distance, whereas two highly divergent, parapatric mitochondrial lineages (>6.6% in ND2) show a discordant longitudinal geographic pattern and experience different climates. Vicariance, incomplete lineage sorting and sex-biased dispersal were shown earlier to be unlikely drivers of the mitonuclear discordance; instead, natural selection on a female-linked trait was the preferred hypothesis. Accordingly, here we tested for signals of positive, divergent selection on mitochondrial genes in E. australis. We used codon models and physicochemical profiles of amino acid replacements to analyse complete mitochondrial genomes of the two mitochondrial lineages in E. australis, its sister species Eopsaltria griseogularis, and outgroups. We found evidence of positive selection on at least five amino acids, encoded by genes of two oxidative phosphorylation pathway complexes NADH dehydrogenase (ND4 and ND4L) and cytochrome bc1 (cyt-b) against a background of widespread purifying selection on all mitochondrial genes. Three of these amino acid replacements were fixed in ND4 of the geographically most widespread E. australis lineage. The other two replacements were fixed in ND4L and cyt-b of the geographically more restricted E. australis lineage. We discuss whether this selection may reflect local environmental adaptation, a by-product of other selective processes, or genetic incompatibilities, and propose how these hypotheses can be tested in future. © 2015 John Wiley & Sons Ltd.

Electric Drive Study. Volume 1

DTIC Science & Technology

1987-12-21

CONDITIONER HIGH VOLTAGE DC ICONDITIONER 3 ,300-50 VOLT5), dCONTROL! Figure 5-4. Typical AC Drive System 20 system usable with an induction motor. The...controlling component in an AC drive is the motor power conditioner . This component changes the high voltage DC power to controlled AC power of...selected voltage and frequency which is applied to the drive motors. Since the vehicle gains stored energy as it is accelerated, the motor power conditioner

40 CFR 1065.307 - Linearity verification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... different flow rates. Use a gravimetric reference measurement (such as a scale, balance, or mass comparator... the gas-division system to divide the span gas with purified air or nitrogen. Select gas divisions... verification for gravimetric PM balances, use external calibration weights that that meet the requirements in...

An Adaptive Rear-End Collision Warning System for Drivers That Estimates Driving Phase and Selects Training Data

NASA Astrophysics Data System (ADS)

Ikeda, Kazushi; Mima, Hiroki; Inoue, Yuta; Shibata, Tomohiro; Fukaya, Naoki; Hitomi, Kentaro; Bando, Takashi

The paper proposes a rear-end collision warning system for drivers, where the collision risk is adaptively set from driving signals. The system employs the inverse of the time-to-collision with a constant relative acceleration as the risk and the one-class support vector machine as the anomaly detector. The system also utilizes brake sequences for outliers detection. When a brake sequence has a low likelihood with respect to trained hidden Markov models, the driving data during the sequence are removed from the training dataset. This data selection is confirmed to increase the robustness of the system by computer simulations.

Heliostat field cost reduction by `slope drive' optimization

NASA Astrophysics Data System (ADS)

Arbes, Florian; Weinrebe, Gerhard; Wöhrbach, Markus

2016-05-01

An algorithm to optimize power tower heliostat fields employing heliostats with so-called slope drives is presented. It is shown that a field using heliostats with the slope drive axes configuration has the same performance as a field with conventional azimuth-elevation tracking heliostats. Even though heliostats with the slope drive configuration have a limited tracking range, field groups of heliostats with different axes or different drives are not needed for different positions in the heliostat field. The impacts of selected parameters on a benchmark power plant (PS10 near Seville, Spain) are analyzed.

Combined Optimal Control System for excavator electric drive

NASA Astrophysics Data System (ADS)

Kurochkin, N. S.; Kochetkov, V. P.; Platonova, E. V.; Glushkin, E. Y.; Dulesov, A. S.

2018-03-01

The article presents a synthesis of the combined optimal control algorithms of the AC drive rotation mechanism of the excavator. Synthesis of algorithms consists in the regulation of external coordinates - based on the theory of optimal systems and correction of the internal coordinates electric drive using the method "technical optimum". The research shows the advantage of optimal combined control systems for the electric rotary drive over classical systems of subordinate regulation. The paper presents a method for selecting the optimality criterion of coefficients to find the intersection of the range of permissible values of the coordinates of the control object. There is possibility of system settings by choosing the optimality criterion coefficients, which allows one to select the required characteristics of the drive: the dynamic moment (M) and the time of the transient process (tpp). Due to the use of combined optimal control systems, it was possible to significantly reduce the maximum value of the dynamic moment (M) and at the same time - reduce the transient time (tpp).

Digest of impaired driving and selected beverage control laws

DOT National Transportation Integrated Search

2007-08-01

This digest reports the status of State laws that are concerned with impaired driving offenses and alcoholic beverage control. Unless otherwise indicated, the status of the laws reported is January 1, 2007.

Digest of impaired driving and selected beverage control laws

DOT National Transportation Integrated Search

2006-04-01

This digest reports the status of State laws that are concerned with impaired driving offenses and alcoholic beverage control. Unless otherwise indicated, the status of the laws reported is January 1, 2006.

Controlled Speed Accessory Drive demonstration program

NASA Technical Reports Server (NTRS)

Hoehn, F. W.

1981-01-01

A Controlled Speed Accessory Drive System was examined in an effort to improve the fuel economy of passenger cars. Concept feasibility and the performance of a typical system during actual road driving conditions were demonstrated. The CSAD system is described as a mechanical device which limits engine accessory speeds, thereby reducing parasitic horsepower losses and improving overall vehicle fuel economy. Fuel consumption data were compiled for fleets of GSA vehicles. Various motor pool locations were selected, each representing different climatic conditions. On the basis of a total accumulated fleet usage of nearly three million miles, an overall fuel economy improvement of 6 percent to 7 percent was demonstrated. Coincident chassis dynamometer tests were accomplished on selected vehicles to establish the effect of different accessory drive systems on exhaust emissions, and to evaluate the magnitude of the mileage benefits which could be derived.

The neural substrates of driving at a safe distance: a functional MRI study.

PubMed

Uchiyama, Yuji; Ebe, Kazutoshi; Kozato, Akio; Okada, Tomohisa; Sadato, Norihiro

2003-12-11

An important driving skill is the ability to maintain a safe distance from a preceding car. To determine the neural substrates of this skill we performed functional magnetic resonance imaging of simulated driving in 21 subjects. Subjects used a joystick to adjust their own driving speed in order to maintain a constant distance from a preceding car traveling at varying speeds. The task activated multiple brain regions. Activation of the cerebellum may reflect visual feedback during smooth tracking of the preceding car. Co-activation of the basal ganglia, thalamus and premotor cortex is related to movement selection. Activation of a premotor-parietal network is related to visuo-motor co-ordination. Task performance was negatively correlated with anterior cingulate activity, consistent with the role of this region in error detection and response selection.

An Evolutionary Algorithm for Feature Subset Selection in Hard Disk Drive Failure Prediction

ERIC Educational Resources Information Center

Bhasin, Harpreet

2011-01-01

Hard disk drives are used in everyday life to store critical data. Although they are reliable, failure of a hard disk drive can be catastrophic, especially in applications like medicine, banking, air traffic control systems, missile guidance systems, computer numerical controlled machines, and more. The use of Self-Monitoring, Analysis and…

Mechanism and active variety of allelochemicals

USGS Publications Warehouse

Peng, S.-L.; Wen, J.; Guo, Q.-F.

2004-01-01

This article summarizes allelochemicals' active variety, its potential causes and function mechanisms. Allelochemicals' activity varies with temperature, photoperiod, water and soils during natural processes, with its initial concentration, compound structure and mixed degree during functional processes, with plant accessions, tissues and maturity within-species, and with research techniques and operation processes. The prospective developmental aspects of allelopathy studies in the future are discussed. Future research should focus on: (1) to identify and purify allelochemicals more effectively, especially for agriculture, (2) the functions of allelopathy at the molecular structure level, (3) using allelopathy to explain plant species interactions, (4) allelopathy as a driving force of succession, and (5) the significance of allelopathy in the evolutionary processes.

Creating new β cells: cellular transmutation by genomic alchemy.

PubMed

Moss, Larry G

2013-03-01

To address insulin insufficiency, diabetes research has long focused on techniques for replacing insulin-producing β cells. Studies in mice have suggested that, under some conditions, α cells possess the capacity to transdifferentiate into β cells, although the mechanisms that drive this conversion are unclear. In this issue, Bramswig et al. analyzed the methylation states of purified human α, β, and acinar cells and found α cells exhibit intrinsic phenotypic plasticity associated with specific histone methylation profiles. In addition to expanding our understanding of this potential source of β cells, this compendium of carefully generated human gene expression and epigenomic data in islet cell subtypes constitutes a truly valuable resource for the field.

Creating new β cells: cellular transmutation by genomic alchemy

PubMed Central

Moss, Larry G.

2013-01-01

To address insulin insufficiency, diabetes research has long focused on techniques for replacing insulin-producing β cells. Studies in mice have suggested that, under some conditions, α cells possess the capacity to transdifferentiate into β cells, although the mechanisms that drive this conversion are unclear. In this issue, Bramswig et al. analyzed the methylation states of purified human α, β, and acinar cells and found α cells exhibit intrinsic phenotypic plasticity associated with specific histone methylation profiles. In addition to expanding our understanding of this potential source of β cells, this compendium of carefully generated human gene expression and epigenomic data in islet cell subtypes constitutes a truly valuable resource for the field. PMID:23434598

Development of a water purifier for radioactive cesium removal from contaminated natural water by radiation-induced graft polymerization

NASA Astrophysics Data System (ADS)

Seko, Noriaki; Hoshina, Hiroyuki; Kasai, Noboru; Shibata, Takuya; Saiki, Seiichi; Ueki, Yuji

2018-02-01

Six years after the Fukushima-nuclear accident, the dissolved radioactive cesium (Cs) is now hardly detected in environmental natural waters. These natural waters are directly used as source of drinking and domestic waters in disaster-stricken areas in Fukushima. However, the possibility that some radioactive Cs adsorbed on soil or leaves will contaminate these natural waters during heavy rains or typhoon is always present. In order for the returning residents to live with peace of mind, it is important to demonstrate the safety of the domestic waters that they will use for their daily life. For this purpose, we have synthesized a material for selective removal of radioactive Cs by introducing ammonium 12-molybdophosphate (AMP) onto polyethylene nonwoven fabric through radiation-induced emulsion graft polymerization technique. Water purifiers filled with the grafted Cs adsorbent were installed in selected houses in Fukushima. The capability of the grafted adsorbent to remove Cs from domestic waters was evaluated for a whole year. The results showed that the tap water filtered through the developed water purifier contained no radioactive Cs, signifying the very effective adsorption performance of the developed grafted adsorbent. From several demonstrations, we have commercialized the water purifier named "KranCsair®". Furthermore, we have also developed a method for the mass production of the grafted nonwoven fabric. Using a 30 L grafting reactor, it was possible to produce the grafted nonwoven fabric with a suitable range of degree of grafting. When an irradiated roll of nonwoven trunk fabric with a length of 10 m and a width of 30 cm was set in the reactor filled with glycidyl methacrylate (GMA), AMP, Tween 80 monomer emulsion solution at 40 °C for 1 h, the difference of Dgs in the length and the width on roll of fabrics was negligible.

Selective recruitment of nuclear factors to productively replicating herpes simplex virus genomes.

PubMed

Dembowski, Jill A; DeLuca, Neal A

2015-05-01

Much of the HSV-1 life cycle is carried out in the cell nucleus, including the expression, replication, repair, and packaging of viral genomes. Viral proteins, as well as cellular factors, play essential roles in these processes. Isolation of proteins on nascent DNA (iPOND) was developed to label and purify cellular replication forks. We adapted aspects of this method to label viral genomes to both image, and purify replicating HSV-1 genomes for the identification of associated proteins. Many viral and cellular factors were enriched on viral genomes, including factors that mediate DNA replication, repair, chromatin remodeling, transcription, and RNA processing. As infection proceeded, packaging and structural components were enriched to a greater extent. Among the more abundant proteins that copurified with genomes were the viral transcription factor ICP4 and the replication protein ICP8. Furthermore, all seven viral replication proteins were enriched on viral genomes, along with cellular PCNA and topoisomerases, while other cellular replication proteins were not detected. The chromatin-remodeling complexes present on viral genomes included the INO80, SWI/SNF, NURD, and FACT complexes, which may prevent chromatinization of the genome. Consistent with this conclusion, histones were not readily recovered with purified viral genomes, and imaging studies revealed an underrepresentation of histones on viral genomes. RNA polymerase II, the mediator complex, TFIID, TFIIH, and several other transcriptional activators and repressors were also affinity purified with viral DNA. The presence of INO80, NURD, SWI/SNF, mediator, TFIID, and TFIIH components is consistent with previous studies in which these complexes copurified with ICP4. Therefore, ICP4 is likely involved in the recruitment of these key cellular chromatin remodeling and transcription factors to viral genomes. Taken together, iPOND is a valuable method for the study of viral genome dynamics during infection and provides a comprehensive view of how HSV-1 selectively utilizes cellular resources.

Anti-CDR3 Therapy for B-Cell Malignancies

DTIC Science & Technology

2013-10-01

1-5 in the report). The "Tomlinson" human antibody phage library will be used to pan for antibodies that bind these target CDR3s and not the parent...selection of phage to a test antigen. Successful expression will lead directly to the selection of CDR3-specific antibody-encoding phage : from which we... phage that bind to the purified candidate antibody and not to irrelevant antibodies. Phage are from single chain Fv library. Sequence phage that

Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences.

PubMed

Pang, Erli; Wu, Xiaomei; Lin, Kui

2016-06-01

Protein evolution plays an important role in the evolution of each genome. Because of their functional nature, in general, most of their parts or sites are differently constrained selectively, particularly by purifying selection. Most previous studies on protein evolution considered individual proteins in their entirety or compared protein-coding sequences with non-coding sequences. Less attention has been paid to the evolution of different parts within each protein of a given genome. To this end, based on PfamA annotation of all human proteins, each protein sequence can be split into two parts: domains or unassigned regions. Using this rationale, single nucleotide polymorphisms (SNPs) in protein-coding sequences from the 1000 Genomes Project were mapped according to two classifications: SNPs occurring within protein domains and those within unassigned regions. With these classifications, we found: the density of synonymous SNPs within domains is significantly greater than that of synonymous SNPs within unassigned regions; however, the density of non-synonymous SNPs shows the opposite pattern. We also found there are signatures of purifying selection on both the domain and unassigned regions. Furthermore, the selective strength on domains is significantly greater than that on unassigned regions. In addition, among all of the human protein sequences, there are 117 PfamA domains in which no SNPs are found. Our results highlight an important aspect of protein domains and may contribute to our understanding of protein evolution.

Purifying Selection on Exonic Splice Enhancers in Intronless Genes

PubMed Central

Savisaar, Rosina; Hurst, Laurence D.

2016-01-01

Exonic splice enhancers (ESEs) are short nucleotide motifs, enriched near exon ends, that enhance the recognition of the splice site and thus promote splicing. Are intronless genes under selection to avoid these motifs so as not to attract the splicing machinery to an mRNA that should not be spliced, thereby preventing the production of an aberrant transcript? Consistent with this possibility, we find that ESEs in putative recent retrocopies are at a higher density and evolving faster than those in other intronless genes, suggesting that they are being lost. Moreover, intronless genes are less dense in putative ESEs than intron-containing ones. However, this latter difference is likely due to the skewed base composition of intronless sequences, a skew that is in line with the general GC richness of few exon genes. Indeed, after controlling for such biases, we find that both intronless and intron-containing genes are denser in ESEs than expected by chance. Importantly, nucleotide-controlled analysis of evolutionary rates at synonymous sites in ESEs indicates that the ESEs in intronless genes are under purifying selection in both human and mouse. We conclude that on the loss of introns, some but not all, ESE motifs are lost, the remainder having functions beyond a role in splice promotion. These results have implications for the design of intronless transgenes and for understanding the causes of selection on synonymous sites. PMID:26802218

Theory of prokaryotic genome evolution.

PubMed

Sela, Itamar; Wolf, Yuri I; Koonin, Eugene V

2016-10-11

Bacteria and archaea typically possess small genomes that are tightly packed with protein-coding genes. The compactness of prokaryotic genomes is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. Here, by fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. These results suggest that the number of genes in prokaryotic genomes reflects the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias (i.e., the rate of deletion of genetic material being slightly greater than the rate of acquisition). Thus, new genes acquired by microbial genomes, on average, appear to be adaptive. The tight spacing of protein-coding genes likely results from a combination of the deletion bias and purifying selection that efficiently eliminates nonfunctional, noncoding sequences.

40 CFR 1065.307 - Linearity verification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... different flow rates. Use a gravimetric reference measurement (such as a scale, balance, or mass comparator... the gas-division system to divide the span gas with purified air or nitrogen. Select gas divisions... PM balance, m max refers to the typical mass of a PM filter. (ii) For linearity verification of...

Host-parasite interactions and purifying selection in a microsporidian parasite of honey bees

USDA-ARS?s Scientific Manuscript database

Nosema ceranae is a microsporidian parasite that infects honey bee mid-gut epithelial cells. Infection can impair honey bee cognitive function, shorten lifespan, suppress the innate immune response and inhibit the apoptosis of infected gut cells. However, the virulence factors of this parasite are s...

Method for removal of phosgene from boron trichloride

DOEpatents

Freund, Samuel M.

1983-01-01

Selective ultraviolet photolysis using an unfiltered mercury arc lamp has been used to substantially reduce the phosgene impurity in a mixture of boron trichloride and phosgene. Infrared spectrophotometric analysis of the sample before and after irradiation shows that is is possible to highly purify commercially available boron trichloride with this method.

PURIFICATION AND PARTIAL CHARACTERIZATION OF AN ACID PHOSPHATASE FROM SPIRODELA OLIGORRHIZA AND ITS AFFINITY FOR SELECTED ORGANOPHOSPHATE PESTICIDES

EPA Science Inventory

An acid phosphatase from the aquatic plant Spirodela oligorrhiza (duckweed) was isolated by fast protein liquid chromatography (FPLC) and partially characterized. The enzyme was purified 1871-fold with a total yield of 40%. SDS-PAGE electrophoresis of the pure acid phosphatase ...

A cDNA Immunization Strategy to Generate Nanobodies against Membrane Proteins in Native Conformation

PubMed Central

Eden, Thomas; Menzel, Stephan; Wesolowski, Janusz; Bergmann, Philine; Nissen, Marion; Dubberke, Gudrun; Seyfried, Fabienne; Albrecht, Birte; Haag, Friedrich; Koch-Nolte, Friedrich

2018-01-01

Nanobodies (Nbs) are soluble, versatile, single-domain binding modules derived from the VHH variable domain of heavy-chain antibodies naturally occurring in camelids. Nbs hold huge promise as novel therapeutic biologics. Membrane proteins are among the most interesting targets for therapeutic Nbs because they are accessible to systemically injected biologics. In order to be effective, therapeutic Nbs must recognize their target membrane protein in native conformation. However, raising Nbs against membrane proteins in native conformation can pose a formidable challenge since membrane proteins typically contain one or more hydrophobic transmembrane regions and, therefore, are difficult to purify in native conformation. Here, we describe a highly efficient genetic immunization strategy that circumvents these difficulties by driving expression of the target membrane protein in native conformation by cells of the immunized camelid. The strategy encompasses ballistic transfection of skin cells with cDNA expression plasmids encoding one or more orthologs of the membrane protein of interest and, optionally, other costimulatory proteins. The plasmid is coated onto 1 µm gold particles that are then injected into the shaved and depilated skin of the camelid. A gene gun delivers a helium pulse that accelerates the DNA-coated particles to a velocity sufficient to penetrate through multiple layers of cells in the skin. This results in the exposure of the extracellular domains of the membrane protein on the cell surface of transfected cells. Repeated immunization drives somatic hypermutation and affinity maturation of target-specific heavy-chain antibodies. The VHH/Nb coding region is PCR-amplified from B cells obtained from peripheral blood or a lymph node biopsy. Specific Nbs are selected by phage display or by screening of Nb-based heavy-chain antibodies expressed as secretory proteins in transfected HEK cells. Using this strategy, we have successfully generated agonistic and antagonistic Nbs against several cell surface ecto-enzymes and ligand-gated ion channels. PMID:29410663

The Rise and Fall of an Evolutionary Innovation: Contrasting Strategies of Venom Evolution in Ancient and Young Animals

PubMed Central

Sunagar, Kartik; Moran, Yehu

2015-01-01

Animal venoms are theorized to evolve under the significant influence of positive Darwinian selection in a chemical arms race scenario, where the evolution of venom resistance in prey and the invention of potent venom in the secreting animal exert reciprocal selection pressures. Venom research to date has mainly focused on evolutionarily younger lineages, such as snakes and cone snails, while mostly neglecting ancient clades (e.g., cnidarians, coleoids, spiders and centipedes). By examining genome, venom-gland transcriptome and sequences from the public repositories, we report the molecular evolutionary regimes of several centipede and spider toxin families, which surprisingly accumulated low-levels of sequence variations, despite their long evolutionary histories. Molecular evolutionary assessment of over 3500 nucleotide sequences from 85 toxin families spanning the breadth of the animal kingdom has unraveled a contrasting evolutionary strategy employed by ancient and evolutionarily young clades. We show that the venoms of ancient lineages remarkably evolve under the heavy constraints of negative selection, while toxin families in lineages that originated relatively recently rapidly diversify under the influence of positive selection. We propose that animal venoms mostly employ a ‘two-speed’ mode of evolution, where the major influence of diversifying selection accompanies the earlier stages of ecological specialization (e.g., diet and range expansion) in the evolutionary history of the species–the period of expansion, resulting in the rapid diversification of the venom arsenal, followed by longer periods of purifying selection that preserve the potent toxin pharmacopeia–the period of purification and fixation. However, species in the period of purification may re-enter the period of expansion upon experiencing a major shift in ecology or environment. Thus, we highlight for the first time the significant roles of purifying and episodic selections in shaping animal venoms. PMID:26492532

Paper-based device for separation and cultivation of single microalga.

PubMed

Chen, Chih-Chung; Liu, Yi-Ju; Yao, Da-Jeng

2015-12-01

Single-cell separation is among the most useful techniques in biochemical research, diagnosis and various industrial applications. Microalgae species have great economic importance as industrial raw materials. Microalgae species collected from environment are typically a mixed and heterogeneous population of species that must be isolated and purified for examination and further application. Conventional methods, such as serial dilution and a streaking-plate method, are intensive of labor and inefficient. We developed a paper-based device for separation and cultivation of single microalga. The fabrication was simply conducted with a common laser printer and required only a few minutes without lithographic instruments and clean-room. The driving force of the paper device was simple capillarity without a complicated pump connection that is part of most devices for microfluidics. The open-structure design of the paper device makes it operable with a common laboratory micropipette for sample transfer and manipulation with a naked eye or adaptable to a robotic system with functionality of high-throughput retrieval and analysis. The efficiency of isolating a single cell from mixed microalgae species is seven times as great as with a conventional method involving serial dilution. The paper device can serve also as an incubator for microalgae growth on simply rinsing the paper with a growth medium. Many applications such as highly expressed cell selection and various single-cell analysis would be applicable. Copyright © 2015 Elsevier B.V. All rights reserved.

Abalone Hemocyanin Blocks the Entry of Herpes Simplex Virus 1 into Cells: a Potential New Antiviral Strategy

PubMed Central

Talaei Zanjani, Negar; Miranda-Saksena, Monica; Valtchev, Peter; Hueston, Linda; Diefenbach, Eve; Sairi, Fareed; Gomes, Vincent G.

2015-01-01

A marine-derived compound, abalone hemocyanin, from Haliotis rubra was shown to have a unique mechanism of antiviral activity against herpes simplex virus 1 (HSV-1) infections. In vitro assays demonstrated the dose-dependent and inhibitory effect of purified hemocyanin against HSV-1 infection in Vero cells with a 50% effective dose (ED50) of 40 to 50 nM and no significant toxicity. In addition, hemocyanin specifically inhibited viral attachment and entry by binding selectively to the viral surface glycoproteins gD, gB, and gC, probably by mimicking their receptors. However, hemocyanin had no effect on postentry events and did not block infection by binding to cellular receptors for HSV. By the use of different mutants of gD and gB and a competitive heparin binding assay, both protein charge and conformation were shown to be the driving forces of the interaction between hemocyanin and viral glycoproteins. These findings also suggested that hemocyanin may have different motifs for binding to each of the viral glycoproteins B and D. The dimer subunit of hemocyanin with a 10-fold-smaller molecular mass exhibited similar binding to viral surface glycoproteins, showing that the observed inhibition did not require the entire multimer. Therefore, a small hemocyanin analogue could serve as a new antiviral candidate for HSV infections. PMID:26643336

SpyRing interrogation: analyzing how enzyme resilience can be achieved with phytase and distinct cyclization chemistries

PubMed Central

Schoene, Christopher; Bennett, S. Paul; Howarth, Mark

2016-01-01

Enzymes catalyze reactions with exceptional selectivity and rate acceleration but are often limited by instability. Towards a generic route to thermo-resilience, we established the SpyRing approach, cyclizing enzymes by sandwiching between SpyTag and SpyCatcher (peptide and protein partners which lock together via a spontaneous isopeptide bond). Here we first investigated the basis for this resilience, comparing alternative reactive peptide/protein pairs we engineered from Gram-positive bacteria. Both SnoopRing and PilinRing cyclization gave dramatic enzyme resilience, but SpyRing cyclization was the best. Differential scanning calorimetry for each ring showed that cyclization did not inhibit unfolding of the inserted β-lactamase. Cyclization conferred resilience even at 100 °C, where the cyclizing domains themselves were unfolded. Phytases hydrolyze phytic acid and improve dietary absorption of phosphate and essential metal ions, important for agriculture and with potential against human malnutrition. SpyRing phytase (PhyC) resisted aggregation and retained catalytic activity even following heating at 100 °C. In addition, SpyRing cyclization made it possible to purify phytase simply by heating the cell lysate, to drive aggregation of non-cyclized proteins. Cyclization via domains forming spontaneous isopeptide bonds is a general strategy to generate resilient enzymes and may extend the range of conditions for isolation and application of enzymes. PMID:26861173

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

PubMed Central

Yang, Zhenzhen; Zhang, Yeting; Wafula, Eric K.; Honaas, Loren A.; Ralph, Paula E.; Jones, Sam; Clarke, Christopher R.; Liu, Siming; Su, Chun; Zhang, Huiting; Altman, Naomi S.; Schuster, Stephan C.; Timko, Michael P.; Yoder, John I.; dePamphilis, Claude W.

2016-01-01

Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to be much less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-living Lindenbergia. Following initial phylogenetic detection and an extensive validation procedure, 52 high-confidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence. Analyses of intron sequences in putative donor and recipient lineages provide evidence for integration of genomic fragments far more often than retro-processed RNA sequences. Purifying selection predominates in functionally transferred sequences, with a small fraction of adaptively evolving sites. HGT-acquired genes are preferentially expressed in the haustorium—the organ of parasitic plants—and are strongly biased in predicted gene functions, suggesting that expression products of horizontally acquired genes are contributing to the unique adaptive feeding structure of parasitic plants. PMID:27791104

Tissue culture specificity of the tobacco ASA2 promoter driving hpt as a selectable marker for soybean transformation selection.

PubMed

Zernova, Olga; Zhong, Wei; Zhang, Xing-Hai; Widholm, Jack

2008-11-01

This study was carried out to determine if the tobacco anthranilate synthase ASA2 2.3 kb promoter drives tissue culture specific expression and if it is strong enough to drive hpt (hygromycin phosphotransferase) gene expression at a level sufficient to allow selection of transformed soybean embryogenic culture lines. A number of transformed cell lines were selected showing that the promoter was strong enough. Northern blot analysis of plant tissues did not detect hpt mRNA in the untransformed control or in the ASA2-hpt plants except in developing seeds while hpt mRNA was detected in all tissues of the CaMV35S-hpt positive control line plants. However, when the more sensitive RT-PCR assay was used all tissues of the ASA2-hpt plants except roots and mature seeds were found to contain detectable hpt mRNA. Embryogenic tissue cultures initiated from the ASA2-hpt plants contained hpt mRNA detectable by both northern and RT-PCR analysis and the cultures were hygromycin resistant. Friable callus initiated from leaves of ASA2-hpt plants did in some cases contain hpt mRNA that was only barely detectable by northern hybridization even though the callus was very hygromycin resistant. Thus the ASA2 promoter is strong enough to drive sufficient hpt expression in soybean embryogenic cultures for hygromycin selection and only very low levels of expression were found in most plant tissues with none in mature seeds.

Utilization of Electrically Reduced Neutral Red by Actinobacillus succinogenes: Physiological Function of Neutral Red in Membrane-Driven Fumarate Reduction and Energy Conservation

PubMed Central

Park, D. H.; Zeikus, J. G.

1999-01-01

Neutral red (NR) functioned as an electronophore or electron channel enabling either cells or membranes purified from Actinobacillus succinogenes to drive electron transfer and proton translocation by coupling fumarate reduction to succinate production. Electrically reduced NR, unlike methyl or benzyl viologen, bound to cell membranes, was not toxic, and chemically reduced NAD. The cell membrane of A. succinogenes contained high levels of benzyl viologen-linked hydrogenase (12.2 U), fumarate reductase (13.1 U), and diaphorase (109.7 U) activities. Fumarate reductase (24.5 U) displayed the highest activity with NR as the electron carrier, whereas hydrogenase (1.1 U) and diaphorase (0.8 U) did not. Proton translocation by whole cells was dependent on either electrically reduced NR or H2 as the electron donor and on the fumarate concentration. During the growth of Actinobacillus on glucose plus electrically reduced NR in an electrochemical bioreactor system versus on glucose alone, electrically reduced NR enhanced glucose consumption, growth, and succinate production by about 20% while it decreased acetate production by about 50%. The rate of fumarate reduction to succinate by purified membranes was twofold higher with electrically reduced NR than with hydrogen as the electron donor. The addition of 2-(n-heptyl)-4-hydroxyquinoline N-oxide to whole cells or purified membranes inhibited succinate production from H2 plus fumarate but not from electrically reduced NR plus fumarate. Thus, NR appears to replace the function of menaquinone in the fumarate reductase complex, and it enables A. succinogenes to utilize electricity as a significant source of metabolic reducing power. PMID:10198002

A Selected Review of the Literature on Factors and Conditions Driving the High Risk and Dropout Problem. Policy Studies in Language and Cross Cultural Education.

ERIC Educational Resources Information Center

Zachman, Jill M.

This report presents the findings of a review of 45 selected references on issues associated with high risk students and dropouts. The literature was analyzed according to: (1) the manner in which high risk students and dropouts are characterized; (2) the suggested causes and conditions driving the problems of high risk and dropping out; (3) the…

Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

PubMed Central

Mkhitaryan, V. V.; Jelezko, F.; Dobrovitski, V. V.

2015-01-01

We consider an electronic spin, such as a nitrogen-vacancy center in diamond, weakly coupled to a large number of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase. We show that by switching the driving phase synchronously with the precession of a given nuclear spin, the interaction to this spin is selectively enhanced, while the rest of the bath remains decoupled. The enhancement is of resonant character. The key feature of the suggested scheme is that the width of the resonance is adjustable, and can be greatly decreased by increasing the driving strength. Thus, the resonance can be significantly narrowed, by a factor of 10–100 in comparison with the existing detection methods. Significant improvement in selectivity is explained analytically and confirmed by direct numerical many-spin simulations. The method can be applied to a wide range of solid-state systems. PMID:26497777

The Sequence of Hip and Selected Upper-Extremity Joint Movements During the Golf Drive.

ERIC Educational Resources Information Center

Hunter, Charles L.

This study analyzed wrist, elbow, and hip actions of golfers who were accurately driving a golf ball a maximum distance. Electrogoniometry and cinematography were used to measure wrist, forearm, elbow, and hip actions during the downswing of 10 low-handicap golfers who were attempting to drive a minimum of 225 yards within a 50-yard corridor.…

Alcohol- and Drug-Involved Driving in the United States: Methodology for the 2007 National Roadside Survey

ERIC Educational Resources Information Center

Lacey, John H.; Kelley-Baker, Tara; Voas, Robert B.; Romano, Eduardo; Furr-Holden, C. Debra; Torres, Pedro; Berning, Amy

2011-01-01

This article describes the methodology used in the 2007 U.S. National Roadside Survey to estimate the prevalence of alcohol- and drug-impaired driving and alcohol- and drug-involved driving. This study involved randomly stopping drivers at 300 locations across the 48 continental U.S. states at sites selected through a stratified random sampling…

Optimization design of wind turbine drive train based on Matlab genetic algorithm toolbox

NASA Astrophysics Data System (ADS)

Li, R. N.; Liu, X.; Liu, S. J.

2013-12-01

In order to ensure the high efficiency of the whole flexible drive train of the front-end speed adjusting wind turbine, the working principle of the main part of the drive train is analyzed. As critical parameters, rotating speed ratios of three planetary gear trains are selected as the research subject. The mathematical model of the torque converter speed ratio is established based on these three critical variable quantity, and the effect of key parameters on the efficiency of hydraulic mechanical transmission is analyzed. Based on the torque balance and the energy balance, refer to hydraulic mechanical transmission characteristics, the transmission efficiency expression of the whole drive train is established. The fitness function and constraint functions are established respectively based on the drive train transmission efficiency and the torque converter rotating speed ratio range. And the optimization calculation is carried out by using MATLAB genetic algorithm toolbox. The optimization method and results provide an optimization program for exact match of wind turbine rotor, gearbox, hydraulic mechanical transmission, hydraulic torque converter and synchronous generator, ensure that the drive train work with a high efficiency, and give a reference for the selection of the torque converter and hydraulic mechanical transmission.

A Novel Point Mutation at Position 156 of Reverse Transcriptase from Feline Immunodeficiency Virus Confers Resistance to the Combination of (−)-β-2′,3′-Dideoxy-3′-Thiacytidine and 3′-Azido-3′-Deoxythymidine

PubMed Central

Smith, Robert A.; Remington, Kathryn M.; Preston, Bradley D.; Schinazi, Raymond F.; North, Thomas W.

1998-01-01

Mutants of feline immunodeficiency virus (FIV) resistant to (−)-β-2′,3′-dideoxy-3′-thiacytidine (3TC) were selected by culturing virus in the presence of increasing stepwise concentrations of 3TC. Two plaque-purified variants were isolated from the original mutant population, and both of these mutants were resistant to 3TC. Surprisingly, these mutants were also phenotypically resistant to 3′-azido-3′-deoxythymidine (AZT) and to the combination of 3TC and AZT. Purified reverse transcriptase (RT) from one of these plaque-purified mutants was resistant to the 5′-triphosphates of 3TC and AZT. DNA sequence analysis of the RT-encoding region of the pol gene amplified from the plaque-purified mutants revealed a Pro-to-Ser mutation at position 156 of RT. A site-directed mutant of FIV engineered to contain this Pro-156-Ser mutation was resistant to 3TC, AZT, and the combination of 3TC and AZT, confirming the role of the Pro-156-Ser mutation in the resistance of FIV to these two nucleoside analogs. This represents the first report of a lentiviral mutant resistant to the combination of AZT and 3TC due to a single, unique point mutation. PMID:9499094

Isolation of friedelin from black condensate of cork.

PubMed

Pires, Ricardo A; Aroso, Ivo; Silva, Susana P; Mano, João F; Reis, Rui L

2011-11-01

Black condensates (BC) are wastes of the insulation corkboard industry that contain several valuable chemicals, including friedelin, a terpene exhibiting biological activity. Herein, we report a straightforward procedure to extract friedelin from BC. Using this procedure, we were able to extract friedelin with yields between 0.4% and 2.9% and to further purify it obtaining purities from 77.0% to 99.3% (HPLC). The initial BC (2 batches), extracted raw product and purified friedelin were analyzed using FTIR. The extraction yields and purities were found to be directly related to the intensity of the carbonyl vibration at 1713 cm(-1) in the FTIR spectrum of the used BC batch. Therefore, these spectra can be used to screen and select BC batches suitable for friedelin extraction.

Expression, purification, and characterization of an enzymatically active truncated human rho-kinase I (ROCK I) domain expressed in Sf-9 insect cells.

PubMed

Khandekar, Sanjay S; Yi, Tracey; Dul, Ed; Wright, Lois L; Chen, Susan; Scott, Gilbert F; Smith, Gary K; Lee, Dennis; Hu, Erding; Kirkpatrick, Robert B

2006-01-01

Rho Kinase I (ROCK I) is a serine/threonine kinase that is involved in diverse cellular signaling. To further understand the physiological role of ROCK I and to identify and develop potent and selective inhibitors of ROCK I, we have overexpressed and purified a constitutively active dimeric human ROCK I (3-543) kinase domain using the Sf9-baculovirus expression system. In addition, using a limited proteolysis technique, we have identified a minimal functional subdomain of ROCK I that can be used in crystallization studies. The availability of multimilligram amounts of purified and well characterized functional human ROCK I kinase domains will be useful in screening and structural studies.

The Effects of Medical Conditions on Driving Performance

DOT National Transportation Integrated Search

2017-08-01

This project investigated the effect of selected medical conditions on the exposure and performance of older drivers. A review of recent literature, followed by a panel meeting with driving safety experts, prioritized four medical conditions for furt...

Preparative isolation and purification of seven main antioxidants from Eucommia ulmoides Oliv. (Du-zhong) leaves using HSCCC guided by DPPH-HPLC experiment.

PubMed

Dai, Xingping; Huang, Qiong; Zhou, Boting; Gong, Zhicheng; Liu, Zhaoqian; Shi, Shuyun

2013-08-15

Seven antioxidants were purified from Eucommia ulmoides Oliv. leaves using HSCCC guided by DPPH-HPLC experiment. HSCCC was successfully used to separate target antioxidants by three runs with different solvent systems after D101 column chromatography fractionation. Ethyl acetate-n-butanol-water (1:2:3, v/v/v) was selected as the optimum solvent system to purify geniposidic acid. Ethyl acetate-ethanol-water (4:1:5, v/v/v) was used to isolate caffeic acid, chlorogenic acid and ferulic acid. While three flavonoids, quercetin-3-O-sambubioside, rutin and isoquercitrin were purified by petroleum ether-ethyl acetate-methanol-water (1:5:1:5, v/v/v/v). The structures were identified by MS and NMR. Antioxidant activities were assessed, and compounds 2-7 showed strong antioxidant activities. This is the first report about separation of antioxidants from E. ulmoides leaves by HSCCC. The results indicated that the combinative methods using DPPH-HPLC and HSCCC could be widely applied for screening and isolation of antioxidants from complex extracts. Copyright © 2013 Elsevier Ltd. All rights reserved.

Lectins discriminate between pathogenic and nonpathogenic South American trypanosomes

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

de Miranda Santos, I.K.; Pereira, M.E.

1984-09-01

Cell surface carbohydrates of Trypanosoma cruzi, Trypanosoma rangeli, and Trypanosoma conorhini were analyzed by a micro-agglutination assay employing 27 highly purified lectins and by binding assays using various /sup 125/I-labeled lectins. The following seven lectins discriminated between the trypanosomes: 1) tomato lectin (an N-acetyl-D-glucosamine-binding protein), both in purified form and as crude tomato juice; 2) Bauhinea purpurea and Sophora japonica lectins (both N-acetyl-D-galactosamine-binding proteins), which selectively agglutinated T. cruzi; 3) Vicia villosa (an N-acetyl-D-galactosamine-binding protein) which was specific for T. rangeli; 4) peanut lectin (a D-galactose-binding protein) both in purified form and as crude saline extract; and 5) Ulex europaeusmore » and Lotus tetragonolobus (both L-fucose-binding proteins) lectins which reacted only with T. conorhini. Binding studies with 125I-labeled lectins were performed to find whether unagglutinated cells of the three different species of trypanosomes might have receptors for these lectins, in which case absence of agglutination could be due to a peculiar arrangement of the receptors. These assays essentially confirmed the agglutination experiments.« less

Understanding Dali's Slave market with the disappearing bust of Voltaire: a case study in the scale information driving perception.

PubMed

Bonnar, Lizann; Gosselin, Frédéric; Schyns, Philippe G

2002-01-01

A generic problem in vision is to know which information drives the perception of a stimulus. We address this problem in a case study that involves the perceptual reversal of an ambiguous image (here, Dali's painting the Slave Market with the Disappearing Bust of Voltaire 1940). In experiment 1, we use 'bubbles' (Gosselin and Schyns, 2001 Vision Research 41 2261-2271) to disambiguate the image and to determine the specific visual information that drives each possible perception (here, the nuns versus the bust of Voltaire). Experiment 2 validates that this information does determine the selective perception of the ambiguous image. We adapted the spatial-frequency channels of observers selectively to the information that mediates one of the two perceptions, to induce the opposite perception of the ambiguous image in a transfer phase. Together, the results suggest a method of revealing the visual information that drives perception.

Differences between emissions measured in urban driving and certification testing of heavy-duty diesel engines

NASA Astrophysics Data System (ADS)

Dixit, Poornima; Miller, J. Wayne; Cocker, David R.; Oshinuga, Adewale; Jiang, Yu; Durbin, Thomas D.; Johnson, Kent C.

2017-10-01

Emissions from eight heavy-duty diesel trucks (HDDTs) equipped with three different exhaust aftertreatment systems (ATS) for controlling nitrogen oxide (NOx) emissions were quantified on a chassis dynamometer using driving schedules representative of stop-and-go and free-flow driving in metropolitan areas. The three control technologies were: 1) cooled exhaust gas recirculation (CEGR) plus a diesel particulate filter (DPF); 2) CEGR and DPF plus advanced engine controls; and 3) CEGR and DPF plus selective catalytic reduction with ammonia (SCR). Results for all control technologies and driving conditions showed PM emission factors were less than the standard, while selected non-regulated emissions (ammonia, carbonyls, and C4-C12 hydrocarbons) and a greenhouse gas (nitrous oxide) were at measurement detection limits. However, NOx emission factors depended on the control technology, engine calibration, and driving mode. For example, emissions from engines with cooled-exhaust gas recirculation (CEGR) were 239% higher for stop-and-go driving as compared with free-flow. For CEGR plus selective catalytic reduction (SCR), the ratio was 450%. A deeper analysis was carried out with the assumption that emissions measured for a drive cycle on either the chassis or in-use driving would be similar. Applying the same NTE rules to the chassis data showed emissions during stop-and-go driving often exceeded the certification standard and >90% of the driving did not fall within the Not-To-Exceed (NTE) control area suggesting the NTE requirements do not provide sufficient emissions control under in-use conditions. On-road measurement of emissions using the same mobile lab while the vehicle followed a free-flow driving schedule verified the chassis results. These results have implications for scientists who build inventories using certification values instead of real world emission values and for metropolitan populations, who are exposed to elevated emissions. The differences in values between real world emissions and certification cycles should be narrowed. For example, one might use a different mix of cold and hot start testing to greater emphasize low temperature/load operation, a separate cycle to specifically characterize low-load operation, or broaden the in-use compliance testing requirements and associated conformity factors to incorporate a wider envelope of vehicle operation, especially at low load conditions. .

Assessment selection in human-automation interaction studies: The Failure-GAM2E and review of assessment methods for highly automated driving.

PubMed

Grane, Camilla

2018-01-01

Highly automated driving will change driver's behavioural patterns. Traditional methods used for assessing manual driving will only be applicable for the parts of human-automation interaction where the driver intervenes such as in hand-over and take-over situations. Therefore, driver behaviour assessment will need to adapt to the new driving scenarios. This paper aims at simplifying the process of selecting appropriate assessment methods. Thirty-five papers were reviewed to examine potential and relevant methods. The review showed that many studies still relies on traditional driving assessment methods. A new method, the Failure-GAM 2 E model, with purpose to aid assessment selection when planning a study, is proposed and exemplified in the paper. Failure-GAM 2 E includes a systematic step-by-step procedure defining the situation, failures (Failure), goals (G), actions (A), subjective methods (M), objective methods (M) and equipment (E). The use of Failure-GAM 2 E in a study example resulted in a well-reasoned assessment plan, a new way of measuring trust through feet movements and a proposed Optimal Risk Management Model. Failure-GAM 2 E and the Optimal Risk Management Model are believed to support the planning process for research studies in the field of human-automation interaction. Copyright © 2017 Elsevier Ltd. All rights reserved.

Associations between selected state laws and teenagers' drinking and driving behaviors.

PubMed

Cavazos-Rehg, Patricia A; Krauss, Melissa J; Spitznagel, Edward L; Chaloupka, Frank J; Schootman, Mario; Grucza, Richard A; Bierut, Laura Jean

2012-09-01

We examined the associations between selected state-level graduated driving licensing (GDL) laws and use-and-lose laws (laws that allow for the suspension of a driver's license for underage alcohol violations including purchase, possession, or consumption) with individual-level alcohol-related traffic risk behaviors among high school youth. Logistic regression models with fixed effects for state were used to examine the associations between the selected state-level laws and drinking and driving behaviors youth aged 16 to 17 years (obtained from the Youth Risk Behavior Surveillance System (YRBSS); responses dichotomized as "0 times" or "1 or more times") over an extended period of time (1999 to 2009). A total of 11.7% of students reported having driven after drinking any alcohol and 28.2% reported riding in a car with a driver who had been drinking on 1 or more occasions in the past 30 days. Restrictive GDL laws and use-and-lose laws were associated with decreased driving after drinking any alcohol and riding in a car with a driver who had been drinking alcohol. Restrictive GDL and use-and-lose laws may help to bolster societal expectations and values about the hazards of drinking and driving behaviors and are therefore partly responsible for the decline in these alcohol-related traffic risk behaviors. Copyright © 2012 by the Research Society on Alcoholism.

Studies on the selective lysis and purification of Trypanosoma cruzi

PubMed Central

1975-01-01

The mechanism by which culture forms of Trypanosoma cruzi are lysed by normal mammalian sera was examined. Lysis is restricted to the epimastigote form of the organism and is not dependent on the presence of agglutinins. Lysis is a complement-dependent process, the activity being generated by the alternate pathway. The selective lysis by serum was exploited to purify viable trypomastigotes by means of centrifugation in an albumin column. Essentially pure trypomastigote populations are now being employed in cell culture experiments. PMID:807672

Structural equation model analysis for the evaluation of overall driving performance: A driving simulator study focusing on driver distraction.

PubMed

Papantoniou, Panagiotis

2018-04-03

The present research relies on 2 main objectives. The first is to investigate whether latent model analysis through a structural equation model can be implemented on driving simulator data in order to define an unobserved driving performance variable. Subsequently, the second objective is to investigate and quantify the effect of several risk factors including distraction sources, driver characteristics, and road and traffic environment on the overall driving performance and not in independent driving performance measures. For the scope of the present research, 95 participants from all age groups were asked to drive under different types of distraction (conversation with passenger, cell phone use) in urban and rural road environments with low and high traffic volume in a driving simulator experiment. Then, in the framework of the statistical analysis, a correlation table is presented investigating any of a broad class of statistical relationships between driving simulator measures and a structural equation model is developed in which overall driving performance is estimated as a latent variable based on several individual driving simulator measures. Results confirm the suitability of the structural equation model and indicate that the selection of the specific performance measures that define overall performance should be guided by a rule of representativeness between the selected variables. Moreover, results indicate that conversation with the passenger was not found to have a statistically significant effect, indicating that drivers do not change their performance while conversing with a passenger compared to undistracted driving. On the other hand, results support the hypothesis that cell phone use has a negative effect on driving performance. Furthermore, regarding driver characteristics, age, gender, and experience all have a significant effect on driving performance, indicating that driver-related characteristics play the most crucial role in overall driving performance. The findings of this study allow a new approach to the investigation of driving behavior in driving simulator experiments and in general. By the successful implementation of the structural equation model, driving behavior can be assessed in terms of overall performance and not through individual performance measures, which allows an important scientific step forward from piecemeal analyses to a sound combined analysis of the interrelationship between several risk factors and overall driving performance.

In vitro study of histamine and histamine receptor ligands influence on the adhesion of purified human eosinophils to endothelium.

PubMed

Grosicki, Marek; Wójcik, Tomasz; Chlopicki, Stefan; Kieć-Kononowicz, Katarzyna

2016-04-15

It is a well-known fact that histamine is involved in eosinophil-dependent inflammatory responses including cellular chemotaxis and migration. Nevertheless, the relative role of histamine receptors in the mechanisms of eosinophils adhesion to endothelial cells is not known. Therefore the aim of presented study was to examine the effect of selective histamine receptors ligands on eosinophils adhesion to endothelium. For that purpose the highly purified human eosinophils have been isolated from the peripheral blood. The viability and functional integrity of isolated eosinophils have been validated in several tests. Histamine as well as 4-methylhistamine (selective H4 agonist) in concentration-dependent manner significantly increased number of eosinophils that adhere to endothelium. Among the selective histamine receptors antagonist or H1 inverse agonist only JNJ7777120 (histamine H4 antagonist) and thioperamide (dual histamine H3/H4 antagonist) had direct effect on eosinophils adhesion to endothelial cells. Antagonists of H1 (diphenhydramine, mepyramine) H2 (ranitidine and famotidine) and H3 (pitolisant) histamine receptors were ineffective. To the best of our knowledge, this is the first study to demonstrate that histamine receptor H4 plays a dominant role in histamine-induced eosinophils adhesion to endothelium. Copyright © 2016 Elsevier B.V. All rights reserved.

The NS3 proteins of global strains of bluetongue virus evolve into regional topotypes through negative (purifying) selection.

PubMed

Balasuriya, U B R; Nadler, S A; Wilson, W C; Pritchard, L I; Smythe, A B; Savini, G; Monaco, F; De Santis, P; Zhang, N; Tabachnick, W J; Maclachlan, N J

2008-01-01

Comparison of the deduced amino acid sequences of the genes (S10) encoding the NS3 protein of 137 strains of bluetongue virus (BTV) from Africa, the Americas, Asia, Australia and the Mediterranean Basin showed limited variation. Common to all NS3 sequences were potential glycosylation sites at amino acid residues 63 and 150 and a cysteine at residue 137, whereas a cysteine at residue 181 was not conserved. The PPXY and PS/TAP late-domain motifs were conserved in all but three of the viruses. Phylogenetic analyses of these same sequences yielded two principal clades that grouped the viruses irrespective of their serotype or year of isolation (1900-2003). All viruses from Asia and Australia were grouped in one clade, whereas those from the other regions were present in both clades. Each clade segregated into distinct subclades that included viruses from single or multiple regions, and the S10 genes of some field viruses were identical to those of live-attenuated BTV vaccines. There was no evidence of positive selection on the S10 gene as assessed by reconstruction of ancestral codon states on the phylogeny, rather the functional constraints of the NS3 protein are expressed through substantial negative (purifying) selection.

Convergence of biannual moulting strategies across birds and mammals

PubMed Central

Burns, Jennifer M.; Breed, Greg A.

2018-01-01

Birds and mammals have developed numerous strategies for replacing worn feathers and hair. Moulting usually occurs on an annual basis; however, moults that take place twice per year (biannual moults) also occur. Here, we review the forces driving the evolution of various moult strategies, focusing on the special case of the complete biannual moult as a convergence of selection pressures across birds and mammals. Current evidence suggests that harsh environmental conditions or seasonality (e.g. larger variation in temperatures) drive evolution of a biannual moult. In turn, the biannual moult can respond to secondary selection that results in phenotypic alteration such as colour changes for mate choice dynamics (sexual selection) or camouflage requirements (natural selection). We discuss the contributions of natural and sexual selection to the evolution of biannual moulting strategies in the contexts of energetics, niche selection, functionality and physiological mechanisms. Finally, we suggest that moult strategies are directly related to species niche because environmental attributes drive the utility (e.g. thermoregulation, camouflage, social dynamics) of the hair or feathers. Functional efficiency of moult may be undermined if the pace of evolution fails to match that of the changing climate. Thus, future research should seek to understand the plasticity of moult duration and phenology, especially in the context of annual cycles. PMID:29769361

Purification of bioactive phenolics from Phanerochaete chysosporium biomass extract on selected macroporous resins

NASA Astrophysics Data System (ADS)

Idris, Z. M.; Dzahir, M. I. H. M.; Jamal, P.; Barkat, A. A.; Xian, R. L. W.

2017-06-01

In this study, two different types of macroporous resins known as XAD-7HP and HP-20 were evaluated for the adsorption and desorption properties against bioactive phenolics extracted from Phanerochaete chrysosporium. From the previous static sorption studies, it was found that the adsorption capacity for both resins had has no significant difference. Then, the kinetic adsorption data were analyzed with both pseudo-first-order and pseudo-second-order equations and the later performed better. The adsorption isotherm data were fitted well by both Langmuir and Freundlich models. Meanwhile in desorption study, HP-20 and XAD-7HP gave 90.52% and 88.28% recoveries, respectively. Considering the desorption results of the macroporous resins, HP-20 and XAD-7HP were packed in chromatography column to further purify the phenolics. For dynamic adsorption, breakthrough capacity of HP-20 (0.522) was found to be higher than XAD-7HP (0.131). Different ethanol concentrations (30% to 50% (v/v)) were investigated at fixed flowrate (1 ml/min) on phenolics recovery from both types of resins. The highest recovery of bioactive phenolics was 94.3% using XAD-7HP resins at 50% (v/v) of ethanol. Only 77.1% of bioactive phenolics were recovered using HP-20 resin at the same experimental conditions. The purified extract subsequently was analyzed using HPLC. The results showed that three phenolics (gallic acid 3,4-dihydroxybenzoic acid and 4-hydroxybenzoic acid) were identified with higher concentrations as compared to non-purified extract. Finally, the purified extract was tested for scavenging activity against DPPH, and it showed that the activity increased significantly to 90.80% from 59.94% in non-purified extract.

Identification of motivations for unsafe driving actions and potential countermeasures

DOT National Transportation Integrated Search

1982-03-01

This report presents the findings of a preliminary investigation of drivers' motivations for selected unsafe driving actions (UDAs). The general objective of the study was to develop the test methods, procedures, and materials for collecting data for...

Drive-By-Wire Technology

DTIC Science & Technology

2001-05-29

Symposium Intelligent Systems for the Objective Fleet uTransmission controls uSteering (both on-transmission and under-carriage) uBraking (service and...parking) uTransmission select uThrottle uOther Electromechanical Opportunities uTurret drives (elevation, traverse) uAutomatic propellant handling systems

Evolutionary algorithm for vehicle driving cycle generation.

PubMed

Perhinschi, Mario G; Marlowe, Christopher; Tamayo, Sergio; Tu, Jun; Wayne, W Scott

2011-09-01

Modeling transit bus emissions and fuel economy requires a large amount of experimental data over wide ranges of operational conditions. Chassis dynamometer tests are typically performed using representative driving cycles defined based on vehicle instantaneous speed as sequences of "microtrips", which are intervals between consecutive vehicle stops. Overall significant parameters of the driving cycle, such as average speed, stops per mile, kinetic intensity, and others, are used as independent variables in the modeling process. Performing tests at all the necessary combinations of parameters is expensive and time consuming. In this paper, a methodology is proposed for building driving cycles at prescribed independent variable values using experimental data through the concatenation of "microtrips" isolated from a limited number of standard chassis dynamometer test cycles. The selection of the adequate "microtrips" is achieved through a customized evolutionary algorithm. The genetic representation uses microtrip definitions as genes. Specific mutation, crossover, and karyotype alteration operators have been defined. The Roulette-Wheel selection technique with elitist strategy drives the optimization process, which consists of minimizing the errors to desired overall cycle parameters. This utility is part of the Integrated Bus Information System developed at West Virginia University.

Method for removal of phosgene from boron trichloride

DOEpatents

Freund, S.M.

1983-09-20

Selective ultraviolet photolysis using an unfiltered mercury arc lamp has been used to substantially reduce the phosgene impurity in a mixture of boron trichloride and phosgene. Infrared spectrophotometric analysis of the sample before and after irradiation shows that it is possible to highly purify commercially available boron trichloride with this method. 5 figs.

Driving ability in sleep apnoea patients before and after CPAP treatment: evaluation on a road safety platform.

PubMed

Mazza, S; Pépin, J-L; Naëgelé, B; Rauch, E; Deschaux, C; Ficheux, P; Lévy, P

2006-11-01

Sleepiness is considered to be the major cause of increased traffic accidents in patients with obstructive sleep apnoea syndrome (OSAS). Until now, OSAS patients' driving ability has been assessed using driving simulators, but no assessment in a more natural driving environment has been carried out to date. The aim of the present study was to evaluate driving parameters in OSAS and in controls on a road safety platform, and to compare them with attentional in-laboratory measures before and after continuous positive airway pressure treatment. The parameters measured were: reaction time; distance to stop and number of collisions on the platform; maintenance of wakefulness; and sustained, selective and divided attention in laboratory. Patients exhibited much longer reaction times than controls, leading to a lengthening of the vehicle's stopping distance of 8.8 m at 40 km.h(-1) and to twice the number of collisions. Patients did not demonstrate objective sleepiness or selective and sustained attention deficits. Divided attention deficits were found. However, they did not allow the prediction of real driving impairment. After CPAP treatment, there was no longer any difference between patients and controls regarding driving and attention performances. Driving abilities are significantly impaired in obstructive sleep apnoea syndrome. After continuous positive airway pressure treatment, deficits were normalised. This stresses the importance of evaluating attentional parameters in apnoeic patients and of offering continuous positive airway pressure treatment even to non-sleepy subjects.

The TRPM8 Protein Is a Testosterone Receptor

PubMed Central

Asuthkar, Swapna; Demirkhanyan, Lusine; Sun, Xiaohui; Elustondo, Pia A.; Krishnan, Vivek; Baskaran, Padmamalini; Velpula, Kiran Kumar; Thyagarajan, Baskaran; Pavlov, Evgeny V.; Zakharian, Eleonora

2015-01-01

Testosterone is a key steroid hormone in the development of male reproductive tissues and the regulation of the central nervous system. The rapid signaling mechanism induced by testosterone affects numerous behavioral traits, including sexual drive, aggressiveness, and fear conditioning. However, the currently identified testosterone receptor(s) is not believed to underlie the fast signaling, suggesting an orphan pathway. Here we report that an ion channel from the transient receptor potential family, TRPM8, commonly known as the cold and menthol receptor is the major component of testosterone-induced rapid actions. Using cultured and primary cell lines along with the purified TRPM8 protein, we demonstrate that testosterone directly activates TRPM8 channel at low picomolar range. Specifically, testosterone induced TRPM8 responses in primary human prostate cells, PC3 prostate cancer cells, dorsal root ganglion neurons, and hippocampal neurons. Picomolar concentrations of testosterone resulted in full openings of the purified TRPM8 channel in planar lipid bilayers. Furthermore, acute applications of testosterone on human skin elicited a cooling sensation. Our data conclusively demonstrate that testosterone is an endogenous and highly potent agonist of TRPM8, suggesting a role of TRPM8 channels well beyond their well established function in somatosensory neurons. This discovery may further imply TRPM8 channel function in testosterone-dependent behavioral traits. PMID:25480785

Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection.

PubMed

Edwards, C T T; Holmes, E C; Pybus, O G; Wilson, D J; Viscidi, R P; Abrams, E J; Phillips, R E; Drummond, A J

2006-11-01

The evolution of the human immunodeficiency virus (HIV-1) during chronic infection involves the rapid, continuous turnover of genetic diversity. However, the role of natural selection, relative to random genetic drift, in governing this process is unclear. We tested a stochastic model of genetic drift using partial envelope sequences sampled longitudinally in 28 infected children. In each case the Bayesian posterior (empirical) distribution of coalescent genealogies was estimated using Markov chain Monte Carlo methods. Posterior predictive simulation was then used to generate a null distribution of genealogies assuming neutrality, with the null and empirical distributions compared using four genealogy-based summary statistics sensitive to nonneutral evolution. Because both null and empirical distributions were generated within a coalescent framework, we were able to explicitly account for the confounding influence of demography. From the distribution of corrected P-values across patients, we conclude that empirical genealogies are more asymmetric than expected if evolution is driven by mutation and genetic drift only, with an excess of low-frequency polymorphisms in the population. This indicates that although drift may still play an important role, natural selection has a strong influence on the evolution of HIV-1 envelope. A negative relationship between effective population size and substitution rate indicates that as the efficacy of selection increases, a smaller proportion of mutations approach fixation in the population. This suggests the presence of deleterious mutations. We therefore conclude that intrahost HIV-1 evolution in envelope is dominated by purifying selection against low-frequency deleterious mutations that do not reach fixation.

Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora

PubMed Central

Steige, Kim A.; Laenen, Benjamin; Reimegård, Johan; Slotte, Tanja

2017-01-01

Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora. We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are under weaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species. PMID:28096395

Selection for low dormancy in annual ryegrass (Lolium rigidum) seeds results in high constitutive expression of a glucose-responsive α-amylase isoform

PubMed Central

Goggin, Danica E.; Powles, Stephen B.

2012-01-01

Background and Aims α-Amylase in grass caryopses (seeds) is usually expressed upon commencement of germination and is rarely seen in dry, mature seeds. A heat-stable α-amylase activity was unexpectedly selected for expression in dry annual ryegrass (Lolium rigidum) seeds during targeted selection for low primary dormancy. The aim of this study was to characterize this constitutive activity biochemically and determine if its presence conferred insensitivity to the germination inhibitors abscisic acid and benzoxazolinone. Methods α-Amylase activity in developing, mature and germinating seeds from the selected (low-dormancy) and a field-collected (dormant) population was characterized by native activity PAGE. The response of seed germination and α-amylase activity to abscisic acid and benzoxazolinone was assessed. Using an alginate affinity matrix, α-amylase was purified from dry and germinating seeds for analysis of its enzymatic properties. Key Results The constitutive α-amylase activity appeared late during seed development and was mainly localized in the aleurone; in germinating seeds, this activity was responsive to both glucose and gibberellin. It migrated differently on native PAGE compared with the major activities in germinating seeds of the dormant population, but the enzymatic properties of α-amylase purified from the low-dormancy and dormant seeds were largely indistinguishable. Seed imbibition on benzoxazolinone had little effect on the low-dormancy seeds but greatly inhibited germination and α-amylase activity in the dormant population. Conclusions The constitutive α-amylase activity in annual ryegrass seeds selected for low dormancy is electrophoretically different from that in germinating seeds and its presence confers insensitivity to benzoxazolinone. The concurrent selection of low dormancy and constitutive α-amylase activity may help to enhance seedling establishment under competitive conditions. PMID:23002268

Wrong-way driving at selected interstate off-ramps.

DOT National Transportation Integrated Search

1980-01-01

This study was designed to evaluate, on interstate roadways in Virginia, the use of a technique developed in California for estimating or determining incidences of wrong-way driving at off-ramps. Also, information gained from a survey of the availabl...

Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology.

PubMed

Belsom, Adam; Schneider, Michael; Fischer, Lutz; Brock, Oliver; Rappsilber, Juri

2016-03-01

Chemical cross-linking combined with mass spectrometry has proven useful for studying protein-protein interactions and protein structure, however the low density of cross-link data has so far precluded its use in determining structures de novo. Cross-linking density has been typically limited by the chemical selectivity of the standard cross-linking reagents that are commonly used for protein cross-linking. We have implemented the use of a heterobifunctional cross-linking reagent, sulfosuccinimidyl 4,4'-azipentanoate (sulfo-SDA), combining a traditional sulfo-N-hydroxysuccinimide (sulfo-NHS) ester and a UV photoactivatable diazirine group. This diazirine yields a highly reactive and promiscuous carbene species, the net result being a greatly increased number of cross-links compared with homobifunctional, NHS-based cross-linkers. We present a novel methodology that combines the use of this high density photo-cross-linking data with conformational space search to investigate the structure of human serum albumin domains, from purified samples, and in its native environment, human blood serum. Our approach is able to determine human serum albumin domain structures with good accuracy: root-mean-square deviation to crystal structure are 2.8/5.6/2.9 Å (purified samples) and 4.5/5.9/4.8Å (serum samples) for domains A/B/C for the first selected structure; 2.5/4.9/2.9 Å (purified samples) and 3.5/5.2/3.8 Å (serum samples) for the best out of top five selected structures. Our proof-of-concept study on human serum albumin demonstrates initial potential of our approach for determining the structures of more proteins in the complex biological contexts in which they function and which they may require for correct folding. Data are available via ProteomeXchange with identifier PXD001692. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Stubborn contaminants: influence of detergents on the purity of the multidrug ABC transporter BmrA.

PubMed

Wiseman, Benjamin; Kilburg, Arnaud; Chaptal, Vincent; Reyes-Mejia, Gina Catalina; Sarwan, Jonathan; Falson, Pierre; Jault, Jean-Michel

2014-01-01

Despite the growing interest in membrane proteins, their crystallization remains a major challenge. In the course of a crystallographic study on the multidrug ATP-binding cassette transporter BmrA, mass spectral analyses on samples purified with six selected detergents revealed unexpected protein contamination visible for the most part on overloaded SDS-PAGE. A major contamination from the outer membrane protein OmpF was detected in purifications with Foscholine 12 (FC12) but not with Lauryldimethylamine-N-oxide (LDAO) or any of the maltose-based detergents. Consequently, in the FC12 purified BmrA, OmpF easily crystallized over BmrA in a new space group, and whose structure is reported here. We therefore devised an optimized protocol to eliminate OmpF during the FC12 purification of BmrA. On the other hand, an additional band visible at ∼110 kDa was detected in all samples purified with the maltose-based detergents. It contained AcrB that crystallized over BmrA despite its trace amounts. Highly pure BmrA preparations could be obtained using either a ΔacrAB E. coli strain and n-dodecyl-β-D-maltopyranoside, or a classical E. coli strain and lauryl maltose neopentyl glycol for the overexpression and purification, respectively. Overall our results urge to incorporate a proteomics-based purity analysis into quality control checks prior to commencing crystallization assays of membrane proteins that are notoriously arduous to crystallize. Moreover, the strategies developed here to selectively eliminate obstinate contaminants should be applicable to the purification of other membrane proteins overexpressed in E. coli.

Stubborn Contaminants: Influence of Detergents on the Purity of the Multidrug ABC Transporter BmrA

PubMed Central

Chaptal, Vincent; Reyes-Mejia, Gina Catalina; Sarwan, Jonathan; Falson, Pierre; Jault, Jean-Michel

2014-01-01

Despite the growing interest in membrane proteins, their crystallization remains a major challenge. In the course of a crystallographic study on the multidrug ATP-binding cassette transporter BmrA, mass spectral analyses on samples purified with six selected detergents revealed unexpected protein contamination visible for the most part on overloaded SDS-PAGE. A major contamination from the outer membrane protein OmpF was detected in purifications with Foscholine 12 (FC12) but not with Lauryldimethylamine-N-oxide (LDAO) or any of the maltose-based detergents. Consequently, in the FC12 purified BmrA, OmpF easily crystallized over BmrA in a new space group, and whose structure is reported here. We therefore devised an optimized protocol to eliminate OmpF during the FC12 purification of BmrA. On the other hand, an additional band visible at ∼110 kDa was detected in all samples purified with the maltose-based detergents. It contained AcrB that crystallized over BmrA despite its trace amounts. Highly pure BmrA preparations could be obtained using either a ΔacrAB E. coli strain and n-dodecyl-β-D-maltopyranoside, or a classical E. coli strain and lauryl maltose neopentyl glycol for the overexpression and purification, respectively. Overall our results urge to incorporate a proteomics-based purity analysis into quality control checks prior to commencing crystallization assays of membrane proteins that are notoriously arduous to crystallize. Moreover, the strategies developed here to selectively eliminate obstinate contaminants should be applicable to the purification of other membrane proteins overexpressed in E. coli. PMID:25517996

A mechanism for the dynamo terms to sustain closed-flux current, including helicity balance, by driving current which crosses the magnetic field

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

Jarboe, T. R.; Nelson, B. A.; Sutherland, D. A.

2015-07-15

An analysis of imposed dynamo current drive (IDCD) [T.R. Jarboe et al., Nucl. Fusion 52 083017 (2012)] reveals: (a) current drive on closed flux surfaces seems possible without relaxation, reconnection, or other flux-surface-breaking large events; (b) the scale size of the key physics may be smaller than is often computationally resolved; (c) helicity can be sustained across closed flux; and (d) IDCD current drive is parallel to the current which crosses the magnetic field to produce the current driving force. In addition to agreeing with spheromak data, IDCD agrees with selected tokamak data.

Evaluation of ionic air purifiers for reducing aerosol exposure in confined indoor spaces.

PubMed

Grinshpun, S A; Mainelis, G; Trunov, M; Adhikari, A; Reponen, T; Willeke, K

2005-08-01

Numerous techniques have been developed over the years for reducing aerosol exposure in indoor air environments. Among indoor air purifiers of different types, ionic emitters have gained increasing attention and are presently used for removing dust particles, aeroallergens and airborne microorganisms from indoor air. In this study, five ionic air purifiers (two wearable and three stationary) that produce unipolar air ions were evaluated with respect to their ability to reduce aerosol exposure in confined indoor spaces. The concentration decay of respirable particles of different properties was monitored in real time inside the breathing zone of a human manikin, which was placed in a relatively small (2.6 m3) walk-in chamber during the operation of an ionic air purifier in calm air and under mixing air condition. The particle removal efficiency as a function of particle size was determined using the data collected with a size-selective optical particle counter. The removal efficiency of the more powerful of the two wearable ionic purifiers reached about 50% after 15 min and almost 100% after 1.5 h of continuous operation in the chamber under calm air conditions. In the absence of external ventilation, air mixing, especially vigorous one (900 CFM), enhanced the air cleaning effect. Similar results were obtained when the manikin was placed inside a partial enclosure that simulated an aircraft seating configuration. All three stationary ionic air purifiers tested in this study were found capable of reducing the aerosol concentration in a confined indoor space. The most powerful stationary unit demonstrated an extremely high particle removal efficiency that increased sharply to almost 90% within 5-6 min, reaching about 100% within 10-12 min for all particle sizes (0.3-3 microm) tested in the chamber. For the units of the same emission rate, the data suggest that the ion polarity per se (negative vs. positive) does not affect the performance but the ion emission rate does. The effects of particle size (within the tested range) and properties (NaCl, PSL, Pseudomonas fluorescens bacteria) as well as the effects of the manikin's body temperature and its breathing on the ionic purifier performance were either small or insignificant. The data suggest that the unipolar ionic air purifiers are particularly efficient in reducing aerosol exposure in the breathing zone when used inside confined spaces with a relatively high surface-to-volume ratio. Ionic air purifiers have become increasingly popular for removing dust particles, aeroallergens and airborne microorganisms from indoor air in various settings. While the indoor air cleaning effect, resulting from unipolar and bipolar ion emission, has been tested by several investigators, there are still controversial claims (favorable and unfavorable) about the performance of commercially available ionic air purifiers. Among the five tested ionic air purifiers (two wearable and three stationary) producing unipolar air ions, the units with a higher ion emission rate provided higher particle removal efficiency. The ion polarity (negative vs. positive), the particle size (0.3-3 microm) and properties (NaCl, PSL, Pseudomonas fluorescens bacteria), as well as the body temperature and breathing did not considerable affected the ionization-driven particle removal. The data suggest that the unipolar ionic air purifiers are particularly efficient in reducing aerosol exposure in the breathing zone when they are used inside confined spaces with a relatively high surface-to-volume ratio (such as automobile cabins, aircraft seating areas, bathrooms, cellular offices, small residential rooms, and animal confinements). Based on our experiments, we proposed that purifiers with a very high ion emission rate be operated in an intermittent mode if used indoors for extended time periods. As the particles migrate to and deposit on indoor surfaces during the operation of ionic air purifiers, some excessive surface contamination may occur, which introduces the need of periodic cleaning these surfaces.

Power system

DOEpatents

Hickam, Christopher Dale [Glasford, IL

2008-03-18

A power system includes a prime mover, a transmission, and a fluid coupler having a selectively engageable lockup clutch. The fluid coupler may be drivingly connected between the prime mover and the transmission. Additionally, the power system may include a motor/generator drivingly connected to at least one of the prime mover and the transmission. The power-system may also include power-system controls configured to execute a control method. The control method may include selecting one of a plurality of modes of operation of the power system. Additionally, the control method may include controlling the operating state of the lockup clutch dependent upon the mode of operation selected. The control method may also include controlling the operating state of the motor/generator dependent upon the mode of operation selected.

Bidirectional Drive-And-Brake Mechanism

NASA Technical Reports Server (NTRS)

Swan, Scott A.

1991-01-01

Vehicle that crawls along monorail combines features of both bicycle and railroad handcar. Bidirectional drive-and-brake mechanism includes selectable-pawl-and-ratchet overrunning clutch (drive mechanism) and mating stationary and rotating conical surfaces pressing against each other (brake mechanism). Operates similarly to bicycle drive-and-brake mechanism except limits rotation of sprocket in both directions and brakes at both limits. Conceived for use by astronaut traveling along structure in outer space, concept also applied on Earth to make very small railraod handcars or crawling vehicles for use on large structures, in pipelines under construction, or underwater.

Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain

PubMed Central

Schrider, Daniel R.; Kern, Andrew D.

2015-01-01

The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely missed by searching for sequence conservation across species. Here we present an analysis based on variation data among human genomes that utilizes a supervised machine learning approach for the identification of human-specific purifying selection in the genome. Using only allele frequency information from the complete low-coverage 1000 Genomes Project data set in conjunction with a support vector machine trained from known functional and nonfunctional portions of the genome, we are able to accurately identify portions of the genome constrained by purifying selection. Our method identifies previously known human-specific gains or losses of function and uncovers many novel candidates. Candidate targets for gain and loss of function along the human lineage include numerous putative regulatory regions of genes essential for normal development of the central nervous system, including a significant enrichment of gain of function events near neurotransmitter receptor genes. These results are consistent with regulatory turnover being a key mechanism in the evolution of human-specific characteristics of brain development. Finally, we show that the majority of the genome is unconstrained by natural selection currently, in agreement with what has been estimated from phylogenetic methods but in sharp contrast to estimates based on transcriptomics or other high-throughput functional methods. PMID:26590212

Selective Perception for Robot Driving

DTIC Science & Technology

1992-05-01

models are theories of human cognitive activity during driving. Van der Molen and Botticher recently reviewed several of these models [ van der Molen 871...how to represent driving knowledge, how to perceive traffic situations, or how to process information to obtain actions. Van der Molen and Botticher...attempted to compare the operations of various models objectively on the same task [Rothengatter 88, van der Molen 87], but the models could be

Psychological and sociodemographic characteristics of accident involved drivers : a survey of the literature.

DOT National Transportation Integrated Search

1976-01-01

This report reviews selected portions of the literature concerning the psychology of negligent driving. In particular, it stresses those studies which attempt to quantify and predict aberrant driving behavior. Reviewed are such topics as the role of ...

Electrochemical Glucose Biosensor Based on Glucose Oxidase Displayed on Yeast Surface.

PubMed

Wang, Hongwei; Lang, Qiaolin; Liang, Bo; Liu, Aihua

2015-01-01

The conventional enzyme-based biosensor requires chemical or physical immobilization of purified enzymes on electrode surface, which often results in loss of enzyme activity and/or fractions immobilized over time. It is also costly. A major advantage of yeast surface display is that it enables the direct utilization of whole cell catalysts with eukaryote-produced proteins being displayed on the cell surface, providing an economic alternative to traditional production of purified enzymes. Herein, we describe the details of the display of glucose oxidase (GOx) on yeast cell surface and its application in the development of electrochemical glucose sensor. In order to achieve a direct electrochemistry of GOx, the entire cell catalyst (yeast-GOx) was immobilized together with multiwalled carbon nanotubes on the electrode, which allowed sensitive and selective glucose detection.

Purification and properties of aryl acylamidase from Pseudomonas fluorescens ATCC 39004.

PubMed

Hammond, P M; Price, C P; Scawen, M D

1983-05-16

Aryl acylamidase has been purified from a strain of Pseudomonas fluorescens ATCC 39004, selected from soil on the basis of its ability to utilise acylanilide compounds as a sole source of carbon. The enzyme was purified to homogeneity by a combination of ion-exchange, hydrophobic and gel-permeation chromatography. A relative molecular mass of about 52 500 was estimated by gel filtration. The native enzyme was shown to be a monomeric protein by sodium dodecyl sulphate/polyacrylamide gel electrophoresis. The enzyme was maximally active at a pH of 8.6 and at a temperature of 45 degrees C. The enzyme shows Michaelis-Menten kinetics; Km values for nitroacetanilide (69 microM) and hydroxyacetanilide (6.1 microM) were low, indicating that the enzyme has a very high affinity for both substrates.

Selection and Reduced Population Size Cannot Explain Higher Amounts of Neandertal Ancestry in East Asian than in European Human Populations

PubMed Central

Kim, Bernard Y.; Lohmueller, Kirk E.

2015-01-01

It has been hypothesized that the greater proportion of Neandertal ancestry in East Asians than in Europeans is due to the fact that purifying selection is less effective at removing weakly deleterious Neandertal alleles from East Asian populations. Using simulations of a broad range of models of selection and demography, we have shown that this hypothesis cannot account for the higher proportion of Neandertal ancestry in East Asians than in Europeans. Instead, more complex demographic scenarios, most likely involving multiple pulses of Neandertal admixture, are required to explain the data. PMID:25683122

Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

DOE PAGES

Mkhitaryan, V. V.; Jelezko, F.; Dobrovitski, V. V.

2015-10-26

We consider an electronic spin, such as a nitrogen-vacancy center in diamond, weakly coupled to a large number of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase. We show that by switching the driving phase synchronously with the precession of a given nuclear spin, the interaction to this spin is selectively enhanced, while the rest of the bath remains decoupled. The enhancement is of resonant character. The key feature of the suggested scheme is that the width of the resonance is adjustable, and can be greatly decreased by increasing the driving strength. Thus, the resonancemore » can be significantly narrowed, by a factor of 10–100 in comparison with the existing detection methods. Significant improvement in selectivity is explained analytically and confirmed by direct numerical many-spin simulations. As a result, the method can be applied to a wide range of solid-state systems.« less

Aptamer facilitated purification of functional proteins.

PubMed

Beloborodov, Stanislav S; Bao, Jiayin; Krylova, Svetlana M; Shala-Lawrence, Agnesa; Johnson, Philip E; Krylov, Sergey N

2018-01-15

DNA aptamers are attractive capture probes for affinity chromatography since, in contrast to antibodies, they can be chemically synthesized and, in contrast to tag-specific capture probes (such as Nickel-NTA or Glutathione), they can be used for purification of proteins free of genetic modifications (such as His or GST tags). Despite these attractive features of aptamers as capture probes, there are only a few reports on aptamer-based protein purification and none of them includes a test of the purified protein's activity, thus, leaving discouraging doubts about method's ability to purify proteins in their active state. The goal of this work was to prove that aptamers could facilitate isolation of active proteins. We refined a complete aptamer-based affinity purification procedure, which takes 4 h to complete. We further applied this procedure to purify two recombinant proteins, MutS and AlkB, from bacterial cell culture: 0.21 mg of 85%-pure AlkB from 4 mL of culture and 0.24 mg of 82%-pure MutS from 0.5 mL of culture. Finally, we proved protein activity by two capillary electrophoresis based assays: an enzymatic assay for AlkB and a DNA-binding assay for MutS. We suggest that in combination with aptamer selection for non-purified protein targets in crude cell lysate, aptamer-based purification provides a means of fast isolation of tag-free recombinant proteins in their native state without the use of antibodies. Copyright © 2017 Elsevier B.V. All rights reserved.

[Identification and production of monoclonal antibody of Siberian tiger's immunoglobulin].

PubMed

Zhang, Yaonglong; Zhang, Duanling; Zhou, Ming; Xue, Yuan; Hua, Yuping; Ma, Jianzhang

2010-03-01

To purify immunoglobulin (Ig) of Siberian Tiger and prepare monoclonal antibody (mAb) against the Ig,which can be used to develop immunological diagnostic kits for diagnosing infectious disease in Siberian Tiger. The Ig of Siberian tigers was purified with saturated ammonium sulfate combined with recombinant Protein G. The C57BL/6 mice were immunized with the purified Ig. Spleno-cytes of the mice immunized were collected and fused with the mouse myeloma cell line (Sp2/0-Ag14). The positive hybridoma clones were selected by ELISA and were identified by western blot. The sandwich ELISA was used to detect immunocompetence of the purified Ig and the mAb. We obtained three mouse hybridoma clones that produced mAbs against Ig of Siberian Tiger. The derived McAbs could recognize Ig heavy chain of Siberian Tiger specifically. The biological activity of the Ig and obtained McAbs also could be identified by detecting the antibody induced by panleukopenia virus (FPV-HLJ) vaccine in Siberian Tiger. The antibody also would be useful for assess the vaccine efficacy against the infectious disease on the Siberian Tiger. Protein G can be used in Ig purification of Siberian Tiger. The obtained McAbs from the hybridoma ADT11 in this study owned strong ability to bind Ig of Siberian Tiger and have a stable immunocompetence. They can be used to develop diagnostic methods for detecting infectious disease in Siberian Tiger and vaccine research.

Expression, Identification and Purification of Dictyostelium Acetoacetyl-CoA Thiolase Expressed in Escherichia coli

PubMed Central

Tanaka, Takeshi; Shima, Yasuyuki; Ogawa, Naoki; Nagayama, Koki; Yoshida, Takashi; Ohmachi, Tetsuo

2011-01-01

Acetoacetyl-CoA thiolase (AT) is an enzyme that catalyses the CoA-dependent thiolytic cleavage of acetoacetyl-CoA to yield 2 molecules of acetyl-CoA, or the reverse condensation reaction. A full-length cDNA clone pBSGT-3, which has homology to known thiolases, was isolated from Dictyostelium cDNA library. Expression of the protein encoded in pBSGT-3 in Escherichia coli, its thiolase enzyme activity, and the amino acid sequence homology search revealed that pBSGT-3 encodes an AT. The recombinant AT (r-thiolase) was expressed in an active form in an E. coli expression system, and purified to homogeneity by selective ammonium sulfate fractionation and two steps of column chromatography. The purified enzyme exhibited a specific activity of 4.70 mU/mg protein. Its N-terminal sequence was (NH2)-Arg-Met-Tyr-Thr-Thr-Ala-Lys-Asn-Leu-Glu-, which corresponds to the sequence from positions 15 to 24 of the amino acid sequence deduced from pBSGT-3 clone. The r-thiolase in the inclusion body expressed highly in E. coli was the precursor form, which is slightly larger than the purified r-thiolase. When incubated with the cell-free extract of Dictyostelium cells, the precursor was converted to the same size to the purified r-thiolase, suggesting that the presequence at the N-terminus is removed by a Dictyostelium processing peptidase. PMID:21209787

Application of aqueous biphasic systems as strategy to purify tannase from Aspergillus tamarii URM 7115.

PubMed

de Sena, Amanda Reges; Barros Oliveira, Flávio Manoel; Campos Leite, Tonny Cley; Evaristo da Silva Nascimento, Talita Camila; Moreira, Keila Aparecida; de Assis, Sandra Aparecida

2017-10-21

The aims of the current study are to assess the influence of polyethylene glycol (PEG) concentration, molar mass, pH, and citrate concentrations on aqueous biphasic systems based on 2 4 factorial designs, as well as to check their capacity to purify tannase secreted by Aspergillus tamarii URM 7115. Tannase was produced through submerged fermentation at 26°C for 67 h in Czapeck-Dox modified broth and added with yeast extract and tannic acid. The factorial design was followed to assess the influence of PEG molar mass (M PEG 600; 4,000 and 8,000 g/ mol), and PEG (C PEG 20.0; 22.0 and 24.0% w/w) and citrate concentrations (C CIT 15.0, 17.5, and 20.0%, w/w), as well as of pH (6.0, 7.0, and 8.0) on the response variables; moreover, partition coefficient (K), yield (Y), and purification factor (PF) were analyzed. The most suitable parameters to purify tannase secreted by A. tamarii URM 7115 through a biphasic system were 600 (g/mol) M PEG , 24% (w/w) C PEG , 15% (w/w) C CIT at pH 6.0 and they resulted in 6.33 enzyme partition, 131.25% yield, 19.80 purification factor and 195.08 selectivity. Tannase secreted by A. tamarii URM 7115 purified through aqueous biphasic systems composed of PEG/citrate can be used for industrial purposes, since it presents suitable purification factor and yield.

A Ten-Week Biochemistry Lab Project Studying Wild-Type and Mutant Bacterial Alkaline Phosphatase

ERIC Educational Resources Information Center

Witherow, D. Scott

2016-01-01

This work describes a 10-week laboratory project studying wild-type and mutant bacterial alkaline phosphatase, in which students purify, quantitate, and perform kinetic assays on wild-type and selected mutants of the enzyme. Students also perform plasmid DNA purification, digestion, and gel analysis. In addition to simply learning important…

Method for removal of phosgene from boron trichloride. [DOE patent application; mercury arc lamp

DOEpatents

Freund, S.M.

1981-09-03

Selective ultraviolet photolysis using an unfiltered mercury arc lamp has been used to substantially reduce the phosgene impurity in a mixture of boron trichloride and phosgene. Infrared spectrophotometric analysis of the sample before and after irradiation shows that it is possible to highly purify commercially available boron trichloride with this method.

Molecular and biological characterization of 'Rs551, a filamentous bacteriophage isolated from a race 3 biovar 2 strain of Ralstonia solanacearum

USDA-ARS?s Scientific Manuscript database

A filamentous bacteriophage, designated 'Rs551, was isolated and purified from the quarantine and select agent phytopathogen Ralstonia solanacearum race 3 biovar 2 strain UW551 (phylotype IIB sequevar 1) grown under normal culture conditions. Electron microscopy suggested that 'Rs551 is a member of ...

The drive-wise project: driving simulator training increases real driving performance in healthy older drivers

PubMed Central

Casutt, Gianclaudio; Theill, Nathan; Martin, Mike; Keller, Martin; Jäncke, Lutz

2014-01-01

Background: Age-related cognitive decline is often associated with unsafe driving behavior. We hypothesized that 10 active training sessions in a driving simulator increase cognitive and on-road driving performance. In addition, driving simulator training should outperform cognitive training. Methods: Ninety-one healthy active drivers (62–87 years) were randomly assigned to one of three groups: (1) a driving simulator training group, (2) an attention training group (vigilance and selective attention), or (3) a control group. The main outcome variables were on-road driving and cognitive performance. Seventy-seven participants (85%) completed the training and were included in the analyses. Training gains were analyzed using a multiple regression analysis with planned orthogonal comparisons. Results: The driving simulator-training group showed an improvement in on-road driving performance compared to the attention-training group. In addition, both training groups increased cognitive performance compared to the control group. Conclusion: Driving simulator training offers the potential to enhance driving skills in older drivers. Compared to the attention training, the simulator training seems to be a more powerful program for increasing older drivers' safety on the road. PMID:24860497

A Driving Simulator Evaluation of Cross-Sectional Design Elements and the Resulting Driving Behaviors

DOT National Transportation Integrated Search

2017-09-01

This research explores the relationship between the cross-sectional design elements and the impact on selected driver attributes such as speed profiles and lateral positioning. In this experiment a traditional collector-type base roadway of 1.5 miles...

Identification of countermeasures for unsafe driving actions. Volume 2, A review of selected literature

DOT National Transportation Integrated Search

1981-02-01

Literature on decision-making and social control was reviewed to identify key principles of human behavior that have potential for reducing the incidence of speed-too-fast and other conscious and intentional unsafe driving actions (UDAs). The review ...

A comparison of crashes and fatalities in Texas by age group : selected cities in Texas.

DOT National Transportation Integrated Search

2012-10-01

In recent decades, great strides have been made to lower the number of accidents that occur on Texas roadways through graduated drivers licensing programs, messages against texting and driving, and discouraging drunk driving. Statistics show that you...

A linear magnetic motor and generator

NASA Technical Reports Server (NTRS)

Studer, P. A.

1980-01-01

In linear magnetic motor and generator suitable for remote and hostile environments, magnetic forces drive reciprocating shaft along its axis. Actuator shaft is located in center of cylindrical body and may be supported by either contacting or noncontacting bearings. When device operates as bidirectional motor, drive coil selectively adds and subtracts magnetic flux to and from flux paths, producing forces that drive actuator along axis. When actuator is driven by external reciprocating engine, device becomes ac generator.

Promiscuity drives sexual selection in a socially monogamous bird.

PubMed

Webster, Michael S; Tarvin, Keith A; Tuttle, Elaina M; Pruett-Jones, Stephen

2007-09-01

Many socially monogamous species paradoxically show signs of strong sexual selection, suggesting cryptic sources of sexual competition among males. Darwin argued that sexual selection could operate in monogamous systems if breeding sex ratios are biased or if some males attract highly fecund females. Alternatively, sexual selection might result from promiscuous copulations outside the pair bond, although several recent studies have cast doubt on this possibility, in particular by showing that variance in apparent male reproductive success (number of social young) differs little from variance in actual male reproductive success (number of young sired). Our results from a long-term study of the socially monogamous splendid fairy-wren (Malurus splendens) demonstrate that such comparisons are misleading and do not adequately assess the effects of extra-pair paternity (EPP). By partitioning the opportunity for selection and calculating Bateman gradients, we show that EPP has a strong effect on male annual and lifetime fitness, whereas other proposed mechanisms of sexual selection do not. Thus, EPP drives sexual selection in this, and possibly other, socially monogamous species.

Effects of Cognitive Load on Driving Performance: The Cognitive Control Hypothesis.

PubMed

Engström, Johan; Markkula, Gustav; Victor, Trent; Merat, Natasha

2017-08-01

The objective of this paper was to outline an explanatory framework for understanding effects of cognitive load on driving performance and to review the existing experimental literature in the light of this framework. Although there is general consensus that taking the eyes off the forward roadway significantly impairs most aspects of driving, the effects of primarily cognitively loading tasks on driving performance are not well understood. Based on existing models of driver attention, an explanatory framework was outlined. This framework can be summarized in terms of the cognitive control hypothesis: Cognitive load selectively impairs driving subtasks that rely on cognitive control but leaves automatic performance unaffected. An extensive literature review was conducted wherein existing results were reinterpreted based on the proposed framework. It was demonstrated that the general pattern of experimental results reported in the literature aligns well with the cognitive control hypothesis and that several apparent discrepancies between studies can be reconciled based on the proposed framework. More specifically, performance on nonpracticed or inherently variable tasks, relying on cognitive control, is consistently impaired by cognitive load, whereas the performance on automatized (well-practiced and consistently mapped) tasks is unaffected and sometimes even improved. Effects of cognitive load on driving are strongly selective and task dependent. The present results have important implications for the generalization of results obtained from experimental studies to real-world driving. The proposed framework can also serve to guide future research on the potential causal role of cognitive load in real-world crashes.

α-l-rhamnosidase selective for rutin to isoquercitrin transformation from Penicillium griseoroseum MTCC-9224.

PubMed

Yadav, Sarita; Yadava, Sudha; Yadav, Kapil D S

2017-02-01

An α-l-rhamnosidase secreting fungal strain has been isolated from the decaying goose berry (Emblica officinalis) fruit peel. The fungal strain has been identified as Penicillium greoroseum MTCC-9224. The α-l-rhamnosidase of this fungal strain has been purified to homogeneity using a simple procedure involving concentration by ultra filtration and an anion exchange chromatography on DEAE-cellulose. The purified enzyme gave a single protein band corresponding to molecular mass of 97kDa in SDS-PAGE analysis. The native-PAGE analysis also gave a single protein band confirming the purity of the enzyme. Using p-nitrophenyl-α-l-rhamnopyranoside as the substrate, K m and k cat values of the enzyme were 0.65mM and 43.65s -1 , respectively. The pH and temperature optima of the enzyme were 6.5 and 57°C, respectively. The activation energy for the thermal denaturation of the enzyme was 27.9kJ/mol. The purified α-l-rhamnosidase hydrolyzed rutin to isoquercitrin and l-rhamnose but has no effect on naringin and hesperidin. Copyright © 2017 Elsevier Inc. All rights reserved.

Derivation of highly purified cardiomyocytes from human induced pluripotent stem cells using small molecule-modulated differentiation and subsequent glucose starvation.

PubMed

Sharma, Arun; Li, Guang; Rajarajan, Kuppusamy; Hamaguchi, Ryoko; Burridge, Paul W; Wu, Sean M

2015-03-18

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have become an important cell source to address the lack of primary cardiomyocytes available for basic research and translational applications. To differentiate hiPSCs into cardiomyocytes, various protocols including embryoid body (EB)-based differentiation and growth factor induction have been developed. However, these protocols are inefficient and highly variable in their ability to generate purified cardiomyocytes. Recently, a small molecule-based protocol utilizing modulation of Wnt/β-Catenin signaling was shown to promote cardiac differentiation with high efficiency. With this protocol, greater than 50%-60% of differentiated cells were cardiac troponin-positive cardiomyocytes were consistently observed. To further increase cardiomyocyte purity, the differentiated cells were subjected to glucose starvation to specifically eliminate non-cardiomyocytes based on the metabolic differences between cardiomyocytes and non-cardiomyocytes. Using this selection strategy, we consistently obtained a greater than 30% increase in the ratio of cardiomyocytes to non-cardiomyocytes in a population of differentiated cells. These highly purified cardiomyocytes should enhance the reliability of results from human iPSC-based in vitro disease modeling studies and drug screening assays.

Metabolism of aspartame by human and pig intestinal microvillar peptidases.

PubMed Central

Hooper, N M; Hesp, R J; Tieku, S

1994-01-01

The artificial sweetener aspartame (N-L-alpha-aspartyl-L-phenyl-alanine-1-methyl ester; Nutrasweet), its decomposition product alpha Asp-Phe and the related peptide alpha Asp-PheNH2 were rapidly hydrolysed by microvillar membranes prepared from human duodenum, jejunum and ileum, and from pig duodenum and kidney. The metabolism of aspartame by the human and pig intestinal microvillar membrane preparations was inhibited significantly (> 78%) by amastatin or 1,10-phenanthroline, and partially (> 38%) by actinonin or bestatin, and was activated 2.9-4.5-fold by CaCl2. The inhibition by amastatin and 1,10-phenanthroline, and the activation by CaCl2 are characteristic of the cell-surface ectoenzyme aminopeptidase A (EC 3.4.11.7) and a purified preparation of this enzyme hydrolysed aspartame with a Km of 0.25 mM and a Vmax of 126 mumol/min per mg. A purified preparation of aminopeptidase W (EC 3.4.11.16) also hydrolysed aspartame but with a Km of 4.96 mM and a Vmax of 110 mumol/min per mg. However, rentiapril, an inhibitor of aminopeptidase W, caused only slight inhibition (maximally 19%) of the hydrolysis of aspartame by the microvillar membrane preparations. Similar patterns of inhibition and kinetic parameters were observed for alpha Asp-Phe and alpha Asp-PheNH2. Two other decomposition products of aspartame, beta Asp-PheMe and cyclo-Asp-Phe, were essentially resistant to hydrolysis by both the human and pig intestinal microvillar membrane preparations and the purified preparations of aminopeptidases A and W. Although the relatively selective inhibitor of aminopeptidase N (EC 3.4.11.2), actinonin, partially inhibited the metabolism of aspartame, alpha Asp-Phe and alpha Asp-PheNH2 by the human and pig intestinal microvillar membrane preparations, these peptides were not hydrolysed by a purified preparation of aminopeptidase N. Membrane dipeptidase (EC 3.4.13.19) only hydrolysed the unblocked dipeptide, alpha Asp-Phe, but the selective inhibitor of this enzyme, cilastatin, did not block the metabolism of alpha Asp-Phe by the microvillar membrane preparations. PMID:8141778

Robust Fault Diagnosis in Electric Drives Using Machine Learning

DTIC Science & Technology

2004-09-08

detection of fault conditions of the inverter. A machine learning framework is developed to systematically select torque-speed domain operation points...were used to generate various fault condition data for machine learning . The technique is viable for accurate, reliable and fast fault detection in electric drives.

A Quantitative Evaluation of Drive Pattern Selection for Optimizing EIT-Based Stretchable Sensors

PubMed Central

Nefti-Meziani, Samia; Carbonaro, Nicola

2017-01-01

Electrical Impedance Tomography (EIT) is a medical imaging technique that has been recently used to realize stretchable pressure sensors. In this method, voltage measurements are taken at electrodes placed at the boundary of the sensor and are used to reconstruct an image of the applied touch pressure points. The drawback with EIT-based sensors, however, is their low spatial resolution due to the ill-posed nature of the EIT reconstruction. In this paper, we show our performance evaluation of different EIT drive patterns, specifically strategies for electrode selection when performing current injection and voltage measurements. We compare voltage data with Signal-to-Noise Ratio (SNR) and Boundary Voltage Changes (BVC), and study image quality with Size Error (SE), Position Error (PE) and Ringing (RNG) parameters, in the case of one-point and two-point simultaneous contact locations. The study shows that, in order to improve the performance of EIT based sensors, the electrode selection strategies should dynamically change correspondingly to the location of the input stimuli. In fact, the selection of one drive pattern over another can improve the target size detection and position accuracy up to 4.7% and 18%, respectively. PMID:28858252

A Quantitative Evaluation of Drive Pattern Selection for Optimizing EIT-Based Stretchable Sensors.

PubMed

Russo, Stefania; Nefti-Meziani, Samia; Carbonaro, Nicola; Tognetti, Alessandro

2017-08-31

Electrical Impedance Tomography (EIT) is a medical imaging technique that has been recently used to realize stretchable pressure sensors. In this method, voltage measurements are taken at electrodes placed at the boundary of the sensor and are used to reconstruct an image of the applied touch pressure points. The drawback with EIT-based sensors, however, is their low spatial resolution due to the ill-posed nature of the EIT reconstruction. In this paper, we show our performance evaluation of different EIT drive patterns, specifically strategies for electrode selection when performing current injection and voltage measurements. We compare voltage data with Signal-to-Noise Ratio (SNR) and Boundary Voltage Changes (BVC), and study image quality with Size Error (SE), Position Error (PE) and Ringing (RNG) parameters, in the case of one-point and two-point simultaneous contact locations. The study shows that, in order to improve the performance of EIT based sensors, the electrode selection strategies should dynamically change correspondingly to the location of the input stimuli. In fact, the selection of one drive pattern over another can improve the target size detection and position accuracy up to 4.7% and 18%, respectively.

Redundant motor drive system

NASA Technical Reports Server (NTRS)

Calvert, J. A. (Inventor)

1980-01-01

A drive system characterized by a base supporting a pair of pillars arranged in spaced parallelism, a shaft extended between and supported by the pillars for rotation about the longitudinal axis thereof, a worm gear affixed to the shaft and supported in coaxial relation therewith is described. A bearing housing of a sleeve like configuration is concentrically related to the shaft and is supported thereby for free rotation. A first and a second quiescent drive train, alternatively activatable, is provided for imparting rotation into said bearing housing. Each of the drive trains is characterized by a selectively energizable motor connected to a spur gear.

EVOLUTION OF DIVERGENT FEMALE MATING PREFERENCE IN RESPONSE TO EXPERIMENTAL SEXUAL SELECTION

PubMed Central

Debelle, Allan; Ritchie, Michael G; Snook, Rhonda R

2014-01-01

Sexual selection is predicted to drive the coevolution of mating signals and preferences (mating traits) within populations, and could play a role in speciation if sexual isolation arises due to mating trait divergence between populations. However, few studies have demonstrated that differences in mating traits between populations result from sexual selection alone. Experimental evolution is a promising approach to directly examine the action of sexual selection on mating trait divergence among populations. We manipulated the opportunity for sexual selection (low vs. high) in populations of Drosophila pseudoobscura. Previous studies on these experimental populations have shown that sexual selection manipulation resulted in the divergence between sexual selection treatments of several courtship song parameters, including interpulse interval (IPI) which markedly influences male mating success. Here, we measure female preference for IPI using a playback design to test for preference divergence between the sexual selection treatments after 130 generations of experimental sexual selection. The results suggest that female preference has coevolved with male signal, in opposite directions between the sexual selection treatments, providing direct evidence of the ability of sexual selection to drive the divergent coevolution of mating traits between populations. We discuss the implications in the context sexual selection and speciation. PMID:24931497

Myosin light chain 2-based selection of human iPSC-derived early ventricular cardiac myocytes

PubMed Central

Bizy, Alexandra; Guerrero-Serna, Guadalupe; Hu, Bin; Ponce-Balbuena, Daniela; Willis, B. Cicero; Zarzoso, Manuel; Ramirez, Rafael J.; Sener, Michelle F.; Mundada, Lakshmi V.; Klos, Matthew; Devaney, Eric J.; Vikstrom, Karen L.; Herron, Todd J.; Jalife, José

2014-01-01

Applications of human induced pluripotent stemcell derived-cardiac myocytes (hiPSC-CMs) would be strengthened by the ability to generate specific cardiac myocyte (CM) lineages. However, purification of lineage-specific hiPSC-CMs is limited by the lack of cell marking techniques. Here, we have developed an iPSC-CM marking system using recombinant adenoviral reporter constructs with atrial- or ventricular-specific myosin light chain-2 (MLC-2) promoters. MLC-2a and MLC-2v selected hiPSC-CMs were purified by fluorescence-activated cell sorting and their biochemical and electrophysiological phenotypes analyzed. We demonstrate that the phenotype of both populations remained stable in culture and they expressed the expected sarcomeric proteins, gap junction proteins and chamber-specific transcription factors. Compared to MLC-2a cells, MLC-2v selected CMs had larger action potential amplitudes and durations. In addition, by immunofluorescence, we showed that MLC-2 isoform expression can be used to enrich hiPSC-CM consistent with early atrial and ventricularmyocyte lineages. However, only the ventricular myosin light chain-2 promoter was able to purify a highly homogeneous population of iPSC-CMs. Using this approach, it is now possible to develop ventricular-specific disease models using iPSC-CMs while atrial-specific iPSC-CM cultures may require additional chamber-specific markers. PMID:24095945

Myosin light chain 2-based selection of human iPSC-derived early ventricular cardiac myocytes.

PubMed

Bizy, Alexandra; Guerrero-Serna, Guadalupe; Hu, Bin; Ponce-Balbuena, Daniela; Willis, B Cicero; Zarzoso, Manuel; Ramirez, Rafael J; Sener, Michelle F; Mundada, Lakshmi V; Klos, Matthew; Devaney, Eric J; Vikstrom, Karen L; Herron, Todd J; Jalife, José

2013-11-01

Applications of human induced pluripotent stem cell derived-cardiac myocytes (hiPSC-CMs) would be strengthened by the ability to generate specific cardiac myocyte (CM) lineages. However, purification of lineage-specific hiPSC-CMs is limited by the lack of cell marking techniques. Here, we have developed an iPSC-CM marking system using recombinant adenoviral reporter constructs with atrial- or ventricular-specific myosin light chain-2 (MLC-2) promoters. MLC-2a and MLC-2v selected hiPSC-CMs were purified by fluorescence-activated cell sorting and their biochemical and electrophysiological phenotypes analyzed. We demonstrate that the phenotype of both populations remained stable in culture and they expressed the expected sarcomeric proteins, gap junction proteins and chamber-specific transcription factors. Compared to MLC-2a cells, MLC-2v selected CMs had larger action potential amplitudes and durations. In addition, by immunofluorescence, we showed that MLC-2 isoform expression can be used to enrich hiPSC-CM consistent with early atrial and ventricular myocyte lineages. However, only the ventricular myosin light chain-2 promoter was able to purify a highly homogeneous population of iPSC-CMs. Using this approach, it is now possible to develop ventricular-specific disease models using iPSC-CMs while atrial-specific iPSC-CM cultures may require additional chamber-specific markers. © 2013.

Magnetically multiplexed heating of single domain nanoparticles

NASA Astrophysics Data System (ADS)

Christiansen, M. G.; Senko, A. W.; Chen, R.; Romero, G.; Anikeeva, P.

2014-05-01

Selective hysteretic heating of multiple collocated types of single domain magnetic nanoparticles (SDMNPs) by alternating magnetic fields (AMFs) may offer a useful tool for biomedical applications. The possibility of "magnetothermal multiplexing" has not yet been realized, in part due to prevalent use of linear response theory to model SDMNP heating in AMFs. Dynamic hysteresis modeling suggests that specific driving conditions play an underappreciated role in determining optimal material selection strategies for high heat dissipation. Motivated by this observation, magnetothermal multiplexing is theoretically predicted and empirically demonstrated by selecting SDMNPs with properties that suggest optimal hysteretic heat dissipation at dissimilar AMF driving conditions. This form of multiplexing could effectively offer multiple channels for minimally invasive biological signaling applications.

Characterizing ultrafine particles and other air pollutants in and around school buses.

PubMed

Zhu, Yifang; Zhang, Qunfang

2014-03-01

Increasing evidence has demonstrated toxic effects of ultrafine particles (UFP*, diameter < 100 nm). Children are particularly at risk because of their immature respiratory systems and higher breathing rates per body mass. This study aimed to characterize UFP, PM2.5 (particulate matter < or = 2.5 microm in aerodynamic diameter), and other vehicular-emitted pollutants in and around school buses. Four sub-studies were conducted, including: 1. On-road tests to measure in-cabin air pollutant levels while school buses were being driven; 2. Idling tests to determine the contributions of tailpipe emissions from idling school buses to air pollutant levels in and around school buses under different scenarios; 3. Retrofit tests to evaluate the performance of two retrofit systems, a diesel oxidation catalyst (DOC) muffler and a crankcase filtration system (CFS), on reducing tailpipe emissions and in-cabin air pollutant concentrations under idling and driving conditions; and 4. High efficiency particulate air (HEPA) filter air purifier tests to evaluate the effectiveness of in-cabin filtration. In total, 24 school buses were employed to cover a wide range of school buses commonly used in the United States. Real-time air quality measurements included particle number concentration (PNC), fine and UFP size distribution in the size range 7.6-289 nm, PM2.5 mass concentration, black carbon (BC) concentration, and carbon monoxide (CO) and carbon dioxide (CO2) concentrations. For in-cabin measurements, instruments were placed on a platform secured to the rear seats inside the school buses. For all other tests, a second set of instruments was deployed to simultaneously measure the ambient air pollutant levels. For tailpipe emission measurements, the exhaust was diluted and then measured by instruments identical to those used for the in-cabin measurements. The results show that when driving on roads, in-cabin PNC, fine and UFP size distribution, PM2.5, BC, and CO varied by engine age, window position, driving speed, driving route, and operating conditions. Emissions from idling school buses increased the PNC close to the tailpipe by a factor of up to 26.0. Under some circumstances, tailpipe emissions of idling school buses increased the in-cabin PNC by factors ranging from 1.2 to 5.8 in the 10-30 nm particle size range. Retrofit systems significantly reduced the tailpipe emissions of idling school buses. With both DOC and CFS installed, PNC in tailpipe emissions dropped by 20%-94%. No unequivocal decrease was observed for in-cabin air pollutants after retrofitting. The operation of the air conditioning (AC) unit and the pollutant concentrations in the surrounding ambient air played more important roles than retrofit technologies in determining in-cabin air quality. The use of a HEPA air purifier removed up to 50% of in-cabin particles. Because each sub-study tested only a subset of the 24 school buses, the results should be seen as more exploratory than definitive.

Exploration of the SHRP2 naturalistic driving study data to identify factors related to the selection of freeway ramp design speed.

DOT National Transportation Integrated Search

2017-03-01

This research explored the second Strategic Highway Research Program (SHRP2) Naturalistic Driving Study (NDS) database for the potential to identify freeway entrance and exit ramps and teen drivers behavior while traveling those ramps. This is in ...

A nanobody directed to a functional epitope on VEGF, as a novel strategy for cancer treatment

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

Farajpour, Zahra; Rahbarizadeh, Fatemeh, E-mail: rahbarif@modares.ac.ir; Kazemi, Bahram

Highlights: • A novel nanobody directed to antigenic regions on VEGF was identified. • Our nanobody was successfully purified. • Our nanobody significantly inhibited VEGF-induced proliferation of HUVECs in a dose dependent manner. - Abstract: Compelling evidence suggests that vascular endothelial growth factor (VEGF), due to its essential role in angiogenesis, is a critical target for cancer treatment. Neutralizing monoclonal antibodies against VEGF are important class of drugs used in cancer therapy. However, the cost of production, large size, and immunogenicity are main drawbacks of conventional monoclonal therapy. Nanobodies are the smallest antigen-binding antibody fragments, which occur naturally in camelidae.more » Because of their remarkable features, we decided to use an immune library of nanobody to direct phage display to recognition of novel functional epitopes on VEGF. Four rounds of selection were performed and six phage-displayed nanobodies were obtained from an immune phage library. The most reactive clone in whole-cell ELISA experiments, was purified and assessed in proliferation inhibition assay. Purified ZFR-5 not only blocked interaction of VEGF with its receptor in cell ELISA experiments, but also was able to significantly inhibit proliferation response of human umbilical vein endothelial cells to VEGF in a dose-dependent manner. Taken together, our study demonstrates that by using whole-cell ELISA experiments, nanobodies against antigenic regions included in interaction of VEGF with its receptors can be directed. Because of unique and intrinsic properties of a nanobody and the ability of selected nanobody for blocking the epitope that is important for biological function of VEGF, it represents novel potential drug candidate.« less

A robust robotic high-throughput antibody purification platform.

PubMed

Schmidt, Peter M; Abdo, Michael; Butcher, Rebecca E; Yap, Min-Yin; Scotney, Pierre D; Ramunno, Melanie L; Martin-Roussety, Genevieve; Owczarek, Catherine; Hardy, Matthew P; Chen, Chao-Guang; Fabri, Louis J

2016-07-15

Monoclonal antibodies (mAbs) have become the fastest growing segment in the drug market with annual sales of more than 40 billion US$ in 2013. The selection of lead candidate molecules involves the generation of large repertoires of antibodies from which to choose a final therapeutic candidate. Improvements in the ability to rapidly produce and purify many antibodies in sufficient quantities reduces the lead time for selection which ultimately impacts on the speed with which an antibody may transition through the research stage and into product development. Miniaturization and automation of chromatography using micro columns (RoboColumns(®) from Atoll GmbH) coupled to an automated liquid handling instrument (ALH; Freedom EVO(®) from Tecan) has been a successful approach to establish high throughput process development platforms. Recent advances in transient gene expression (TGE) using the high-titre Expi293F™ system have enabled recombinant mAb titres of greater than 500mg/L. These relatively high protein titres reduce the volume required to generate several milligrams of individual antibodies for initial biochemical and biological downstream assays, making TGE in the Expi293F™ system ideally suited to high throughput chromatography on an ALH. The present publication describes a novel platform for purifying Expi293F™-expressed recombinant mAbs directly from cell-free culture supernatant on a Perkin Elmer JANUS-VariSpan ALH equipped with a plate shuttle device. The purification platform allows automated 2-step purification (Protein A-desalting/size exclusion chromatography) of several hundred mAbs per week. The new robotic method can purify mAbs with high recovery (>90%) at sub-milligram level with yields of up to 2mg from 4mL of cell-free culture supernatant. Copyright © 2016 Elsevier B.V. All rights reserved.

Selective Expansion of Memory CD4+ T cells By Mitogenic Human CD28 Generates Inflammatory Cytokines and Regulatory T cells

PubMed Central

Singh, Manisha; Basu, Sreemanti; Camell, Christina; Couturier, Jacob; Nudelman, Rodolfo J.; Medina, Miguel A.; Rodgers, John R.; Lewis, Dorothy E.

2009-01-01

Co-stimulatory signals are important for development of effector and regulatory T cells. In this case, CD28 signaling is usually considered inert in the absence of signaling through the TCR. By contrast, mitogenic rat CD28 mAbs reportedly expand regulatory T cells without TCR stimulation. We found that a commercially available human CD28 mAb (ANC28) stimulated PBMCs without TCR co-ligation or cross-linking; ANC28 selectively expanded CD4+CD25+FoxP3−(T effector) and CD4+CD25+FoxP3+ (Treg) cells. ANC28 stimulated the CD45RO+ CD4+ (memory) population whereas CD45RA+CD4+ (naïve) cells did not respond. ANC28 also induced inflammatory cytokines. Treg induced by ANC28 retain the Treg phenotype longer than did co-stimulated Treg. Treg induced by ANC28 suppressed CD25− T cells through a contact-dependent mechanism. Purity influenced the response of CD4+CD25+ cells because bead-purified CD4+CD25+ cells (85–90% pure) responded strongly to ANC28, whereas 98% pure FACS-sorted CD4+CD25 bright (T-reg) did not respond. Purified CD4+CD25int cells responded similarly to the bead-purified CD4+CD25+ cells. Thus, pre-activated CD4+ T cells (CD25int) respond to ANC28 rather than Treg (CD25bright). The ability of ANC28 to expand both effectors producing inflammatory cytokines as well as suppressive regulatory T cells might be useful for ex vivo expansion of therapeutic T cells. PMID:18446791

Fossil rhabdoviral sequences integrated into arthropod genomes: ontogeny, evolution, and potential functionality.

PubMed

Fort, Philippe; Albertini, Aurélie; Van-Hua, Aurélie; Berthomieu, Arnaud; Roche, Stéphane; Delsuc, Frédéric; Pasteur, Nicole; Capy, Pierre; Gaudin, Yves; Weill, Mylène

2012-01-01

Retroelements represent a considerable fraction of many eukaryotic genomes and are considered major drives for adaptive genetic innovations. Recent discoveries showed that despite not normally using DNA intermediates like retroviruses do, Mononegaviruses (i.e., viruses with nonsegmented, negative-sense RNA genomes) can integrate gene fragments into the genomes of their hosts. This was shown for Bornaviridae and Filoviridae, the sequences of which have been found integrated into the germ line cells of many vertebrate hosts. Here, we show that Rhabdoviridae sequences, the major Mononegavirales family, have integrated only into the genomes of arthropod species. We identified 185 integrated rhabdoviral elements (IREs) coding for nucleoproteins, glycoproteins, or RNA-dependent RNA polymerases; they were mostly found in the genomes of the mosquito Aedes aegypti and the blacklegged tick Ixodes scapularis. Phylogenetic analyses showed that most IREs in A. aegypti derived from multiple independent integration events. Since RNA viruses are submitted to much higher substitution rates as compared with their hosts, IREs thus represent fossil traces of the diversity of extinct Rhabdoviruses. Furthermore, analyses of orthologous IREs in A. aegypti field mosquitoes sampled worldwide identified an integrated polymerase IRE fragment that appeared under purifying selection within several million years, which supports a functional role in the host's biology. These results show that A. aegypti was subjected to repeated Rhabdovirus infectious episodes during its evolution history, which led to the accumulation of many integrated sequences. They also suggest that like retroviruses, integrated rhabdoviral sequences may participate actively in the evolution of their hosts.

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

Mays, Suzanne G.; Okafor, C. Denise; Tuntland, Micheal L.

Peroxisome proliferator-activated gamma coactivator 1-α (PGC1α) regulates energy metabolism by directly interacting with transcription factors to modulate gene expression. Among the PGC1α binding partners is liver receptor homolog 1 (LRH-1; NR5A2), an orphan nuclear hormone receptor that controls lipid and glucose homeostasis. Although PGC1α is known to bind and activate LRH-1, mechanisms through which PGC1α changes LRH-1 conformation to drive transcription are unknown. Here, we used biochemical and structural methods to interrogate the LRH-1–PGC1α complex. Purified, full-length LRH-1, as well as isolated ligand binding domain, bound to PGC1α with higher affinity than to the coactivator, nuclear receptor coactivator-2 (Tif2), inmore » coregulator peptide recruitment assays. We present the first crystal structure of the LRH-1–PGC1α complex, which depicts several hydrophobic contacts and a strong charge clamp at the interface between these partners. In molecular dynamics simulations, PGC1α induced correlated atomic motion throughout the entire LRH-1 activation function surface, which was dependent on charge-clamp formation. In contrast, Tif2 induced weaker signaling at the activation function surface than PGC1α but promoted allosteric signaling from the helix 6/β-sheet region of LRH-1 to the activation function surface. These studies are the first to probe mechanisms underlying the LRH-1–PGC1α interaction and may illuminate strategies for selective therapeutic targeting of PGC1α-dependent LRH-1 signaling pathways.« less

Antibody Characterization Process | Office of Cancer Clinical Proteomics Research

Cancer.gov

The goal of the NCI's Antibody Characterization Program (ACP) is to have three monoclonal antibodies produced for each successfully expressed/purified recombinant antigen and one antibody per peptide (1 to 3 peptides per protein). To date, over 4000 clones have been screened before selecting the current 393 antibodies. They are winnowed down based on the projected end use of the antibody.

Antimalarial drug discovery: screening of Brazilian medicinal plants and purified compounds.

PubMed

Krettli, Antoniana Ursine

2009-02-01

Malaria is the most important parasitic disease and its control depends on specific chemotherapy, now complicated by Plasmodium falciparum that has become resistant to most commonly available antimalarials. Treatment of the disease requires quinine or drug combinations of artemisinin derivatives and other antimalarials. Further drug resistance is expected. New active compounds need to be discovered. To find new antimalarials from medicinal and randomly collected plants, crude extracts are screened against P. falciparum in cultures and in malaria animal models, following bioassays of purified fractions, and cytotoxicity tests. For antimalarial research, screening medicinal plants is more efficient than screening randomly chosen plants. Biomonitored fractionation allows selection of new active molecules identified as potential antimalarials in multidisciplinary projects in Brazil; no new molecule is available for human testing. The advantages of projects based on ethnopharmacology are discussed.

Anti-tumour potential of a gallic acid-containing phenolic fraction from Oenothera biennis.

PubMed

Pellegrina, Chiara Dalla; Padovani, Giorgia; Mainente, Federica; Zoccatelli, Gianni; Bissoli, Gaetano; Mosconi, Silvia; Veneri, Gianluca; Peruffo, Angelo; Andrighetto, Giancarlo; Rizzi, Corrado; Chignola, Roberto

2005-08-08

A phenolic fraction purified form defatted seeds of Oenothera biennis promoted selective apoptosis of human and mouse bone marrow-derived cell lines following first-order kinetics through a caspase-dependent pathway. In non-leukemia tumour cell lines, such as human colon carcinoma CaCo(2) cells and mouse fibrosarcoma WEHI164 cells, this fraction inhibited (3)H-thymidine incorporation but not cell death or cell cycle arrest. Human peripheral blood mononuclear cells showed low sensitivity to treatment. Single bolus injection of the phenolic fraction could delay the growth of established myeloma tumours in syngeneic animals. HPLC and mass spectrometry analysis revealed that the fraction contains gallic acid. However, the biological activity of the fraction differs from the activity of this phenol and hence it should be attributed to other co-purified molecules which remain still unidentified.

Process for forming a nickel foil with controlled and predetermined permeability to hydrogen

DOEpatents

Engelhaupt, Darell E.

1981-09-22

The present invention provides a novel process for forming a nickel foil having a controlled and predetermined hydrogen permeability. This process includes the steps of passing a nickel plating bath through a suitable cation exchange resin to provide a purified nickel plating bath free of copper and gold cations, immersing a nickel anode and a suitable cathode in the purified nickel plating bath containing a selected concentration of an organic sulfonic acid such as a napthalene-trisulfonic acid, electrodepositing a nickel layer having the thickness of a foil onto the cathode, and separating the nickel layer from the cathode to provide a nickel foil. The anode is a readily-corrodible nickel anode. The present invention also provides a novel nickel foil having a greater hydrogen permeability than palladium at room temperature.

Anti-Legionella activity of staphylococcal hemolytic peptides.

PubMed

Marchand, A; Verdon, J; Lacombe, C; Crapart, S; Héchard, Y; Berjeaud, J M

2011-05-01

A collection of various Staphylococci was screened for their anti-Legionella activity. Nine of the tested strains were found to secrete anti-Legionella compounds. The culture supernatants of the strains, described in the literature to produce hemolytic peptides, were successfully submitted to a two step purification process. All the purified compounds, except one, corresponded to previously described hemolytic peptides and were not known for their anti-Legionella activity. By comparison of the minimal inhibitory concentrations, minimal permeabilization concentrations, decrease in the number of cultivable bacteria, hemolytic activity and selectivity, the purified peptides could be separated in two groups. First group, with warnericin RK as a leader, corresponds to the more hemolytic and bactericidal peptides. The peptides of the second group, represented by the PSMα from Staphylococcus epidermidis, appeared bacteriostatic and poorly hemolytic. Copyright © 2011 Elsevier Inc. All rights reserved.

Induction of specific immune unresponsiveness with purified mixed leukocyte culture-activated T lymphoblasts as autoimmunogen. II. An analysis of the effects measured at the cellular and serological levels

PubMed Central

1978-01-01

T lymphoblasts specific for foreign histocompatibility antigens and purified via mixed leukocyte culture (MLC) and 1 g velocity sedimentation procedures can be used as autoimmunogen to produce specific immunological unresponsiveness in adult animals. This unresponsiveness is positively correlated to the production of autoanti- idiotypic antibodies in the blast immunized animals and no evidence of coexisting alloimmunity was found. We consider this autoanti-idiotypic immunity to be the specific inducing agent of the immune tolerance. The blast immunization procedure will lead to selective reduction in T-cell reactivity against the relevant alloantigens as measured by MLC, cell- mediated lympholysis, or graft-versus-host assays. However, in individual animals, dichtomy in suppression between two T-cell assays could sometimes be observed indicating elimination of only a select group of idiotypic functionally distinct population of T cells in these blast-immunized animals. Attempts to abrogate already immune animals by the autoblast procedure were successful, in part suggesting the use of the present procedure when trying to induce in accelerated reversion of such immunity. PMID:75235

Accumulation of slightly deleterious mutations in the mitochondrial genome: a hallmark of animal domestication.

PubMed

Hughes, Austin L

2013-02-15

The hypothesis that domestication leads to a relaxation of purifying selection on mitochondrial (mt) genomes was tested by comparative analysis of mt genes from dog, pig, chicken, and silkworm. The three vertebrate species showed mt genome phylogenies in which domestic and wild isolates were intermingled, whereas the domestic silkworm (Bombyx mori) formed a distinct cluster nested within its closest wild relative (Bombyx mandarina). In spite of these differences in phylogenetic pattern, significantly greater proportions of nonsynonymous SNPs than of synonymous SNPs were unique to the domestic populations of all four species. Likewise, in all four species, significantly greater proportions of RNA-encoding SNPs than of synonymous SNPs were unique to the domestic populations. Thus, domestic populations were characterized by an excess of unique polymorphisms in two categories generally subject to purifying selection: nonsynonymous sites and RNA-encoding sites. Many of these unique polymorphisms thus seem likely to be slightly deleterious; the latter hypothesis was supported by the generally lower gene diversities of polymorphisms unique to domestic populations in comparison to those of polymorphisms shared by domestic and wild populations. Copyright © 2012 Elsevier B.V. All rights reserved.

An integrated map of genetic variation from 1,092 human genomes

PubMed Central

2012-01-01

Summary Through characterising the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help understand the genetic contribution to disease. We describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methodologies to integrate information across multiple algorithms and diverse data sources we provide a validated haplotype map of 38 million SNPs, 1.4 million indels and over 14 thousand larger deletions. We show that individuals from different populations carry different profiles of rare and common variants and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways and that each individual harbours hundreds of rare non-coding variants at conserved sites, such as transcription-factor-motif disrupting changes. This resource, which captures up to 98% of accessible SNPs at a frequency of 1% in populations of medical genetics focus, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations. PMID:23128226

Neurocognitive Correlates in Driving Under the Influence of Cannabis.

PubMed

Busardò, Francesco P; Pellegrini, Manuela; Klein, Julia; di Luca, Natale M

2017-01-01

Delta (9)-tetrahydrocannabinol (THC) is the main psychoactive compound in cannabis and is frequently identified in blood samples from apprehended drivers suspected for driving under the influence of drugs. Changing social norms towards cannabis and higher acceptability towards the drug emphasize the need for in-depth understanding of the acute neurocognitive and psychomotor effects caused by cannabis and how these effects are correlated to driving skills and performance. In this review, PubMed, Cochrane Central, Scopus, Web of Science, Science Direct, EMBASE and Google Scholar databases were used to identify and select publications up to January 2017 dealing with acute and chronic neurocognitive effects induced by cannabis and ability to drive. Thirty-six publications were selected for this review. The studies conducted were experimental, using simulators or on-road studies and brain imaging (structural and functional) to better understand the acute and chronic effects on cognitive functions comprised in the short and long-term fitness to drive after cannabis consumption. In a case-crossover self-report study a significant odds ratio increase was found for driving- related injury after combined exposure to cannabis and alcohol compared to cannabis alone (OR of 10.9 and 5.8 respectively). Both, experimental and epidemiological studies have revealed that THC affects negatively both, psychomotor skills and cognitive functions. Studies of the acute effects of cannabis on driving have shown that drivers under the influence of this substance are impaired. Indeed, driving under the influence of cannabis doubles or triples the risk of a crash. Specifically, cannabis use impairs critical-tracking tasks, increases lane weaving, decreases reaction time, and divided attention. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Lessons Learned form Selecting and Testing Spaceflight Potentiometers

NASA Technical Reports Server (NTRS)

Iskenderian, T.

1994-01-01

A solar array drive (SAD) was designed for operation on the TOPEX/POSEIDON spacecraft that was launched in August of 1992. The experience gained in selecting, specifying, testing to failure, and redesigning its position sensor produced valuable lessons for future component selection and qualification.

Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection.

PubMed

Ojosnegros, Samuel; Agudo, Rubén; Sierra, Macarena; Briones, Carlos; Sierra, Saleta; González-López, Claudia; Domingo, Esteban; Cristina, Juan

2008-07-17

The molecular events and evolutionary forces underlying lethal mutagenesis of virus (or virus extinction through an excess of mutations) are not well understood. Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ) to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV) quasispecies subjected to mutagenesis by base and nucleoside analogues. Phylogenetic and PAQ analyses have revealed a highly dynamic variation of intrapopulation diversity of FMDV quasispecies. The population diversity first suffers striking expansions in the presence of mutagens and then compressions either when the presence of the mutagenic analogue was discontinued or when a mutation that decreased sensitivity to a mutagen was selected. The pattern of mutations found in the populations was in agreement with the behavior of the corresponding nucleotide analogues with FMDV in vitro. Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying) selection in populations subjected to mutagenesis. No evidence of unusually elevated genetic distances has been obtained for FMDV populations approaching extinction. Phylogenetic and PAQ analysis provide adequate procedures to describe the evolution of viral sequences subjected to lethal mutagenesis. These methods define the changes of intra-population structure more precisely than mutation frequencies and Shannon entropies. PAQ is very sensitive to variations of intrapopulation genetic distances. Strong negative (or purifying) selection operates in FMDV populations subjected to enhanced mutagenesis. The quantifications provide evidence that extinction does not imply unusual increases of intrapopulation complexity, in support of the lethal defection model of virus extinction.

Bent shaft motor

DOEpatents

Benavides, Gilbert L.

1998-01-01

A nonelectromagnetic motor comprising a base, a bent shaft which is rotable relative to the base wherein the bent shaft comprises a straight portion aligned with a main axis and an offset portion that is offset with respect to the main axis; and a drive means for driving the offset portion of the bent shaft along a generally circular path in a plane perpendicular to the main axis to rotate the bent shaft. The bent shaft and drive means for driving the bent shaft can be selected from piezoelectric, magnetostrictive, rheological and shape memory alloys. The drive means of the nonelectromagnetic motor can additionally comprise a shell which shell surrounds and houses the bent shaft and precesses or gyrates which in turn causes the bent drive shaft to rotate. The nonelectromagnetic motor does not rely on friction for the application of torque upon a rotor.

Bent shaft motor

DOEpatents

Benavides, G.L.

1998-05-05

A nonelectromagnetic motor comprising a base, a bent shaft which is rotatable relative to the base wherein the bent shaft comprises a straight portion aligned with a main axis and an offset portion that is offset with respect to the main axis; and a drive means for driving the offset portion of the bent shaft along a generally circular path in a plane perpendicular to the main axis to rotate the bent shaft. The bent shaft and drive means for driving the bent shaft can be selected from piezoelectric, magnetostrictive, rheological and shape memory alloys. The drive means of the nonelectromagnetic motor can additionally comprise a shell which shell surrounds and houses the bent shaft and precesses or gyrates which in turn causes the bent drive shaft to rotate. The nonelectromagnetic motor does not rely on friction for the application of torque upon a rotor. 11 figs.

Balancing Vibrations at Harmonic Frequencies by Injecting Harmonic Balancing Signals into the Armature of a Linear Motor/Alternator Coupled to a Stirling Machine

NASA Technical Reports Server (NTRS)

Holliday, Ezekiel S. (Inventor)

2014-01-01

Vibrations at harmonic frequencies are reduced by injecting harmonic balancing signals into the armature of a linear motor/alternator coupled to a Stirling machine. The vibrations are sensed to provide a signal representing the mechanical vibrations. A harmonic balancing signal is generated for selected harmonics of the operating frequency by processing the sensed vibration signal with adaptive filter algorithms of adaptive filters for each harmonic. Reference inputs for each harmonic are applied to the adaptive filter algorithms at the frequency of the selected harmonic. The harmonic balancing signals for all of the harmonics are summed with a principal control signal. The harmonic balancing signals modify the principal electrical drive voltage and drive the motor/alternator with a drive voltage component in opposition to the vibration at each harmonic.

On the application of frequency selective common mode feedback for multifrequency EIT.

PubMed

Langlois, Peter J; Wu, Yu; Bayford, Richard H; Demosthenous, Andreas

2015-06-01

Common mode voltages are frequently a problem in electrical impedance tomography (EIT) and other bioimpedance applications. To reduce their amplitude common mode feedback is employed. Formalised analyses of both current and voltage feedback is presented in this paper for current drives. Common mode effects due to imbalances caused by the current drives, the electrode connections to the body load and the introduction of the body impedance to ground are considered. Frequency selective narrowband common mode feedback previously proposed to provide feedback stability is examined. As a step towards multifrequency applications the use of narrowband feedback is experimentally demonstrated for two simultaneous current drives. Measured results using standard available components show a reduction of 62 dB for current feedback and 31 dB for voltage feedback. Frequencies ranged from 50 kHz to 1 MHz.

The TRPM8 protein is a testosterone receptor: II. Functional evidence for an ionotropic effect of testosterone on TRPM8.

PubMed

Asuthkar, Swapna; Demirkhanyan, Lusine; Sun, Xiaohui; Elustondo, Pia A; Krishnan, Vivek; Baskaran, Padmamalini; Velpula, Kiran Kumar; Thyagarajan, Baskaran; Pavlov, Evgeny V; Zakharian, Eleonora

2015-01-30

Testosterone is a key steroid hormone in the development of male reproductive tissues and the regulation of the central nervous system. The rapid signaling mechanism induced by testosterone affects numerous behavioral traits, including sexual drive, aggressiveness, and fear conditioning. However, the currently identified testosterone receptor(s) is not believed to underlie the fast signaling, suggesting an orphan pathway. Here we report that an ion channel from the transient receptor potential family, TRPM8, commonly known as the cold and menthol receptor is the major component of testosterone-induced rapid actions. Using cultured and primary cell lines along with the purified TRPM8 protein, we demonstrate that testosterone directly activates TRPM8 channel at low picomolar range. Specifically, testosterone induced TRPM8 responses in primary human prostate cells, PC3 prostate cancer cells, dorsal root ganglion neurons, and hippocampal neurons. Picomolar concentrations of testosterone resulted in full openings of the purified TRPM8 channel in planar lipid bilayers. Furthermore, acute applications of testosterone on human skin elicited a cooling sensation. Our data conclusively demonstrate that testosterone is an endogenous and highly potent agonist of TRPM8, suggesting a role of TRPM8 channels well beyond their well established function in somatosensory neurons. This discovery may further imply TRPM8 channel function in testosterone-dependent behavioral traits. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Selection and reduced population size cannot explain higher amounts of Neandertal ancestry in East Asian than in European human populations.

PubMed

Kim, Bernard Y; Lohmueller, Kirk E

2015-03-05

It has been hypothesized that the greater proportion of Neandertal ancestry in East Asians than in Europeans is due to the fact that purifying selection is less effective at removing weakly deleterious Neandertal alleles from East Asian populations. Using simulations of a broad range of models of selection and demography, we have shown that this hypothesis cannot account for the higher proportion of Neandertal ancestry in East Asians than in Europeans. Instead, more complex demographic scenarios, most likely involving multiple pulses of Neandertal admixture, are required to explain the data. Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Impact of mobile phone use on car-following behaviour of young drivers.

PubMed

Saifuzzaman, Mohammad; Haque, Md Mazharul; Zheng, Zuduo; Washington, Simon

2015-09-01

Multitasking, such as the concurrent use of a mobile phone and operating a motor vehicle, is a significant distraction that impairs driving performance and is becoming a leading cause of motor vehicle crashes. This study investigates the impact of mobile phone conversations on car-following behaviour. The CARRS-Q Advanced Driving Simulator was used to test a group of young Australian drivers aged 18-26 years on a car-following task in three randomised phone conditions: baseline (no phone conversation), hands-free and handheld. Repeated measure ANOVA was applied to examine the effect of mobile phone distraction on selected car-following variables such as driving speed, spacing, and time headway. Overall, drivers tended to select slower driving speeds, larger vehicle spacings, and longer time headways when they were engaged in either hands-free or handheld phone conversations, suggesting possible risk compensatory behaviour. In addition, phone conversations while driving influenced car-following behaviour such that variability was increased in driving speeds, vehicle spacings, and acceleration and decelerations. To further investigate car-following behaviour of distracted drivers, driver time headways were modelled using Generalized Estimation Equation (GEE). After controlling for various exogenous factors, the model predicts an increase of 0.33s in time headway when a driver is engaged in hands-free phone conversation and a 0.75s increase for handheld phone conversation. The findings will improve the collective understanding of distraction on driving performance, in particular car following behaviour which is most critical in the determination of rear-end crashes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Indirect Vision Driving with Fixed Flat Panel Displays for Near Unity, Wide, and Extended Fields of Camera View

DTIC Science & Technology

2001-06-01

The choice of camera FOV may depend on the task being performed. The driver may prefer a unity view for driving along a known route to...increase his or her perception of potential road hazards. On the other hand, the driver may prefer a compressed image at road turns for route selection...with a supervisory evaluation of the road ahead and the impact on the driving schema. Included in this

Single cell gene expression profiling of cortical osteoblast lineage cells.

PubMed

Flynn, James M; Spusta, Steven C; Rosen, Clifford J; Melov, Simon

2013-03-01

In tissues with complex architectures such as bone, it is often difficult to purify and characterize specific cell types via molecular profiling. Single cell gene expression profiling is an emerging technology useful for characterizing transcriptional profiles of individual cells isolated from heterogeneous populations. In this study we describe a novel procedure for the isolation and characterization of gene expression profiles of single osteoblast lineage cells derived from cortical bone. Mixed populations of different cell types were isolated from adult long bones of C57BL/6J mice by enzymatic digestion, and subsequently subjected to FACS to purify and characterize osteoblast lineage cells via a selection strategy using antibodies against CD31, CD45, and alkaline phosphatase (AP), specific for mature osteoblasts. The purified individual osteoblast lineage cells were then profiled at the single cell level via nanofluidic PCR. This method permits robust gene expression profiling on single osteoblast lineage cells derived from mature bone, potentially from anatomically distinct sites. In conjunction with this technique, we have also shown that it is possible to carry out single cell profiling on cells purified from fixed and frozen bone samples without compromising the gene expression signal. The latter finding means the technique can be extended to biopsies of bone from diseased individuals. Our approach for single cell expression profiling provides a new dimension to the transcriptional profile of the primary osteoblast lineage population in vivo, and has the capacity to greatly expand our understanding of how these cells may function in vivo under normal and diseased states. Copyright © 2012 Elsevier Inc. All rights reserved.

A model for prediction of the transient rolling resistance of tyres based on inner-liner temperatures

NASA Astrophysics Data System (ADS)

Greiner, Matthias; Unrau, Hans-Joachim; Gauterin, Frank

2018-01-01

Measurements of rolling resistance in thermal equilibrium of a tyre, like measurements according to ISO 28580, do not allow statements about rolling resistances under other driving conditions. Such statements, however, are necessary to determine the energy consumption in driving cycles. Especially for the proper calculation of electric-vehicle remaining ranges and the selection of the respective driving strategies, the real amount of energy consumption is required. This paper presents a model approach, which by means of only one standardised rolling resistance measurement can be parameterised and, considering the present driving speed and tyre temperature, can predict the respective current rolling resistance.

The effects of using a portable music player on simulated driving performance and task-sharing strategies.

PubMed

Young, Kristie L; Mitsopoulos-Rubens, Eve; Rudin-Brown, Christina M; Lenné, Michael G

2012-07-01

This study examined the effects of performing scrollable music selection tasks using a portable music player (iPod Touch™) on simulated driving performance and task-sharing strategies, as evidenced through eye glance behaviour and secondary task performance. A total of 37 drivers (18-48 yrs) completed the PC-based MUARC Driver Distraction Test (DDT) while performing music selection tasks on an iPod Touch. Drivers' eye glance behaviour was examined using faceLAB eye tracking equipment. Results revealed that performing music search tasks while driving increased the amount of time that drivers spent with their eyes off the roadway and decreased their ability to maintain a constant lane position and time headway from a lead vehicle. There was also evidence, however, that drivers attempted to regulate their behaviour when distracted by decreasing their speed and taking a large number of short glances towards the device. Overall, results suggest that performing music search tasks while driving is problematic and steps to prohibit this activity should be taken. Copyright © 2011 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Origin, evolution, and population genetics of the selfish Segregation Distorter gene duplication in European and African populations of Drosophila melanogaster.

PubMed

Brand, Cara L; Larracuente, Amanda M; Presgraves, Daven C

2015-05-01

Meiotic drive elements are a special class of evolutionarily "selfish genes" that subvert Mendelian segregation to gain preferential transmission at the expense of homologous loci. Many drive elements appear to be maintained in populations as stable polymorphisms, their equilibrium frequencies determined by the balance between drive (increasing frequency) and selection (decreasing frequency). Here we show that a classic, seemingly balanced, drive system is instead characterized by frequent evolutionary turnover giving rise to dynamic, rather than stable, equilibrium frequencies. The autosomal Segregation Distorter (SD) system of the fruit fly Drosophila melanogaster is a selfish coadapted meiotic drive gene complex in which the major driver corresponds to a partial duplication of the gene Ran-GTPase activating protein (RanGAP). SD chromosomes segregate at similar, low frequencies of 1-5% in natural populations worldwide, consistent with a balanced polymorphism. Surprisingly, our population genetic analyses reveal evidence for parallel, independent selective sweeps of different SD chromosomes in populations on different continents. These findings suggest that, rather than persisting at a single stable equilibrium, SD chromosomes turn over frequently within populations. © 2015 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Phenotypic selection varies with pollination intensity across populations of Sabatia angularis.

PubMed

Emel, Sarah L; Franks, Steven J; Spigler, Rachel B

2017-07-01

Pollinators are considered primary selective agents acting on plant traits, and thus variation in the strength of the plant-pollinator interaction might drive variation in the opportunity for selection and selection intensity across plant populations. Here, we examine whether these critical evolutionary parameters covary with pollination intensity across wild populations of the biennial Sabatia angularis. We quantified pollination intensity in each of nine S. angularis populations as mean stigmatic pollen load per population. For female fitness and three components, fruit number, fruit set (proportion of flowers setting fruit) and number of seeds per fruit, we evaluated whether the opportunity for selection varied with pollination intensity. We used phenotypic selection analyses to test for interactions between pollination intensity and selection gradients for five floral traits, including flowering phenology. The opportunity for selection via fruit set and seeds per fruit declined significantly with increasing pollen receipt, as expected. We demonstrated significant directional selection on multiple traits across populations. We also found that selection intensity for all traits depended on pollination intensity. Consistent with general theory about the relationship between biotic interaction strength and the intensity of selection, our study suggests that variation in pollination intensity drives variation in selection across S. angularis populations. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Evolution of divergent female mating preference in response to experimental sexual selection.

PubMed

Debelle, Allan; Ritchie, Michael G; Snook, Rhonda R

2014-09-01

Sexual selection is predicted to drive the coevolution of mating signals and preferences (mating traits) within populations, and could play a role in speciation if sexual isolation arises due to mating trait divergence between populations. However, few studies have demonstrated that differences in mating traits between populations result from sexual selection alone. Experimental evolution is a promising approach to directly examine the action of sexual selection on mating trait divergence among populations. We manipulated the opportunity for sexual selection (low vs. high) in populations of Drosophila pseudoobscura. Previous studies on these experimental populations have shown that sexual selection manipulation resulted in the divergence between sexual selection treatments of several courtship song parameters, including interpulse interval (IPI) which markedly influences male mating success. Here, we measure female preference for IPI using a playback design to test for preference divergence between the sexual selection treatments after 130 generations of experimental sexual selection. The results suggest that female preference has coevolved with male signal, in opposite directions between the sexual selection treatments, providing direct evidence of the ability of sexual selection to drive the divergent coevolution of mating traits between populations. We discuss the implications in the context sexual selection and speciation. © 2014 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

The critical limiting temperature and selective brain cooling: neuroprotection during exercise?

PubMed

Marino, Frank E

2011-01-01

There is wide consensus that long duration exercise in the heat is impaired compared with cooler conditions. A common observation when examining exercise tolerance in the heat in laboratory studies is the critical limiting core temperature (CLT) and the apparent attenuation in central nervous system (CNS) drive leading to premature fatigue. Selective brain cooling (SBC) purportedly confers neuroprotection during exercise heat stress by attenuating the increase in brain temperature. As the CLT is dependent on heating to invoke a reduction in efferent drive, it is thus not compatible with SBC which supposedly attenuates the rise in brain temperature. Therefore, the CLT and SBC hypotheses cannot be complimentary if the goal is to confer neuroprotection from thermal insult as it is counter-intuitive to selectively cool the brain if the purpose of rising brain temperature is to down-regulate skeletal muscle recruitment. This presents a circular model for which there is no apparent end to the ultimate physiological outcome; a 'hot brain' selectively cooled in order to reduce the CNS drive to skeletal muscle. This review will examine the postulates of the CLT and SBC with their relationship to the avoidance of a 'hot brain' which together argue for a theoretical position against neuroprotection as the key physiological strategy in exercise-induced hyperthermia.

Family feuds: social competition and sexual conflict in complex societies.

PubMed

Rubenstein, Dustin R

2012-08-19

Darwin was initially puzzled by the processes that led to ornamentation in males-what he termed sexual selection-and those that led to extreme cooperation and altruism in complex animal societies-what was later termed kin selection. Here, I explore the relationships between sexual and kin selection theory by examining how social competition for reproductive opportunities-particularly in females-and sexual conflict over mating partners are inherent and critical parts of complex altruistic societies. I argue that (i) patterns of reproductive sharing within complex societies can drive levels of social competition and reproductive conflict not only in males but also in females living in social groups, and ultimately the evolution of female traits such as ornaments and armaments; (ii) mating conflict over female choice of sexual partners can influence kin structure within groups and drive the evolution of complex societies; and (iii) patterns of reproductive sharing and conflict among females may also drive the evolution of complex societies by influencing kin structure within groups. Ultimately, complex societies exhibiting altruistic behaviour appear to have only arisen in taxa where social competition over reproductive opportunities and sexual conflict over mating partners were low. Once such societies evolved, there were important selective feedbacks on traits used to regulate and mediate intra-sexual competition over reproductive opportunities, particularly in females.

Comparative study on the selective chalcopyrite bioleaching of a molybdenite concentrate with mesophilic and thermophilic bacteria.

PubMed

Romano, P; Blázquez, M L; Alguacil, F J; Muñoz, J A; Ballester, A; González, F

2001-03-01

This study evaluates different bioleaching treatments of a molybdenite concentrate using mesophilic and thermophilic bacterial cultures. Further studies on the chemical leaching and the electrochemical behavior of the MoS(2) concentrate were carried out. Bioleaching tests showed a progressive removal of chalcopyrite from the molybdenite concentrate with an increase in temperature. Chemical leaching tests support the idea of an indirect attack of the concentrate. Electrochemical tests indicate that chalcopyrite dissolution is favored when molybdenite is present. Therefore, this type of bioleaching treatment could be applied to purify molybdenite flotation concentrates by selectively dissolving chalcopyrite.

Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene

PubMed Central

Erixon, Per; Oxelman, Bengt

2008-01-01

Background Synonymous DNA substitution rates in the plant chloroplast genome are generally relatively slow and lineage dependent. Non-synonymous rates are usually even slower due to purifying selection acting on the genes. Positive selection is expected to speed up non-synonymous substitution rates, whereas synonymous rates are expected to be unaffected. Until recently, positive selection has seldom been observed in chloroplast genes, and large-scale structural rearrangements leading to gene duplications are hitherto supposed to be rare. Methodology/Principle Findings We found high substitution rates in the exons of the plastid clpP1 gene in Oenothera (the Evening Primrose family) and three separate lineages in the tribe Sileneae (Caryophyllaceae, the Carnation family). Introns have been lost in some of the lineages, but where present, the intron sequences have substitution rates similar to those found in other introns of their genomes. The elevated substitution rates of clpP1 are associated with statistically significant whole-gene positive selection in three branches of the phylogeny. In two of the lineages we found multiple copies of the gene. Neighboring genes present in the duplicated fragments do not show signs of elevated substitution rates or positive selection. Although non-synonymous substitutions account for most of the increase in substitution rates, synonymous rates are also markedly elevated in some lineages. Whereas plant clpP1 genes experiencing negative (purifying) selection are characterized by having very conserved lengths, genes under positive selection often have large insertions of more or less repetitive amino acid sequence motifs. Conclusions/Significance We found positive selection of the clpP1 gene in various plant lineages to correlated with repeated duplication of the clpP1 gene and surrounding regions, repetitive amino acid sequences, and increase in synonymous substitution rates. The present study sheds light on the controversial issue of whether negative or positive selection is to be expected after gene duplications by providing evidence for the latter alternative. The observed increase in synonymous substitution rates in some of the lineages indicates that the detection of positive selection may be obscured under such circumstances. Future studies are required to explore the functional significance of the large inserted repeated amino acid motifs, as well as the possibility that synonymous substitution rates may be affected by positive selection. PMID:18167545

Molecular evolution of the odorant and gustatory receptor genes in lepidopteran insects: implications for their adaptation and speciation.

PubMed

Engsontia, Patamarerk; Sangket, Unitsa; Chotigeat, Wilaiwan; Satasook, Chutamas

2014-08-01

Lepidoptera (comprised of butterflies and moths) is one of the largest groups of insects, including more than 160,000 described species. Chemoreception plays important roles in the adaptation of these species to a wide range of niches, e.g., plant hosts, egg-laying sites, and mates. This study investigated the molecular evolution of the lepidopteran odorant (Or) and gustatory receptor (Gr) genes using recently identified genes from Bombyx mori, Danaus plexippus, Heliconius melpomene, Plutella xylostella, Heliothis virescens, Manduca sexta, Cydia pomonella, and Spodoptera littoralis. A limited number of cases of large lineage-specific gene expansion are observed (except in the P. xylostella lineage), possibly due to selection against tandem gene duplication. There has been strong purifying selection during the evolution of both lepidopteran odorant and gustatory genes, as shown by the low ω values estimated through CodeML analysis, ranging from 0.0093 to 0.3926. However, purifying selection has been relaxed on some amino acid sites in these receptors, leading to sequence divergence, which is a precursor of positive selection on these sequences. Signatures of positive selection were detected only in a few loci from the lineage-specific analysis. Estimation of gene gains and losses suggests that the common ancestor of the Lepidoptera had fewer Or genes compared to extant species and an even more reduced number of Gr genes, particularly within the bitter receptor clade. Multiple gene gains and a few gene losses occurred during the evolution of Lepidoptera. Gene family expansion may be associated with the adaptation of lepidopteran species to plant hosts, especially after angiosperm radiation. Phylogenetic analysis of the moth sex pheromone receptor genes suggested that chromosomal translocations have occurred several times. New sex pheromone receptors have arisen through tandem gene duplication. Positive selection was detected at some amino acid sites predicted to be in the extracellular and transmembrane regions of the newly duplicated genes, which might be associated with the evolution of the new pheromone receptors.

Production of capsular polysaccharide of Streptococcus pneumoniae type 14 and its purification by affinity chromatography.

PubMed

Suárez, N; Fraguas, L F; Texeira, E; Massaldi, H; Batista-Viera, F; Ferreira, F

2001-02-01

We describe a rapid and efficient method for producing the capsular polysaccharide of Streptococcus pneumoniae by fermentation on tryptic soy broth and purification of this compound by using immobilized soybean lectin as an affinity adsorbent. In principle, the same strategy can be used to produce purified capsular polysaccharides from other streptococcal serotypes by selecting the appropriate lectin adsorbents.

Production of Capsular Polysaccharide of Streptococcus pneumoniae Type 14 and Its Purification by Affinity Chromatography

PubMed Central

Suárez, Norma; Fraguas, Laura Franco; Texeira, Esther; Massaldi, Hugo; Batista-Viera, Francisco; Ferreira, Fernando

2001-01-01

We describe a rapid and efficient method for producing the capsular polysaccharide of Streptococcus pneumoniae by fermentation on tryptic soy broth and purification of this compound by using immobilized soybean lectin as an affinity adsorbent. In principle, the same strategy can be used to produce purified capsular polysaccharides from other streptococcal serotypes by selecting the appropriate lectin adsorbents. PMID:11157270

Early detection of tumor cells by innate immune cells leads to T(reg) recruitment through CCL22 production by tumor cells.

PubMed

Faget, Julien; Biota, Cathy; Bachelot, Thomas; Gobert, Michael; Treilleux, Isabelle; Goutagny, Nadège; Durand, Isabelle; Léon-Goddard, Sophie; Blay, Jean Yves; Caux, Christophe; Ménétrier-Caux, Christine

2011-10-01

In breast carcinomas, patient survival seems to be negatively affected by the recruitment of regulatory T cells (T(reg)) within lymphoid aggregates by CCL22. However, the mechanisms underpinning this process, which may be of broader significance in solid tumors, have yet to be described. In this study, we determined how CCL22 production is controlled in tumor cells. In human breast carcinoma cell lines, CCL22 was secreted at low basal levels that were strongly increased in response to inflammatory signals [TNF-α, IFN-γ, and interleukin (IL)-1β], contrasting with CCL17. Primary breast tumors and CD45(+) infiltrating immune cells appeared to cooperate in driving CCL22 secretion, as shown clearly in cocultures of breast tumor cell lines and peripheral blood mononuclear cells (PBMC) or their supernatants. We determined that monocyte-derived IL-1β and TNF-α are key players as monocyte depletion or neutralization of these cytokines attenuated secretion of CCL22. However, when purified monocytes were used, exogenous human IFN-γ was also required to generate this response suggesting a role for IFN-γ-producing cells within PBMCs. In this setting, we found that human IFN-γ could be replaced by the addition of (i) IL-2 or K562-activated natural killer (NK) cells or (ii) resting NK cells in the presence of anti-MHC class I antibody. Taken together, our results show a dialogue between NK and tumor cells leading to IFN-γ secretion, which in turn associates with monocyte-derived IL-1β and TNF-α to drive production of CCL22 by tumor cells and subsequent recruitment of T(reg). As one validation of this conclusion in primary breast tumors, we showed that NK cells and macrophages tend to colocalize within tumors. In summary, our findings suggest that at early times during tumorigenesis, the detection of tumor cells by innate effectors (monocytes and NK cells) imposes a selection for CCL22 secretion that recruits T(reg) to evade this early antitumor immune response.

Hydrogen bonds are a primary driving force for de novo protein folding

DOE PAGES

Lee, Schuyler; Wang, Chao; Liu, Haolin; ...

2017-11-10

The protein-folding mechanism remains a major puzzle in life science. Purified soluble activation-induced cytidine deaminase (AID) is one of the most difficult proteins to obtain. Starting from inclusion bodies containing a C-terminally truncated version of AID (residues 1–153; AID 153 ), an optimized in vitro folding procedure was derived to obtain large amounts of AID 153 , which led to crystals with good quality and to final structural determination. Interestingly, it was found that the final refolding yield of the protein is proline residue-dependent. The difference in the distribution of cis and trans configurations of proline residues in the proteinmore » after complete denaturation is a major determining factor of the final yield. A point mutation of one of four proline residues to an asparagine led to a near-doubling of the yield of refolded protein after complete denaturation. It was concluded that the driving force behind protein folding could not overcome the cis -to- trans proline isomerization, or vice versa , during the protein-folding process. Furthermore, it was found that successful refolding of proteins optimally occurs at high pH values, which may mimic protein folding in vivo . It was found that high pH values could induce the polarization of peptide bonds, which may trigger the formation of protein secondary structures through hydrogen bonds. It is proposed that a hydrophobic environment coupled with negative charges is essential for protein folding. Combined with our earlier discoveries on protein-unfolding mechanisms, it is proposed that hydrogen bonds are a primary driving force for de novo protein folding.« less

Hydrogen bonds are a primary driving force for de novo protein folding

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

Lee, Schuyler; Wang, Chao; Liu, Haolin

The protein-folding mechanism remains a major puzzle in life science. Purified soluble activation-induced cytidine deaminase (AID) is one of the most difficult proteins to obtain. Starting from inclusion bodies containing a C-terminally truncated version of AID (residues 1–153; AID 153 ), an optimized in vitro folding procedure was derived to obtain large amounts of AID 153 , which led to crystals with good quality and to final structural determination. Interestingly, it was found that the final refolding yield of the protein is proline residue-dependent. The difference in the distribution of cis and trans configurations of proline residues in the proteinmore » after complete denaturation is a major determining factor of the final yield. A point mutation of one of four proline residues to an asparagine led to a near-doubling of the yield of refolded protein after complete denaturation. It was concluded that the driving force behind protein folding could not overcome the cis -to- trans proline isomerization, or vice versa , during the protein-folding process. Furthermore, it was found that successful refolding of proteins optimally occurs at high pH values, which may mimic protein folding in vivo . It was found that high pH values could induce the polarization of peptide bonds, which may trigger the formation of protein secondary structures through hydrogen bonds. It is proposed that a hydrophobic environment coupled with negative charges is essential for protein folding. Combined with our earlier discoveries on protein-unfolding mechanisms, it is proposed that hydrogen bonds are a primary driving force for de novo protein folding.« less

The use of a driving simulator to determine how time pressures impact driver aggressiveness.

PubMed

Fitzpatrick, Cole D; Samuel, Siby; Knodler, Michael A

2017-11-01

Speeding greatly attributes to traffic safety with approximately a third of fatal crashes in the United States being speeding-related. Previous research has identified being late as a primary cause of speeding. In this driving simulator study, a virtual drive was constructed to evaluate how time pressures, or hurried driving, affected driver speed choice and driver behavior. In particular, acceleration profiles, gap acceptance, willingness to pass, and dilemma zone behavior were used, in addition to speed, as measures to evaluate whether being late increased risky and aggressive driving behaviors. Thirty-six drivers were recruited with an equal male/female split and a broad distribution of ages. Financial incentives and completion time goals calibrated from a control group were used to generate a Hurried and Very Hurried experimental group. As compared to the control group, Very Hurried drivers selected higher speeds, accelerated faster after red lights, accepted smaller gaps on left turns, were more likely to pass a slow vehicle, and were more likely to run a yellow light in a dilemma zone situation. These trends were statistically significant and were also evident with the Hurried group but a larger sample would be needed to show statistical significance. The findings from this study provide evidence that hurried drivers select higher speeds and exhibit riskier driving behaviors. These conclusive results have possible implications in areas such as transportation funding and commercial motor vehicle safety. Published by Elsevier Ltd.

Osvaldo and Isis retrotransposons as markers of the Drosophila buzzatii colonisation in Australia.

PubMed

Guerreiro, María Pilar García; Fontdevila, Antonio

2011-04-24

Transposable elements (TEs) constitute an important source of genetic variability owing to their jumping and regulatory properties, and are considered to drive species evolution. Several factors that are able to induce TE transposition in genomes have been documented (for example environmental stress and inter- and intra-specific crosses) but in many instances the reasons for TE mobilisation have yet to be elucidated. Colonising populations constitute an ideal model for studying TE behaviour and distribution as they are exposed to different environmental and new demographic conditions. In this study, the distribution of two TEs, Osvaldo and Isis, was examined in two colonising populations of D. buzzatii from Australia. Comparing Osvaldo copy numbers between Australian and Old World (reported in previous studies) colonisations provides a valuable tool for elucidating the colonisation process and the effect of new conditions encountered by colonisers on TEs. The chromosomal distributions of Osvaldo and Isis retrotransposons in two colonising populations of D. buzzatii from Australia revealed sites of high insertion frequency (>10%) and low frequency sites. Comparisons between Osvaldo insertion profiles in colonising populations from the Old World and Australia demonstrate a tendency towards a higher number of highly occupied sites with higher insertion frequency in the Old World than in Australian populations. Tests concerning selection against deleterious TE insertions indicate that Isis is more controlled by purifying selection than Osvaldo. The distribution of both elements on chromosomal arms follows a Poisson distribution and there are non-significant positive correlations between highly occupied sites and chromosomal inversions. The occupancy profile of Osvaldo and Isis retrotransposons is characterised by the existence of high and low insertion frequency sites in the populations. These results demonstrate that Australian D. buzzatii populations were subjected to a founder effect during the colonisation process. Moreover, there are more sites with high insertion frequency in the Old World colonisation than in the Australian colonisation, indicating a probable stronger bottleneck effect in Australia. The results suggest that selection does not seem to play a major role, compared to demography, in the distribution of transposable elements in the Australian populations.

Osvaldo and Isis retrotransposons as markers of the Drosophila buzzatii colonisation in Australia

PubMed Central

2011-01-01

Background Transposable elements (TEs) constitute an important source of genetic variability owing to their jumping and regulatory properties, and are considered to drive species evolution. Several factors that are able to induce TE transposition in genomes have been documented (for example environmental stress and inter- and intra-specific crosses) but in many instances the reasons for TE mobilisation have yet to be elucidated. Colonising populations constitute an ideal model for studying TE behaviour and distribution as they are exposed to different environmental and new demographic conditions. In this study, the distribution of two TEs, Osvaldo and Isis, was examined in two colonising populations of D. buzzatii from Australia. Comparing Osvaldo copy numbers between Australian and Old World (reported in previous studies) colonisations provides a valuable tool for elucidating the colonisation process and the effect of new conditions encountered by colonisers on TEs. Results The chromosomal distributions of Osvaldo and Isis retrotransposons in two colonising populations of D. buzzatii from Australia revealed sites of high insertion frequency (>10%) and low frequency sites. Comparisons between Osvaldo insertion profiles in colonising populations from the Old World and Australia demonstrate a tendency towards a higher number of highly occupied sites with higher insertion frequency in the Old World than in Australian populations. Tests concerning selection against deleterious TE insertions indicate that Isis is more controlled by purifying selection than Osvaldo. The distribution of both elements on chromosomal arms follows a Poisson distribution and there are non-significant positive correlations between highly occupied sites and chromosomal inversions. Conclusions The occupancy profile of Osvaldo and Isis retrotransposons is characterised by the existence of high and low insertion frequency sites in the populations. These results demonstrate that Australian D. buzzatii populations were subjected to a founder effect during the colonisation process. Moreover, there are more sites with high insertion frequency in the Old World colonisation than in the Australian colonisation, indicating a probable stronger bottleneck effect in Australia. The results suggest that selection does not seem to play a major role, compared to demography, in the distribution of transposable elements in the Australian populations. PMID:21513573

Identification of conformational epitopes for human IgG on Chemotaxis inhibitory protein of Staphylococcus aureus

PubMed Central

Gustafsson, Erika; Haas, Pieter-Jan; Walse, Björn; Hijnen, Marcel; Furebring, Christina; Ohlin, Mats; van Strijp, Jos AG; van Kessel, Kok PM

2009-01-01

Background The Chemotaxis inhibitory protein of Staphylococcus aureus (CHIPS) blocks the Complement fragment C5a receptor (C5aR) and formylated peptide receptor (FPR) and is thereby a potent inhibitor of neutrophil chemotaxis and activation of inflammatory responses. The majority of the healthy human population has antibodies against CHIPS that have been shown to interfere with its function in vitro. The aim of this study was to define potential epitopes for human antibodies on the CHIPS surface. We also initiate the process to identify a mutated CHIPS molecule that is not efficiently recognized by preformed anti-CHIPS antibodies and retains anti-inflammatory activity. Results In this paper, we panned peptide displaying phage libraries against a pool of CHIPS specific affinity-purified polyclonal human IgG. The selected peptides could be divided into two groups of sequences. The first group was the most dominant with 36 of the 48 sequenced clones represented. Binding to human affinity-purified IgG was verified by ELISA for a selection of peptide sequences in phage format. For further analysis, one peptide was chemically synthesized and antibodies affinity-purified on this peptide were found to bind the CHIPS molecule as studied by ELISA and Surface Plasmon Resonance. Furthermore, seven potential conformational epitopes responsible for antibody recognition were identified by mapping phage selected peptide sequences on the CHIPS surface as defined in the NMR structure of the recombinant CHIPS31–121 protein. Mapped epitopes were verified by in vitro mutational analysis of the CHIPS molecule. Single mutations introduced in the proposed antibody epitopes were shown to decrease antibody binding to CHIPS. The biological function in terms of C5aR signaling was studied by flow cytometry. A few mutations were shown to affect this biological function as well as the antibody binding. Conclusion Conformational epitopes recognized by human antibodies have been mapped on the CHIPS surface and amino acid residues involved in both antibody and C5aR interaction could be defined. This information has implications for the development of an effective anti-inflammatory agent based on a functional CHIPS molecule with low interaction with human IgG. PMID:19284584

Synthetically engineered Medea gene drive system in the worldwide crop pest Drosophila suzukii

PubMed Central

Buchman, Anna; Marshall, John M.; Ostrovski, Dennis; Yang, Ting; Akbari, Omar S.

2018-01-01

Synthetic gene drive systems possess enormous potential to replace, alter, or suppress wild populations of significant disease vectors and crop pests; however, their utility in diverse populations remains to be demonstrated. Here, we report the creation of a synthetic Medea gene drive system in a major worldwide crop pest, Drosophila suzukii. We demonstrate that this drive system, based on an engineered maternal “toxin” coupled with a linked embryonic “antidote,” is capable of biasing Mendelian inheritance rates with up to 100% efficiency. However, we find that drive resistance, resulting from naturally occurring genetic variation and associated fitness costs, can be selected for and hinder the spread of such a drive. Despite this, our results suggest that this gene drive could maintain itself at high frequencies in a wild population and spread to fixation if either its fitness costs or toxin resistance were reduced, providing a clear path forward for developing future such systems in this pest. PMID:29666236

Combination and selection of traffic safety expert judgments for the prevention of driving risks.

PubMed

Cabello, Enrique; Conde, Cristina; de Diego, Isaac Martín; Moguerza, Javier M; Redchuk, Andrés

2012-11-02

In this paper, we describe a new framework to combine experts’ judgments for the prevention of driving risks in a cabin truck. In addition, the methodology shows how to choose among the experts the one whose predictions fit best the environmental conditions. The methodology is applied over data sets obtained from a high immersive cabin truck simulator in natural driving conditions. A nonparametric model, based in Nearest Neighbors combined with Restricted Least Squared methods is developed. Three experts were asked to evaluate the driving risk using a Visual Analog Scale (VAS), in order to measure the driving risk in a truck simulator where the vehicle dynamics factors were stored. Numerical results show that the methodology is suitable for embedding in real time systems.

Effects of altruism and burnout on driving behavior of bus drivers.

PubMed

Shi, Xia; Zhang, Liang

2017-05-01

Personality traits predict driving behaviors. However, the mechanism underlying this relationship has not been adequately investigated in professional drivers. The current study investigated the relationship between altruistic personality and aberrant driving behaviors, and the potential role of burnout. A total of 194 bus drivers completed questionnaires including measures of altruism, burnout and aberrant driving behaviors (aggressive violations, ordinary violations, errors, and lapses). The results showed that altruism was negatively correlated with burnout, and with all the four subcategories of aberrant driving behavior. Burnout fully mediated the relationship between altruism and aggressive violations, and partially mediated the relationship between altruism and lapses. These findings can be applied in the bus drivers' selection and interventions for burnout in order to improve the safety of public transport. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mounting arrangement for the drive system of an air-bearing spindle on a machine tool

DOEpatents

Lunsford, J.S.; Crisp, D.W.; Petrowski, P.L.

1987-12-07

The present invention is directed to a mounting arrangement for the drive system of an air-bearing spindle utilized on a machine tool such as a lathe. The mounting arrangement of the present invention comprises a housing which is secured to the casing of the air bearing in such a manner that the housing position can be selectively adjusted to provide alignment of the air-bearing drive shaft supported by the housing and the air-bearing spindle. Once this alignment is achieved the air between spindle and the drive arrangement is maintained in permanent alignment so as to overcome misalignment problems encountered in the operation of the machine tool between the air-bearing spindle and the shaft utilized for driving the air-bearing spindle.

Vehicle ownership and other predictors of teenagers risky driving behavior: Evidence from a naturalistic driving study.

PubMed

Gershon, Pnina; Ehsani, Johnathon; Zhu, Chunming; O'Brien, Fearghal; Klauer, Sheila; Dingus, Tom; Simons-Morton, Bruce

2018-06-08

Risky driving behavior may contribute to the high crash risk among teenage drivers. The current naturalistic driving study assessed predictors for teenagers' kinematic risky driving (KRD) behavior and the interdependencies between them. The private vehicles of 81 novice teenage drivers were equipped with data acquisition system that recorded driving kinematics, miles driven, and video recordings of the driver, passengers and the driving environment. Psychosocial measures were collected using questionnaires administered at licensure. Poisson regression analyses and model selection were used to assess factors associated with teens' risky driving behavior and the interactions between them. Driving own vs shared vehicle, driving during the day vs at night, and driving alone vs with passengers were significantly associated with higher KRD rates (Incidence rate ratios (IRRs) of 1.60, 1.41, and 1.28, respectively). Teenagers reporting higher vs lower levels of parental trust had significantly lower KRD rates (IRR = 0.58). KRD rates were 88% higher among teenagers driving with a passenger in their own vehicle compared to teenagers driving with a passenger in a shared vehicle. Similarly, KRD rates during the day were 74% higher among teenagers driving their own vehicle compared to those driving a shared vehicle. Novice teenagers' risky driving behavior varied according to driver attributes and contextual aspects of the driving environment. As such, examining teenagers' risky driving behavior should take into account multiple contributing factors and their interactions. The variability in risky driving according to the driving context can inform the development of targeted interventions to reduce the crash risk of novice teenage drivers. Copyright © 2018 Elsevier Ltd. All rights reserved.

Active colloids as mobile microelectrodes for unified label-free selective cargo transport.

PubMed

Boymelgreen, Alicia M; Balli, Tov; Miloh, Touvia; Yossifon, Gilad

2018-02-22

Utilization of active colloids to transport both biological and inorganic cargo has been widely examined in the context of applications ranging from targeted drug delivery to sample analysis. In general, carriers are customized to load one specific target via a mechanism distinct from that driving the transport. Here we unify these tasks and extend loading capabilities to include on-demand selection of multiple nano/micro-sized targets without the need for pre-labelling or surface functionalization. An externally applied electric field is singularly used to drive the active cargo carrier and transform it into a mobile floating electrode that can attract (trap) or repel specific targets from its surface by dielectrophoresis, enabling dynamic control of target selection, loading and rate of transport via the electric field parameters. In the future, dynamic selectivity could be combined with directed motion to develop building blocks for bottom-up fabrication in applications such as additive manufacturing and soft robotics.

Content Characteristics Driving the Diffusion of Antismoking Messages: Implications for Cancer Prevention in the Emerging Public Communication Environment

PubMed Central

2013-01-01

This study examined how content characteristics of antitobacco messages affect smokers’ selective exposure to and social sharing of those messages. Results from an experiment revealed that content features predicting smokers’ selection of antismoking messages are different from those predicting whether those messages are shared. Antismoking messages smokers tend to select are characterized by strong arguments (odds ratio = 2.02, P = .02) and positive sentiments (odds ratio = 3.08, P = .03). Once selected, the messages more likely to be retransmitted by smokers were those with novel arguments (B = .83, P = .002) and positive sentiments (B = 1.65, P = .005). This research adds to the literature about the content characteristics driving the social diffusion of antitobacco messages and contributes to our understanding of the role of persuasive messages about smoking cessation in the emerging public communication environment. PMID:24395989

Ball Screw Actuator Including a Stop with an Integral Guide

NASA Technical Reports Server (NTRS)

Wingett, Paul T. (Inventor); Perek, John (Inventor); Geck, Kellan (Inventor)

2015-01-01

An actuator includes a housing assembly, a ball nut, a ball screw, and a ball screw stop. The ball nut is rotationally mounted in the housing assembly, is adapted to receive an input torque, and is configured, upon receipt thereof, to rotate and supply a drive force. The ball screw is mounted within the housing assembly and extends through the ball nut. The ball screw has a first end and a second end, and is coupled to receive the drive force from the ball nut. The ball screw is configured, upon receipt of the drive force, to selectively translate between a stow position and a deploy position. The ball screw stop is mounted on the ball screw to translate therewith and is configured to at selectively engage the housing assembly while the ball screw is translating, and engage the ball nut when the ball screw is in the deploy position.

Main drive selection for the Windstorm Simulation Center

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

Lacy, J.M.; Earl, J.S.

1998-02-01

Operated by the Partnership for Natural Disaster Reduction, the Windstorm Simulation Center (WSC) will be a structural test center dedicated to studying the performance of civil structural systems subjected to hurricanes, tornadoes, and other storm winds. Within the WSC, a bank of high-power fans, the main drive, will produce the high velocity wind necessary to reproduce these storms. Several options are available for the main drive, each with advantages and liabilities. This report documents a study to identify and evaluate all candidates available, and to select the most promising system such that the best possible combination of real-world performance attributesmore » is achieved at the best value. Four broad classes of candidate were identified: electric motors, turbofan aircraft engines, turboshaft aircraft engines, and turboshaft industrial engines. Candidate systems were evaluated on a basis of technical feasibility, availability, power, installed cost, and operating cost.« less

Electrodrift purification of materials for room temperature radiation detectors

DOEpatents

James, R.B.; Van Scyoc, J.M. III; Schlesinger, T.E.

1997-06-24

A method of purifying nonmetallic, crystalline semiconducting materials useful for room temperature radiation detecting devices by applying an electric field across the material is disclosed. The present invention discloses a simple technology for producing purified ionic semiconducting materials, in particular PbI{sub 2} and preferably HgI{sub 2}, which produces high yields of purified product, requires minimal handling of the material thereby reducing the possibility of introducing or reintroducing impurities into the material, is easy to control, is highly selective for impurities, retains the stoichiometry of the material and employs neither high temperatures nor hazardous materials such as solvents or liquid metals. An electric field is applied to a bulk sample of the material causing impurities present in the sample to drift in a preferred direction. After all of the impurities have been transported to the ends of the sample the current flowing through the sample, a measure of the rate of transport of mobile impurities, falls to a low, steady state value, at which time the end sections of the sample where the impurities have concentrated are removed leaving a bulk sample of higher purity material. Because the method disclosed here only acts on the electrically active impurities, the stoichiometry of the host material remains substantially unaffected. 4 figs.

Electrodrift purification of materials for room temperature radiation detectors

DOEpatents

James, Ralph B.; Van Scyoc, III, John M.; Schlesinger, Tuviah E.

1997-06-24

A method of purifying nonmetallic, crystalline semiconducting materials useful for room temperature radiation detecting devices by applying an electric field across the material. The present invention discloses a simple technology for producing purified ionic semiconducting materials, in particular PbI.sub.2 and preferably HgI.sub.2, which produces high yields of purified product, requires minimal handling of the material thereby reducing the possibility of introducing or reintroducing impurities into the material, is easy to control, is highly selective for impurities, retains the stoichiometry of the material and employs neither high temperatures nor hazardous materials such as solvents or liquid metals. An electric field is applied to a bulk sample of the material causing impurities present in the sample to drift in a preferred direction. After all of the impurities have been transported to the ends of the sample the current flowing through the sample, a measure of the rate of transport of mobile impurities, falls to a low, steady state value, at which time the end sections of the sample where the impurities have concentrated are removed leaving a bulk sample of higher purity material. Because the method disclosed here only acts on the electrically active impurities, the stoichiometry of the host material remains substantially unaffected.

Purification and characterization of an alginate lyase from marine Bacterium Vibrio sp. mutant strain 510-64.

PubMed

Hu, Xiaoke; Jiang, Xiaolu; Hwang, Huey-Min

2006-08-01

Marine Vibrio sp. 510 was chosen as a parent strain for screening high producers of alginate lyase using the complex mutagenesis of Ethyl Methanesulphonate and UV radiation treatments. The mutant strain Vibrio sp. 510-64 was selected and its alginate lyase activity was increased by 3.87-fold (reaching 46.12 EU/mg) over that of the parent strain. An extracellular alginate lyase was purified from Vibrio sp. 510-64 cultural supernatant by successive fractionation on DEAE Sepharose FF and two steps of Superdex 75. The purified enzyme yielded a single band on SDS-PAGE with the molecular weight of 34.6 kDa. Data of the N-terminal amino acid sequence indicated that this protein might be a novel alginate lyase. The substrate specificity results demonstrated that the alginate lyase had the specificity for poly G block.

Bacterial Reaction Centers Purified with Styrene Maleic Acid Copolymer Retain Native Membrane Functional Properties and Display Enhanced Stability**

PubMed Central

Swainsbury, David J K; Scheidelaar, Stefan; van Grondelle, Rienk; Killian, J Antoinette; Jones, Michael R

2014-01-01

Integral membrane proteins often present daunting challenges for biophysical characterization, a fundamental issue being how to select a surfactant that will optimally preserve the individual structure and functional properties of a given membrane protein. Bacterial reaction centers offer a rare opportunity to compare the properties of an integral membrane protein in different artificial lipid/surfactant environments with those in the native bilayer. Here, we demonstrate that reaction centers purified using a styrene maleic acid copolymer remain associated with a complement of native lipids and do not display the modified functional properties that typically result from detergent solubilization. Direct comparisons show that reaction centers are more stable in this copolymer/lipid environment than in a detergent micelle or even in the native membrane, suggesting a promising new route to exploitation of such photovoltaic integral membrane proteins in device applications. PMID:25212490

The metabolism of neuropeptides. Neurokinin A (substance K) is a substrate for endopeptidase-24.11 but not for peptidyl dipeptidase A (angiotensin-converting enzyme).

PubMed Central

Hooper, N M; Kenny, A J; Turner, A J

1985-01-01

Both endopeptidase-24.11 and peptidyl dipeptidase A have previously been shown to hydrolyse the neuropeptide substance P. The structurally related peptide neurokinin A is also shown to be hydrolysed by pig kidney endopeptidase-24.11. The identified products indicated hydrolysis at two sites, Ser5-Phe6 and Gly8-Leu9, consistent with the known specificity of the enzyme. The pattern of hydrolysis of neurokinin A by synaptic membranes prepared from pig striatum was similar to that observed with purified endopeptidase-24.11, and hydrolysis was substantially abolished by the selective inhibitor phosphoramidon. Peptidyl dipeptidase A purified from pig kidney was shown to hydrolyse substance P but not neurokinin A. It is concluded that endopeptidase-24.11 has the general capacity to hydrolyse and inactivate the family of tachykinin peptides, including substance P and neurokinin A. PMID:2998348

The metabolism of neuropeptides. Neurokinin A (substance K) is a substrate for endopeptidase-24.11 but not for peptidyl dipeptidase A (angiotensin-converting enzyme).

PubMed

Hooper, N M; Kenny, A J; Turner, A J

1985-10-15

Both endopeptidase-24.11 and peptidyl dipeptidase A have previously been shown to hydrolyse the neuropeptide substance P. The structurally related peptide neurokinin A is also shown to be hydrolysed by pig kidney endopeptidase-24.11. The identified products indicated hydrolysis at two sites, Ser5-Phe6 and Gly8-Leu9, consistent with the known specificity of the enzyme. The pattern of hydrolysis of neurokinin A by synaptic membranes prepared from pig striatum was similar to that observed with purified endopeptidase-24.11, and hydrolysis was substantially abolished by the selective inhibitor phosphoramidon. Peptidyl dipeptidase A purified from pig kidney was shown to hydrolyse substance P but not neurokinin A. It is concluded that endopeptidase-24.11 has the general capacity to hydrolyse and inactivate the family of tachykinin peptides, including substance P and neurokinin A.

Molecular Evolution of the Neural Crest Regulatory Network in Ray-Finned Fish

PubMed Central

Kratochwil, Claudius F.; Geissler, Laura; Irisarri, Iker; Meyer, Axel

2015-01-01

Abstract Gene regulatory networks (GRN) are central to developmental processes. They are composed of transcription factors and signaling molecules orchestrating gene expression modules that tightly regulate the development of organisms. The neural crest (NC) is a multipotent cell population that is considered a key innovation of vertebrates. Its derivatives contribute to shaping the astounding morphological diversity of jaws, teeth, head skeleton, or pigmentation. Here, we study the molecular evolution of the NC GRN by analyzing patterns of molecular divergence for a total of 36 genes in 16 species of bony fishes. Analyses of nonsynonymous to synonymous substitution rate ratios (dN/dS) support patterns of variable selective pressures among genes deployed at different stages of NC development, consistent with the developmental hourglass model. Model-based clustering techniques of sequence features support the notion of extreme conservation of NC-genes across the entire network. Our data show that most genes are under strong purifying selection that is maintained throughout ray-finned fish evolution. Late NC development genes reveal a pattern of increased constraints in more recent lineages. Additionally, seven of the NC-genes showed signs of relaxation of purifying selection in the famously species-rich lineage of cichlid fishes. This suggests that NC genes might have played a role in the adaptive radiation of cichlids by granting flexibility in the development of NC-derived traits—suggesting an important role for NC network architecture during the diversification in vertebrates. PMID:26475317

Stearoyl-acyl carrier protein desaturases are associated with floral isolation in sexually deceptive orchids

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

Schluter, P.M.; Shanklin, J.; Xu, S.

The orchids Ophrys sphegodes and O. exaltata are reproductively isolated from each other by the attraction of two different, highly specific pollinator species. For pollinator attraction, flowers chemically mimic the pollinators sex pheromones, the key components of which are alkenes with different double-bond positions. This study identifies genes likely involved in alkene biosynthesis, encoding stearoyl-acyl carrier protein (ACP) desaturase (SAD) homologs. The expression of two isoforms, SAD1 and SAD2, is flower-specific and broadly parallels alkene production during flower development. SAD2 shows a significant association with alkene production, and in vitro assays show that O. sphegodes SAD2 has activity both asmore » an 18:0-ACP {Delta}{sup 9} and a 16:0-ACP {Delta}{sup 4} desaturase. Downstream metabolism of the SAD2 reaction products would give rise to alkenes with double-bonds at position 9 or position 12, matching double-bond positions observed in alkenes in the odor bouquet of O. sphegodes. SAD1 and SAD2 show evidence of purifying selection before, and positive or relaxed purifying selection after gene duplication. By contributing to the production of species-specific alkene bouquets, SAD2 is suggested to contribute to differential pollinator attraction and reproductive isolation among these species. Taken together, these data are consistent with the hypothesis that SAD2 is a florally expressed barrier gene of large phenotypic effect and, possibly, a genic target of pollinator-mediated selection.« less

Stearoyl-acyl carrier protein desaturases are associated with floral isolation in sexually deceptive orchids

PubMed Central

Schlüter, Philipp M.; Xu, Shuqing; Gagliardini, Valeria; Whittle, Edward; Shanklin, John; Grossniklaus, Ueli; Schiestl, Florian P.

2011-01-01

The orchids Ophrys sphegodes and O. exaltata are reproductively isolated from each other by the attraction of two different, highly specific pollinator species. For pollinator attraction, flowers chemically mimic the pollinators’ sex pheromones, the key components of which are alkenes with different double-bond positions. This study identifies genes likely involved in alkene biosynthesis, encoding stearoyl-acyl carrier protein (ACP) desaturase (SAD) homologs. The expression of two isoforms, SAD1 and SAD2, is flower-specific and broadly parallels alkene production during flower development. SAD2 shows a significant association with alkene production, and in vitro assays show that O. sphegodes SAD2 has activity both as an 18:0-ACP Δ9 and a 16:0-ACP Δ4 desaturase. Downstream metabolism of the SAD2 reaction products would give rise to alkenes with double-bonds at position 9 or position 12, matching double-bond positions observed in alkenes in the odor bouquet of O. sphegodes. SAD1 and SAD2 show evidence of purifying selection before, and positive or relaxed purifying selection after gene duplication. By contributing to the production of species-specific alkene bouquets, SAD2 is suggested to contribute to differential pollinator attraction and reproductive isolation among these species. Taken together, these data are consistent with the hypothesis that SAD2 is a florally expressed barrier gene of large phenotypic effect and, possibly, a genic target of pollinator-mediated selection. PMID:21436056

Purification of flavonoids from licorice using an off-line preparative two-dimensional normal-phase liquid chromatography/reversed-phase liquid chromatography method.

PubMed

Fan, Yunpeng; Fu, Yanhui; Fu, Qing; Cai, Jianfeng; Xin, Huaxia; Dai, Mei; Jin, Yu

2016-07-01

An orthogonal (71.9%) off-line preparative two-dimensional normal-phase liquid chromatography/reversed-phase liquid chromatography method coupled with effective sample pretreatment was developed for separation and purification of flavonoids from licorice. Most of the nonflavonoids were firstly removed using a self-made Click TE-Cys (60 μm) solid-phase extraction. In the first dimension, an industrial grade preparative chromatography was employed to purify the crude flavonoids. Click TE-Cys (10 μm) was selected as the stationary phase that provided an excellent separation with high reproducibility. Ethyl acetate/ethanol was selected as the mobile phase owing to their excellent solubility for flavonoids. Flavonoids co-eluted in the first dimension were selected for further purification using reversed-phase liquid chromatography. Multiple compounds could be isolated from one normal-phase fraction and some compounds with bad resolution in one-dimensional liquid chromatography could be prepared in this two-dimensional system owing to the orthogonal separation. Moreover, this two-dimensional liquid chromatography method was beneficial for the preparation of relatively trace flavonoid compounds, which were enriched in the first dimension and further purified in the second dimension. Totally, 24 flavonoid compounds with high purity were obtained. The results demonstrated that the off-line two-dimensional liquid chromatography method was effective for the preparative separation and purification of flavonoids from licorice. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

RESONANT CAVITY EXCITATION SYSTEM

DOEpatents

Baker, W.R.

1959-08-01

A cavity excitation circuit is described for rapidly building up and maintaining high-level oscillations in a resonant cavity. The circuit overcomes oscillation buildup slowing effects such as ion locking in the cavity by providing for the selective application of an amplified accelerating drive signal to the main cavity exciting oscillator during oscillation buildup and a direct drive signal to the oscillator thereafter.

Statistical Physics of Adaptation

DTIC Science & Technology

2016-08-23

Statistical Physics of Adaptation Nikolay Perunov, Robert A. Marsland, and Jeremy L. England Department of Physics , Physics of Living Systems Group...Subject Areas: Biological Physics , Complex Systems, Statistical Physics I. INTRODUCTION It has long been understood that nonequilibrium driving can...equilibrium may appear to have been specially selected for physical properties connected to their ability to absorb work from the particular driving environment

Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides

PubMed Central

Hopwood, Paul E.; Head, Megan L.; Jordan, Eleanor J.; Carter, Mauricio J.; Davey, Emma; Moore, Allen J.; Royle, Nick J.

2016-01-01

Male and female genital morphology varies widely across many taxa, and even among populations. Disentangling potential sources of selection on genital morphology is problematic because each sex is predicted to respond to adaptations in the other due to reproductive conflicts of interest. To test how variation in this sexual conflict trait relates to variation in genital morphology we used our previously developed artificial selection lines for high and low repeated mating rates. We selected for high and low repeated mating rates using monogamous pairings to eliminate contemporaneous female choice and male–male competition. Male and female genital shape responded rapidly to selection on repeated mating rate. High and low mating rate lines diverged from control lines after only 10 generations of selection. We also detected significant patterns of male and female genital shape coevolution among selection regimes. We argue that because our selection lines differ in sexual conflict, these results support the hypothesis that sexually antagonistic coevolution can drive the rapid divergence of genital morphology. The greatest divergence in morphology corresponded with lines in which the resolution of sexual conflict over mating rate was biased in favor of male interests. PMID:27144373

Increased parent limits on teen driving: positive effects from a brief intervention administered at the Motor Vehicle Administration.

PubMed

Simons-Morton, Bruce G; Hartos, Jessica L; Beck, Kenneth H

2004-06-01

The purpose of this study was to determine whether exposure to a brief intervention administered at the Motor Vehicle Administration (MVA) increases parental limits on teen driving. A total of 658 parents and their 16-year-old adolescents were recruited from a local MVA site as adolescents successfully tested for provisional licenses. At the MVA, participating parents completed written surveys about expected teen driving during the 1st month of provisional licensure. One month later, 579 parent-teen dyads completed follow-up telephone interviews about teen driving within the past month. On weeks assigned as intervention, parents were exposed to a video and given the video and a driving agreement to take home. In multivariate linear regression analyses, the results indicated that when controlling for selected demographic and baseline psychosocial variables, intervention parents reported more driving rules, restricted driving, limits for high-speed roads, weekend night restrictions, and overall driving limits than did parents in the control group. When compared to control teens, intervention teens reported more limits on passengers, high-speed roads, and night driving, and on overall driving limits, but there were no differences for overall driving or driving under high-risk conditions. In addition, intervention parents were about 3 times, and intervention teens were about 5 times, more likely than controls to report using a parent-teen driving agreement. These results indicate that brief exposure to intervention at an MVA office may help increase parental limits on teen driving.

Identifying the principal driving factors of water ecosystem dependence and the corresponding indicator species in a pilot City, China

NASA Astrophysics Data System (ADS)

Zhao, C. S.; Shao, N. F.; Yang, S. T.; Xiang, H.; Lou, H. Z.; Sun, Y.; Yang, Z. Y.; Zhang, Y.; Yu, X. Y.; Zhang, C. B.; Yu, Q.

2018-01-01

The world's aquatic ecosystems yield numerous vital services, which are essential to human existence but have deteriorated seriously in recent years. By studying the mechanisms of interaction between ecosystems and habitat processes, the constraining factors can be identified, and this knowledge can be used to improve the success rate of ecological restoration initiatives. At present, there is insufficient data on the link between hydrological, water quality factors and the changes in the structure of aquatic communities to allow any meaningful study of driving factors of aquatic ecosystems. In this study, the typical monitoring stations were selected by fuzzy clustering analysis based on the spatial and temporal distribution characteristics of water ecology in Jinan City, the first pilot city for the construction of civilized aquatic ecosystems in China. The dominant species identification model was used to identify the dominant species of the aquatic community. The driving effect of hydrological and water quality factors on dominant species was analyzed by Canonical Correspondence Analysis. Then, the principal factors of aquatic ecosystem dependence were selected. The results showed that there were 10 typical monitoring stations out of 59 monitoring sites, which were representative of aquatic ecosystems, 9 dominant fish species, and 20 dominant invertebrate species. The selection of factors for aquatic ecosystem dependence in Jinan were highly influenced by its regional conditions. Chemical environmental parameters influence the temporal and spatial variation of invertebrate much more than that of fish in Jinan City. However, the methodologies coupling typical monitoring stations selection, dominant species determination and driving factors identification were certified to be a cost-effective way, which can provide in-deep theoretical and technical directions for the restoration of aquatic ecosystems elsewhere.

R2d2 Drives Selfish Sweeps in the House Mouse.

PubMed

Didion, John P; Morgan, Andrew P; Yadgary, Liran; Bell, Timothy A; McMullan, Rachel C; Ortiz de Solorzano, Lydia; Britton-Davidian, Janice; Bult, Carol J; Campbell, Karl J; Castiglia, Riccardo; Ching, Yung-Hao; Chunco, Amanda J; Crowley, James J; Chesler, Elissa J; Förster, Daniel W; French, John E; Gabriel, Sofia I; Gatti, Daniel M; Garland, Theodore; Giagia-Athanasopoulou, Eva B; Giménez, Mabel D; Grize, Sofia A; Gündüz, İslam; Holmes, Andrew; Hauffe, Heidi C; Herman, Jeremy S; Holt, James M; Hua, Kunjie; Jolley, Wesley J; Lindholm, Anna K; López-Fuster, María J; Mitsainas, George; da Luz Mathias, Maria; McMillan, Leonard; Ramalhinho, Maria da Graça Morgado; Rehermann, Barbara; Rosshart, Stephan P; Searle, Jeremy B; Shiao, Meng-Shin; Solano, Emanuela; Svenson, Karen L; Thomas-Laemont, Patricia; Threadgill, David W; Ventura, Jacint; Weinstock, George M; Pomp, Daniel; Churchill, Gary A; Pardo-Manuel de Villena, Fernando

2016-06-01

A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether "selfish" genes are capable of fixation-thereby leaving signatures identical to classical selective sweeps-despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2(HC)) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2(HC) rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2(HC) is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Recurrent selection on the Winters sex-ratio genes in Drosophila simulans.

PubMed

Kingan, Sarah B; Garrigan, Daniel; Hartl, Daniel L

2010-01-01

Selfish genes, such as meiotic drive elements, propagate themselves through a population without increasing the fitness of host organisms. X-linked (or Y-linked) meiotic drive elements reduce the transmission of the Y (X) chromosome and skew progeny and population sex ratios, leading to intense conflict among genomic compartments. Drosophila simulans is unusual in having a least three distinct systems of X chromosome meiotic drive. Here, we characterize naturally occurring genetic variation at the Winters sex-ratio driver (Distorter on the X or Dox), its progenitor gene (Mother of Dox or MDox), and its suppressor gene (Not Much Yang or Nmy), which have been previously mapped and characterized. We survey three North American populations as well as 13 globally distributed strains and present molecular polymorphism data at the three loci. We find that all three genes show signatures of selection in North America, judging from levels of polymorphism and skews in the site-frequency spectrum. These signatures likely result from the biased transmission of the driver and selection on the suppressor for the maintenance of equal sex ratios. Coalescent modeling indicates that the timing of selection is more recent than the age of the alleles, suggesting that the driver and suppressor are coevolving under an evolutionary "arms race." None of the Winters sex-ratio genes are fixed in D. simulans, and at all loci we find ancestral alleles, which lack the gene insertions and exhibit high levels of nucleotide polymorphism compared to the derived alleles. In addition, we find several "null" alleles that have mutations on the derived Dox background, which result in loss of drive function. We discuss the possible causes of the maintenance of presence-absence polymorphism in the Winters sex-ratio genes.

R2d2 Drives Selfish Sweeps in the House Mouse

PubMed Central

Didion, John P.; Morgan, Andrew P.; Yadgary, Liran; Bell, Timothy A.; McMullan, Rachel C.; Ortiz de Solorzano, Lydia; Britton-Davidian, Janice; Bult, Carol J.; Campbell, Karl J.; Castiglia, Riccardo; Ching, Yung-Hao; Chunco, Amanda J.; Crowley, James J.; Chesler, Elissa J.; Förster, Daniel W.; French, John E.; Gabriel, Sofia I.; Gatti, Daniel M.; Garland, Theodore; Giagia-Athanasopoulou, Eva B.; Giménez, Mabel D.; Grize, Sofia A.; Gündüz, İslam; Holmes, Andrew; Hauffe, Heidi C.; Herman, Jeremy S.; Holt, James M.; Hua, Kunjie; Jolley, Wesley J.; Lindholm, Anna K.; López-Fuster, María J.; Mitsainas, George; da Luz Mathias, Maria; McMillan, Leonard; Ramalhinho, Maria da Graça Morgado; Rehermann, Barbara; Rosshart, Stephan P.; Searle, Jeremy B.; Shiao, Meng-Shin; Solano, Emanuela; Svenson, Karen L.; Thomas-Laemont, Patricia; Threadgill, David W.; Ventura, Jacint; Weinstock, George M.; Pomp, Daniel; Churchill, Gary A.; Pardo-Manuel de Villena, Fernando

2016-01-01

A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether “selfish” genes are capable of fixation—thereby leaving signatures identical to classical selective sweeps—despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2HC) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2HC rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2HC is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution. PMID:26882987

Modular multimorphic kinematic arm structure and pitch and yaw joint for same

DOEpatents

Martin, H. Lee; Williams, Daniel M.; Holt, W. Eugene

1989-01-01

A multimorphic kinematic manipulator arm is provided with seven degrees of freedom and modular kinematic redundancy through identical pitch/yaw, shoulder, elbow and wrist joints and a wrist roll device at the wrist joint, which further provides to the manipulator arm an obstacle avoidance capability. The modular pitch/yaw joints are traction drive devices which provide backlash free operation with smooth torque transmission and enhanced rigidity. A dual input drive arrangement is provided for each joint resulting in a reduction of the load required to be assumed by each drive and providing selective pitch and yaw motions by control of the relative rotational directions of the input drive.

Modular multimorphic kinematic arm structure and pitch and yaw joint for same

DOEpatents

Martin, H.L.; Williams, D.M.; Holt, W.E.

1987-04-21

A multimorphic kinematic manipulator arm is provided with seven degrees of freedom and modular kinematic redundancy through identical pitch/yaw, shoulder, elbow and wrist joints and a wrist roll device at the wrist joint, which further provides to the manipulator arm an obstacle avoidance capability. The modular pitch/yaw joints are traction drive devices which provide backlash free operation with smooth torque transmission and enhanced rigidity. A dual input drive arrangement is provided for each joint resulting in a reduction of the load required to be assumed by each drive means and providing selective pitch and yaw motions by control of the relative rotational directions of the input drive means. 12 figs.

Rapid diversification of FoxP2 in teleosts through gene duplication in the teleost-specific whole genome duplication event.

PubMed

Song, Xiaowei; Wang, Yajun; Tang, Yezhong

2013-01-01

As one of the most conserved genes in vertebrates, FoxP2 is widely involved in a number of important physiological and developmental processes. We systematically studied the evolutionary history and functional adaptations of FoxP2 in teleosts. The duplicated FoxP2 genes (FoxP2a and FoxP2b), which were identified in teleosts using synteny and paralogon analysis on genome databases of eight organisms, were probably generated in the teleost-specific whole genome duplication event. A credible classification with FoxP2, FoxP2a and FoxP2b in phylogenetic reconstructions confirmed the teleost-specific FoxP2 duplication. The unavailability of FoxP2b in Danio rerio suggests that the gene was deleted through nonfunctionalization of the redundant copy after the Otocephala-Euteleostei split. Heterogeneity in evolutionary rates among clusters consisting of FoxP2 in Sarcopterygii (Cluster 1), FoxP2a in Teleostei (Cluster 2) and FoxP2b in Teleostei (Cluster 3), particularly between Clusters 2 and 3, reveals asymmetric functional divergence after the gene duplication. Hierarchical cluster analyses of hydrophobicity profiles demonstrated significant structural divergence among the three clusters with verification of subsequent stepwise discriminant analysis, in which FoxP2 of Leucoraja erinacea and Lepisosteus oculatus were classified into Cluster 1, whereas FoxP2b of Salmo salar was grouped into Cluster 2 rather than Cluster 3. The simulated thermodynamic stability variations of the forkhead box domain (monomer and homodimer) showed remarkable divergence in FoxP2, FoxP2a and FoxP2b clusters. Relaxed purifying selection and positive Darwinian selection probably were complementary driving forces for the accelerated evolution of FoxP2 in ray-finned fishes, especially for the adaptive evolution of FoxP2a and FoxP2b in teleosts subsequent to the teleost-specific gene duplication.

Rapid Diversification of FoxP2 in Teleosts through Gene Duplication in the Teleost-Specific Whole Genome Duplication Event

PubMed Central

Song, Xiaowei; Wang, Yajun; Tang, Yezhong

2013-01-01

As one of the most conserved genes in vertebrates, FoxP2 is widely involved in a number of important physiological and developmental processes. We systematically studied the evolutionary history and functional adaptations of FoxP2 in teleosts. The duplicated FoxP2 genes (FoxP2a and FoxP2b), which were identified in teleosts using synteny and paralogon analysis on genome databases of eight organisms, were probably generated in the teleost-specific whole genome duplication event. A credible classification with FoxP2, FoxP2a and FoxP2b in phylogenetic reconstructions confirmed the teleost-specific FoxP2 duplication. The unavailability of FoxP2b in Danio rerio suggests that the gene was deleted through nonfunctionalization of the redundant copy after the Otocephala-Euteleostei split. Heterogeneity in evolutionary rates among clusters consisting of FoxP2 in Sarcopterygii (Cluster 1), FoxP2a in Teleostei (Cluster 2) and FoxP2b in Teleostei (Cluster 3), particularly between Clusters 2 and 3, reveals asymmetric functional divergence after the gene duplication. Hierarchical cluster analyses of hydrophobicity profiles demonstrated significant structural divergence among the three clusters with verification of subsequent stepwise discriminant analysis, in which FoxP2 of Leucoraja erinacea and Lepisosteus oculatus were classified into Cluster 1, whereas FoxP2b of Salmo salar was grouped into Cluster 2 rather than Cluster 3. The simulated thermodynamic stability variations of the forkhead box domain (monomer and homodimer) showed remarkable divergence in FoxP2, FoxP2a and FoxP2b clusters. Relaxed purifying selection and positive Darwinian selection probably were complementary driving forces for the accelerated evolution of FoxP2 in ray-finned fishes, especially for the adaptive evolution of FoxP2a and FoxP2b in teleosts subsequent to the teleost-specific gene duplication. PMID:24349554

Human Variation in Short Regions Predisposed to Deep Evolutionary Conservation

PubMed Central

Loots, Gabriela G.; Ovcharenko, Ivan

2010-01-01

The landscape of the human genome consists of millions of short islands of conservation that are 100% conserved across multiple vertebrate genomes (termed “bricks”), the majority of which are located in noncoding regions. Several hundred thousand bricks are deeply conserved reaching the genomes of amphibians and fish. Deep phylogenetic conservation of noncoding DNA has been reported to be strongly associated with the presence of gene regulatory elements, introducing bricks as a proxy to the functional noncoding landscape of the human genome. Here, we report a significant overrepresentation of bricks in the promoters of transcription factors and developmental genes, where the high level of phylogenetic conservation correlates with an increase in brick overrepresentation. We also found that the presence of a brick dictates a predisposition to evolutionary constraint, with only 0.7% of the amniota brick central nucleotides being diverged within the primate lineage—an 11-fold reduction in the divergence rate compared with random expectation. Human single-nucleotide polymorphism (SNP) data explains only 3% of primate-specific variation in amniota bricks, thus arguing for a widespread fixation of brick mutations within the primate lineage and prior to human radiation. This variation, in turn, might have been utilized as a driving force for primate- and hominoid-specific adaptation. We also discovered a pronounced deviation from the evolutionary predisposition in the human lineage, with over 20-fold increase in the substitution rate at brick SNP sites over expected values. In addition, contrary to typical brick mutations, brick variation commonly encountered in the human population displays limited, if any, signatures of negative selection as measured by the minor allele frequency and population differentiation (F-statistical measure) measures. These observations argue for the plasticity of gene regulatory mechanisms in vertebrates—with evidence of strong purifying selection acting on the gene regulatory landscape of the human genome, where widespread advantageous mutations in putative regulatory elements are likely utilized in functional diversification and adaptation of species. PMID:20093432

The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy.

PubMed

Mao, Kai; Wang, Ke; Liu, Xu; Klionsky, Daniel J

2013-07-15

As the cellular power plant, mitochondria play a significant role in homeostasis. To maintain the proper quality and quantity of mitochondria requires both mitochondrial degradation and division. A selective type of autophagy, mitophagy, drives the degradation of excess or damaged mitochondria, whereas division is controlled by a specific fission complex; however, the relationship between these two processes, especially the role of mitochondrial fission during mitophagy, remains unclear. In this study, we report that mitochondrial fission is important for the progression of mitophagy. When mitophagy is induced, the fission complex is recruited to the degrading mitochondria through an interaction between Atg11 and Dnm1; interfering with this interaction severely blocks mitophagy. These data establish a paradigm for selective organelle degradation. Copyright © 2013 Elsevier Inc. All rights reserved.

Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans.

PubMed

Shen, Tong; Xu, Shixia; Wang, Xiaohong; Yu, Wenhua; Zhou, Kaiya; Yang, Guang

2012-03-24

Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans.

Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans

PubMed Central

2012-01-01

Background Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. Results We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. Conclusions This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans. PMID:22443485

Identification of landscape features influencing gene flow: How useful are habitat selection models?

Treesearch

Gretchen H. Roffler; Michael K. Schwartz; Kristine Pilgrim; Sandra L. Talbot; George K. Sage; Layne G. Adams; Gordon Luikart

2016-01-01

Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is...

Automated Hydrophobic Interaction Chromatography Column Selection for Use in Protein Purification

PubMed Central

Murphy, Patrick J. M.; Stone, Orrin J.; Anderson, Michelle E.

2011-01-01

In contrast to other chromatographic methods for purifying proteins (e.g. gel filtration, affinity, and ion exchange), hydrophobic interaction chromatography (HIC) commonly requires experimental determination (referred to as screening or "scouting") in order to select the most suitable chromatographic medium for purifying a given protein 1. The method presented here describes an automated approach to scouting for an optimal HIC media to be used in protein purification. HIC separates proteins and other biomolecules from a crude lysate based on differences in hydrophobicity. Similar to affinity chromatography (AC) and ion exchange chromatography (IEX), HIC is capable of concentrating the protein of interest as it progresses through the chromatographic process. Proteins best suited for purification by HIC include those with hydrophobic surface regions and able to withstand exposure to salt concentrations in excess of 2 M ammonium sulfate ((NH4)2SO4). HIC is often chosen as a purification method for proteins lacking an affinity tag, and thus unsuitable for AC, and when IEX fails to provide adequate purification. Hydrophobic moieties on the protein surface temporarily bind to a nonpolar ligand coupled to an inert, immobile matrix. The interaction between protein and ligand are highly dependent on the salt concentration of the buffer flowing through the chromatography column, with high ionic concentrations strengthening the protein-ligand interaction and making the protein immobile (i.e. bound inside the column) 2. As salt concentrations decrease, the protein-ligand interaction dissipates, the protein again becomes mobile and elutes from the column. Several HIC media are commercially available in pre-packed columns, each containing one of several hydrophobic ligands (e.g. S-butyl, butyl, octyl, and phenyl) cross-linked at varying densities to agarose beads of a specific diameter 3. Automated column scouting allows for an efficient approach for determining which HIC media should be employed for future, more exhaustive optimization experiments and protein purification runs 4. The specific protein being purified here is recombinant green fluorescent protein (GFP); however, the approach may be adapted for purifying other proteins with one or more hydrophobic surface regions. GFP serves as a useful model protein, due to its stability, unique light absorbance peak at 397 nm, and fluorescence when exposed to UV light 5. Bacterial lysate containing wild type GFP was prepared in a high-salt buffer, loaded into a Bio-Rad DuoFlow medium pressure liquid chromatography system, and adsorbed to HiTrap HIC columns containing different HIC media. The protein was eluted from the columns and analyzed by in-line and post-run detection methods. Buffer blending, dynamic sample loop injection, sequential column selection, multi-wavelength analysis, and split fraction eluate collection increased the functionality of the system and reproducibility of the experimental approach. PMID:21968976

Importance of NADPH oxidase-mediated redox signaling in the detrimental effect of CRP on pancreatic insulin secretion.

PubMed

Chan, Pei-Chi; Wang, Ya-Chin; Chen, Yi-Ling; Hsu, Wan-Ning; Tian, Yu-Feng; Hsieh, Po-Shiuan

2017-11-01

Elevations in C-reactive protein (CRP) levels are positively correlated with the progress of type 2 diabetes mellitus. However, the effect of CRP on pancreatic insulin secretion is unknown. Here, we showed that purified human CRP impaired insulin secretion in isolated mouse islets and NIT-1 insulin-secreting cells in dose- and time-dependent manners. CRP increased NADPH oxidase-mediated ROS (reactive oxygen species) production, which simultaneously promoted the production of nitrotyrosine (an indicator of RNS, reactive nitrogen species) and TNFα, to diminish cell viability, insulin secretion in islets and insulin-secreting cells. These CRP-mediated detrimental effects on cell viability and insulin secretion were significantly reversed by adding NAC (a potent antioxidant), apocynin (a selective NADPH oxidase inhibitor), L-NAME (a non-selective nitric oxide synthase (NOS) inhibitor), aminoguanidine (a selective iNOS inhibitor), PDTC (a selective NFκB inhibitor) or Enbrel (an anti-TNFα fusion protein). However, CRP-induced ROS production failed to change after adding L-NAME, aminoguanidine or PDTC. In isolated islets and NIT-1 cells, the elevated nitrotyrosine contents by CRP pretreatment were significantly suppressed by adding L-NAME but not PDTC. Conversely, CRP-induced increases in TNF-α production were significantly reversed by administration of PDTC but not L-NAME. In addition, wild-type mice treated with purified human CRP showed significant decreases in the insulin secretion index (HOMA-β cells) and the insulin stimulation index in isolated islets that were reversed by the addition of L-NAME, aminoguanidine or NAC. It is suggested that CRP-activated NADPH-oxidase redox signaling triggers iNOS-mediated RNS and NFκB-mediated proinflammatory cytokine production to cause β cell damage in state of inflammation. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae.

PubMed

Mao, Yunrui; Zhang, Yonghua; Xu, Chuan; Qiu, Yingxiong

2016-01-01

Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53,929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa. © 2015 John Wiley & Sons Ltd.

Importance of the residue Asp 290 on chain length selectivity and catalytic efficiency of recombinant Staphylococcus simulans lipase expressed in E. coli.

PubMed

Sayari, Adel; Mosbah, Habib; Gargouri, Youssef

2007-05-01

In addition to their physiological importance, microbial lipases, like staphylococcal ones, are of considerable commercial interest for biotechnological applications such as detergents, food production, and pharmaceuticals and industrial synthesis of fine chemicals. The gene encoding the extracellular lipase of Staphylococcus simulans (SSL) was subcloned in the pET-14b expression vector and expressed in Esherichia coli BL21 (DE3). The wild-type SSL was expressed as amino terminal His6-tagged recombinant protein. One-step purification of the recombinant lipase was achieved with nickel metal affinity column. The purified His-tagged SSL (His6-SSL) is able to hydrolyse triacylglycerols without chain length selectivity. The major differences among lipases are reflected in their chemical specificity in the hydrolysis of peculiar ester bonds, and their respective capacity to hydrolyse substrates having different physico-chemical properties. It has been proposed, using homology alignment, that the region around the residue 290 of Staphylococcus hyicus lipase could be involved in the selection of the substrate. To evaluate the importance of this environment, the residue Asp290 of Staphylococcus simulans lipase was mutated to Ala using site-directed mutagenesis. The mutant expression plasmid was also overexpressed in Esherichia coli and purified with a nickel metal affinity column. The substitution of Asp290 by Ala was accompanied by a significant shift of the acyl-chain length specificity of the mutant towards short chain fatty acid esters. Kinetic studies of wild-type SSL and its mutant D290A were carried out, and show essentially that the catalytic efficiency (k cat /K M ) of the mutant was affected. Our results confirmed that Asp290 is important for the chain length selectivity and catalytic efficiency of Staphylococcus simulans lipase.

Analysis of Serine Codon Conservation Reveals Diverse Phenotypic Constraints on Hepatitis C Virus Glycoprotein Evolution

PubMed Central

Koutsoudakis, George; Urbanowicz, Richard A.; Mirza, Deeman; Ginkel, Corinne; Riebesehl, Nina; Calland, Noémie; Albecka, Anna; Price, Louisa; Hudson, Natalia; Descamps, Véronique; Backx, Matthijs; McClure, C. Patrick; Duverlie, Gilles; Pecheur, Eve-Isabelle; Dubuisson, Jean; Perez-del-Pulgar, Sofia; Forns, Xavier; Steinmann, Eike; Tarr, Alexander W.; Pietschmann, Thomas

2014-01-01

Serine is encoded by two divergent codon types, UCN and AGY, which are not interchangeable by a single nucleotide substitution. Switching between codon types therefore occurs via intermediates (threonine or cysteine) or via simultaneous tandem substitutions. Hepatitis C virus (HCV) chronically infects 2 to 3% of the global population. The highly variable glycoproteins E1 and E2 decorate the surface of the viral envelope, facilitate cellular entry, and are targets for host immunity. Comparative sequence analysis of globally sampled E1E2 genes, coupled with phylogenetic analysis, reveals the signatures of multiple archaic codon-switching events at seven highly conserved serine residues. Limited detection of intermediate phenotypes indicates that associated fitness costs restrict their fixation in divergent HCV lineages. Mutational pathways underlying codon switching were probed via reverse genetics, assessing glycoprotein functionality using multiple in vitro systems. These data demonstrate selection against intermediate phenotypes can act at the structural/functional level, with some intermediates displaying impaired virion assembly and/or decreased capacity for target cell entry. These effects act in residue/isolate-specific manner. Selection against intermediates is also provided by humoral targeting, with some intermediates exhibiting increased epitope exposure and enhanced neutralization sensitivity, despite maintaining a capacity for target cell entry. Thus, purifying selection against intermediates limits their frequencies in globally sampled strains, with divergent functional constraints at the protein level restricting the fixation of deleterious mutations. Overall our study provides an experimental framework for identification of barriers limiting viral substitutional evolution and indicates that serine codon-switching represents a genomic “fossil record” of historical purifying selection against E1E2 intermediate phenotypes. PMID:24173227

Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection

PubMed Central

2008-01-01

Background The molecular events and evolutionary forces underlying lethal mutagenesis of virus (or virus extinction through an excess of mutations) are not well understood. Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ) to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV) quasispecies subjected to mutagenesis by base and nucleoside analogues. Results Phylogenetic and PAQ analyses have revealed a highly dynamic variation of intrapopulation diversity of FMDV quasispecies. The population diversity first suffers striking expansions in the presence of mutagens and then compressions either when the presence of the mutagenic analogue was discontinued or when a mutation that decreased sensitivity to a mutagen was selected. The pattern of mutations found in the populations was in agreement with the behavior of the corresponding nucleotide analogues with FMDV in vitro. Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying) selection in populations subjected to mutagenesis. No evidence of unusually elevated genetic distances has been obtained for FMDV populations approaching extinction. Conclusion Phylogenetic and PAQ analysis provide adequate procedures to describe the evolution of viral sequences subjected to lethal mutagenesis. These methods define the changes of intra-population structure more precisely than mutation frequencies and Shannon entropies. PAQ is very sensitive to variations of intrapopulation genetic distances. Strong negative (or purifying) selection operates in FMDV populations subjected to enhanced mutagenesis. The quantifications provide evidence that extinction does not imply unusual increases of intrapopulation complexity, in support of the lethal defection model of virus extinction. PMID:18637173

Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins.

PubMed

Mallik, Saurav; Kundu, Sudip

2017-04-01

Understanding the molecular evolution of macromolecular complexes in the light of their structure, assembly, and stability is of central importance. Here, we address how the modular organization of native molecular contacts shapes the selection pressure on individual residue sites of ribosomal complexes. The bacterial ribosomal complex is represented as a residue contact network where nodes represent amino acid/nucleotide residues and edges represent their van der Waals interactions. We find statistically overrepresented native amino acid-nucleotide contacts (OaantC, one amino acid contacts one or multiple nucleotides, internucleotide contacts are disregarded). Contact number is defined as the number of nucleotides contacted. Involvement of individual amino acids in OaantCs with smaller contact numbers is more random, whereas only a few amino acids significantly contribute to OaantCs with higher contact numbers. An investigation of structure, stability, and assembly of bacterial ribosome depicts the involvement of these OaantCs in diverse biophysical interactions stabilizing the complex, including high-affinity protein-RNA contacts, interprotein cooperativity, intersubunit bridge, packing of multiple ribosomal RNA domains, etc. Amino acid-nucleotide constituents of OaantCs with higher contact numbers are generally associated with significantly slower substitution rates compared with that of OaantCs with smaller contact numbers. This evolutionary rate heterogeneity emerges from the strong purifying selection pressure that conserves the respective amino acid physicochemical properties relevant to the stabilizing interaction with OaantC nucleotides. An analysis of relative molecular orientations of OaantC residues and their interaction energetics provides the biophysical ground of purifying selection conserving OaantC amino acid physicochemical properties. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Amorphous and nanocrystalline luminescent Si and Ge obtained via a solid-state chemical metathesis synthesis route

NASA Astrophysics Data System (ADS)

McMillan, Paul F.; Gryko, Jan; Bull, Craig; Arledge, Richard; Kenyon, Anthony J.; Cressey, Barbara A.

2005-03-01

A new solid-state metathesis synthesis route was applied to obtain bulk samples of amorphous or microcrystalline Si and Ge. The method involves reaction of Zintl phases such as NaSi or NaGe, with ammonium or metal (e.g., CuCl, CoBr 2) halides. The driving force for the solid-state reaction is provided by the formation of alkali halides and the transition metals or metal silicides, or gaseous ammonia and hydrogen. The semiconductors were purified by washing to remove other solid products. The amorphous semiconductors were obtained in bulk form from reactions carried out at 200-300 °C. Syntheses at higher temperatures gave rise to microcrystalline semiconductors, or to micro-/nanocrystalline particles contained within the amorphous material. Similar crystalline/amorphous composites were obtained after heat treatment of bulk amorphous materials.

Quality assurance after process changes of the production of a therapeutic antibody.

PubMed

Brass, J M; Krummen, K; Moll-Kaufmann, C

1996-12-01

Process development for the production of a therapeutic humanised antibody is a very complex operation. It involves recombinant genetics, verification of a strong expression system, gene amplification, characterisation of a stable host cell expression system, optimisation and design of the mammalian cell culture fermentation system and development of an efficient recovery process resulting in high yields and product quality. Rapid progress in the field and the wish of some pharmaceutical companies for outsourcing their production are the driving forces for process changes relatively late in the development phase. This literature survey is aimed at identifying the limits of acceptable process changes in up scaling of the fermentation and down stream processing of biopharmaceuticals and defining the demand in production validation to prove product equivalency and identity of the isolated, purified therapeutic antibody.

Affinity Proteomics for Fast, Sensitive, Quantitative Analysis of Proteins in Plasma.

PubMed

O'Grady, John P; Meyer, Kevin W; Poe, Derrick N

2017-01-01

The improving efficacy of many biological therapeutics and identification of low-level biomarkers are driving the analytical proteomics community to deal with extremely high levels of sample complexity relative to their analytes. Many protein quantitation and biomarker validation procedures utilize an immunoaffinity enrichment step to purify the sample and maximize the sensitivity of the corresponding liquid chromatography tandem mass spectrometry measurements. In order to generate surrogate peptides with better mass spectrometric properties, protein enrichment is followed by a proteolytic cleavage step. This is often a time-consuming multistep process. Presented here is a workflow which enables rapid protein enrichment and proteolytic cleavage to be performed in a single, easy-to-use reactor. Using this strategy Klotho, a low-abundance biomarker found in plasma, can be accurately quantitated using a protocol that takes under 5 h from start to finish.

Spatial gene drives and pushed genetic waves.

PubMed

Tanaka, Hidenori; Stone, Howard A; Nelson, David R

2017-08-08

Gene drives have the potential to rapidly replace a harmful wild-type allele with a gene drive allele engineered to have desired functionalities. However, an accidental or premature release of a gene drive construct to the natural environment could damage an ecosystem irreversibly. Thus, it is important to understand the spatiotemporal consequences of the super-Mendelian population genetics before potential applications. Here, we use a reaction-diffusion model for sexually reproducing diploid organisms to study how a locally introduced gene drive allele spreads to replace the wild-type allele, although it possesses a selective disadvantage s > 0. Using methods developed by Barton and collaborators, we show that socially responsible gene drives require 0.5 < s < 0.697, a rather narrow range. In this "pushed wave" regime, the spatial spreading of gene drives will be initiated only when the initial frequency distribution is above a threshold profile called "critical propagule," which acts as a safeguard against accidental release. We also study how the spatial spread of the pushed wave can be stopped by making gene drives uniquely vulnerable ("sensitizing drive") in a way that is harmless for a wild-type allele. Finally, we show that appropriately sensitized drives in two dimensions can be stopped, even by imperfect barriers perforated by a series of gaps.

Recombinant production of enzymatically active male contraceptive drug target hTSSK2 - Localization of the TSKS domain phosphorylated by TSSK2.

PubMed

Shetty, Jagathpala; Sinville, Rondedrick; Shumilin, Igor A; Minor, Wladek; Zhang, Jianhai; Hawkinson, Jon E; Georg, Gunda I; Flickinger, Charles J; Herr, John C

2016-05-01

The testis-specific serine/threonine kinase 2 (TSSK2) has been proposed as a candidate male contraceptive target. Development of a selective inhibitor for this kinase first necessitates the production of highly purified, soluble human TSSK2 and its substrate, TSKS, with high yields and retention of biological activity for crystallography and compound screening. Strategies to produce full-length, soluble, biologically active hTSSK2 in baculovirus expression systems were tested and refined. Soluble preparations of TSSK2 were purified by immobilized-metal affinity chromatography (IMAC) followed by gel filtration chromatography. The biological activities of rec.hTSSK2 were verified by in vitro kinase and mobility shift assays using bacterially produced hTSKS (isoform 2), casein, glycogen synthase peptide (GS peptide) and various TSKS peptides as target substrates. Purified recombinant hTSSK2 showed robust kinase activity in the in vitro kinase assay by phosphorylating hTSKS isoform 2 and casein. The ATP Km values were similar for highly and partially purified fractions of hTSSK2 (2.2 and 2.7 μM, respectively). The broad spectrum kinase inhibitor staurosporine was a potent inhibitor of rec.hTSSK2 (IC50 = 20 nM). In vitro phosphorylation experiments carried out with TSKS (isoform 1) fragments revealed particularly strong phosphorylation of a recombinant N-terminal region representing aa 1-150 of TSKS, indicating that the N-terminus of human TSKS is phosphorylated by human TSSK2. Production of full-length enzymatically active recombinant TSSK2 kinase represents the achievement of a key benchmark for future discovery of TSSK inhibitors as male contraceptive agents. Copyright © 2016 Elsevier Inc. All rights reserved.

Safety and immunogenicity of mammalian cell derived and Modified Vaccinia Ankara vectored African swine fever subunit antigens in swine.

PubMed

Lopera-Madrid, Jaime; Osorio, Jorge E; He, Yongqun; Xiang, Zuoshuang; Adams, L Garry; Laughlin, Richard C; Mwangi, Waithaka; Subramanya, Sandesh; Neilan, John; Brake, David; Burrage, Thomas G; Brown, William Clay; Clavijo, Alfonso; Bounpheng, Mangkey A

2017-03-01

A reverse vaccinology system, Vaxign, was used to identify and select a subset of five African Swine Fever (ASF) antigens that were successfully purified from human embryonic kidney 293 (HEK) cells and produced in Modified vaccinia virus Ankara (MVA) viral vectors. Three HEK-purified antigens [B646L (p72), E183L (p54), and O61R (p12)], and three MVA-vectored antigens [B646L, EP153R, and EP402R (CD2v)] were evaluated using a prime-boost immunization regimen swine safety and immunogenicity study. Antibody responses were detected in pigs following prime-boost immunization four weeks apart with the HEK-293-purified p72, p54, and p12 antigens. Notably, sera from the vaccinees were positive by immunofluorescence on ASFV (Georgia 2007/1)-infected primary macrophages. Although MVA-vectored p72, CD2v, and EP153R failed to induce antibody responses, interferon-gamma (IFN-γ + ) spot forming cell responses against all three antigens were detected one week post-boost. The highest IFN-γ + spot forming cell responses were detected against p72 in pigs primed with MVA-p72 and boosted with the recombinant p72. Antigen-specific (p12, p72, CD2v, and EP153R) T-cell proliferative responses were also detected post-boost. Collectively, these results are the first demonstration that ASFV subunit antigens purified from mammalian cells or expressed in MVA vectors are safe and can induce ASFV-specific antibody and T-cell responses following a prime-boost immunization regimen in swine. Copyright © 2017 Elsevier B.V. All rights reserved.

The production and characterization of novel heavy-chain antibodies against the tandem repeat region of MUC1 mucin.

PubMed

Rahbarizadeh, Fatemeh; Rasaee, Mohammad J; Forouzandeh, Mehdi; Allameh, Abdolamir; Sarrami, Ramin; Nasiry, Habib; Sadeghizadeh, Majid

2005-01-01

Camelidae are known to produce immunoglobulins (Igs) devoid of light chains and constant heavy-chain domains (CH1). Antigen-specific fragments of these heavy-chain IgGs (VHH) are of great interest in biotechnology applications. This paper describes the first example of successfully raised heavy-chain antibodies in Camelus dromedarius (single-humped camel) and Camelus bactrianus (two-humped camel) against a MUC1 related peptide that is found to be an important epitope expressed in cancerous tissue. Camels were immunized against a synthetic peptide corresponding to the tandem repeat region of MUC1 mucin and cancerous tissue preparation obtained from patients suffering from breast carcinoma. Three IgG subclasses with different binding properties to protein A and G were purified by affinity chromatography. Both conventional and heavy-chain IgG antibodies were produced in response to MUC1-related peptide. The elicited antibodies could react specifically with the tandem repeat region of MUC1 mucin in an enzyme linked immunosorbant assay (ELISA). Anti-peptide antibodies were purified after passing antiserum over two affinity chromatography columns. Using ELISA, immunocytochemistry and Western blotting, the interaction of purified antibodies with different antigens was evaluated. The antibodies were observed to be selectively bound to antigens namely: MUC1 peptide (tandem repeat region), human milk fat globule membrane (HMFG), deglycosylated human milk fat globule membrane (D-HMFG), homogenized cancerous breast tissue and a native MUC1 purified from ascitic fluid. Ka values of specific polyclonal antipeptide antibodies were estimated in C. dromedarius and C. bactrianus, as 7 x 10(10) M(-1) and 1.4 x 10(10) M(-1) respectively.

Phosphatidylinositol anchor of HeLa cell alkaline phosphatase

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

Jemmerson, R.; Low, M.G.

1987-09-08

Alkaline phosphatase from cancer cells, HeLa TCRC-1, was biosynthetically labeled with either /sup 3/H-fatty acids or (/sup 3/H)ethanolamine as analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and fluorography of immunoprecipitated material. Phosphatidylinositol-specific phospholipase C (PI-PLC) released a substantial proportion of the /sup 3/H-fatty acid label from immunoaffinity-purified alkaline phosphatase but had no effect on the radioactivity of (/sup 3/H)ethanolamine-labeled material. PI-PLC also liberated catalytically active alkaline phosphatase from viable cells, and this could be selectively blocked by monoclonal antibodies to alkaline phosphatase. However, the alkaline phosphatase released from /sup 3/H-fatty acid labeled cells by PI-PLC was not radioactive. By contrast,more » treatment with bromelain removed both the /sup 3/H-fatty acid and the (/sup 3/H)ethanolamine label from purified alkaline phosphatase. Subtilisin was also able to remove the (/sup 3/H)ethanolamine label from the purified alkaline phosphatase. The /sup 3/H radioactivity in alkaline phosphatase purified from (/sup 3/H)ethanolamine-labeled cells comigrated with authentic (/sup 3/H)ethanolamine by anion-exchange chromatography after acid hydrolysis. The data suggest that the /sup 3/H-fatty acid and (/sup 3/H)ethanolamine are covalently attached to the carboxyl-terminal segment since bromelain and subtilisin both release alkaline phosphatase from the membrane by cleavage at that end of the polypeptide chain. The data are consistent with findings for other proteins recently shown to be anchored in the membrane through a glycosylphosphatidylinositol structure and indicate that a similar structure contributes to the membrane anchoring of alkaline phosphatase.« less

Purification of Cardiomyocytes from Differentiating Pluripotent Stem Cells using Molecular Beacons Targeting Cardiomyocyte-Specific mRNA

PubMed Central

Kim, Sangsung; Park, Hun-Jun; Byun, Jaemin; Cho, Kyu-Won; Saafir, Talib; Song, Ming-Ke; Yu, Shan Ping; Wagner, Mary; Bao, Gang; Yoon, Young-Sup

2013-01-01

Background While methods for generating cardiomyocytes (CMs) from pluripotent stem cells (PSCs) have been reported, current methods produce heterogeneous mixtures of CMs and non-CM cells. Here, we report an entirely novel system in which PSC-derived CMs are purified by CM-specific molecular beacons (MBs). MBs are nano-scale probes that emit a fluorescence signal when hybridized to target mRNAs. Method and Results Five MBs targeting mRNAs of either cardiac troponin T or myosin heavy chain 6/7 were generated. Among five MBs, a MB targeting myosin heavy chain 6/7 mRNA (MHC1-MB) identified up to 99% of HL-1 CMs, a mouse CM cell line, but < 3% of four non-CM cell types in flow cytometry analysis, indicating that MHC1-MB is specific for identifying CMs. We delivered MHC1-MB into cardiomyogenically differentiated PSCs through nucleofection. The detection rate of CMs was similar to the percentages of cardiac troponin T (TNNT2) or cardiac troponin I (TNNI3)-positive CMs, supporting the specificity of MBs. Finally, MHC1-MB-positive cells were FACS-sorted from mouse and human PSC differentiating cultures and ~97% cells expressed TNNT2- or TNNI3 determined by flow cytometry. These MB-based sorted cells maintained their CM characteristics verified by spontaneous beating, electrophysiologic studies, and expression of cardiac proteins. When transplanted in a myocardial infarction model, MB-based purified CMs improved cardiac function and demonstrated significant engraftment for 4 weeks without forming tumors. Conclusions We developed a novel CM selection system that allows production of highly purified CMs. These purified CMs and this system can be valuable for cell therapy and drug discovery. PMID:23995537

Purification of cardiomyocytes from differentiating pluripotent stem cells using molecular beacons that target cardiomyocyte-specific mRNA.

PubMed

Ban, Kiwon; Wile, Brian; Kim, Sangsung; Park, Hun-Jun; Byun, Jaemin; Cho, Kyu-Won; Saafir, Talib; Song, Ming-Ke; Yu, Shan Ping; Wagner, Mary; Bao, Gang; Yoon, Young-Sup

2013-10-22

Although methods for generating cardiomyocytes from pluripotent stem cells have been reported, current methods produce heterogeneous mixtures of cardiomyocytes and noncardiomyocyte cells. Here, we report an entirely novel system in which pluripotent stem cell-derived cardiomyocytes are purified by cardiomyocyte-specific molecular beacons (MBs). MBs are nanoscale probes that emit a fluorescence signal when hybridized to target mRNAs. Five MBs targeting mRNAs of either cardiac troponin T or myosin heavy chain 6/7 were generated. Among 5 MBs, an MB that targeted myosin heavy chain 6/7 mRNA (MHC1-MB) identified up to 99% of HL-1 cardiomyocytes, a mouse cardiomyocyte cell line, but <3% of 4 noncardiomyocyte cell types in flow cytometry analysis, which indicates that MHC1-MB is specific for identifying cardiomyocytes. We delivered MHC1-MB into cardiomyogenically differentiated pluripotent stem cells through nucleofection. The detection rate of cardiomyocytes was similar to the percentages of cardiac troponin T- or cardiac troponin I-positive cardiomyocytes, which supports the specificity of MBs. Finally, MHC1-MB-positive cells were sorted by fluorescence-activated cell sorter from mouse and human pluripotent stem cell differentiating cultures, and ≈97% cells expressed cardiac troponin T or cardiac troponin I as determined by flow cytometry. These MB-based sorted cells maintained their cardiomyocyte characteristics, which was verified by spontaneous beating, electrophysiological studies, and expression of cardiac proteins. When transplanted in a myocardial infarction model, MB-based purified cardiomyocytes improved cardiac function and demonstrated significant engraftment for 4 weeks without forming tumors. We developed a novel cardiomyocyte selection system that allows production of highly purified cardiomyocytes. These purified cardiomyocytes and this system can be valuable for cell therapy and drug discovery.

Molecular evolution and expression profile of the chemerine encoding gene RARRES2 in baboon and chimpanzee.

PubMed

González-Alvarez, Rafael; Garza-Rodríguez, María de Lourdes; Delgado-Enciso, Iván; Treviño-Alvarado, Víctor Manuel; Canales-Del-Castillo, Ricardo; Martínez-De-Villarreal, Laura Elia; Lugo-Trampe, Ángel; Tejero, María Elizabeth; Schlabritz-Loutsevitch, Natalia E; Rocha-Pizaña, María Del Refugio; Cole, Shelley A; Reséndez-Pérez, Diana; Moises-Alvarez, Mario; Comuzzie, Anthony G; Barrera-Saldaña, Hugo Alberto; Garza-Guajardo, Raquel; Barboza-Quintana, Oralia; Rodríguez-Sánchez, Irám Pablo

2015-06-12

Chemerin, encoded by the retinoic acid receptor responder 2 (RARRES2) gene is an adipocytesecreted protein with autocrine/paracrine functions in adipose tissue, metabolism and inflammation with a recently described function in vascular tone regulation, liver, steatosis, etc. This molecule is believed to represent a critical endocrine signal linking obesity to diabetes. There are no data available regarding evolution of RARRES2 in non-human primates and great apes. Expression profile and orthology in RARRES2 genes are unknown aspects in the biology of this multigene family in primates. Thus; we attempt to describe expression profile and phylogenetic relationship as complementary knowledge in the function of this gene in primates. To do that, we performed A RT-PCR from different tissues obtained during necropsies. Also we tested the hypotheses of positive evolution, purifying selection, and neutrality. And finally a phylogenetic analysis was made between primates RARRES2 protein. RARRES2 transcripts were present in liver, lung, adipose tissue, ovary, pancreas, heart, hypothalamus and pituitary tissues. Expression in kidney and leukocytes were not detectable in either species. It was determined that the studied genes are orthologous. RARRES2 evolution fits the hypothesis of purifying selection. Expression profiles of the RARRES2 gene are similar in baboons and chimpanzees and are also phylogenetically related.

Common spectrum of polypeptides occurs in secretion granule membranes of different exocrine glands

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

Cameron, R.S.; Cameron, P.L.; Castle, J.D.

1986-10-01

A highly purified membrane preparation from rat parotid secretion granules has been used as a comparative probe to examine the extent of compositional overlap in granule membranes of three other exocrine secretory tissues - pancreatic, lacrimal, and submandibular - from several standpoints. First, indirect immunofluorescent studies using a polyclonal polyspecific anti-parotid granule membrane antiserum has indicated a selective staining of granule membrane profiles in all acinar cells of all tissues. Second, highly purified granule membrane subfractions have been isolated from each exocrine tissue; comparative two-dimensional (isoelectric focusing; SDS) PAGE of radioiodinated granule membranes has identified 10-15 polypeptides of identical pImore » and apparent molecular mass. These species are likely to be integral membrane components since they are not extracted by either saponin-sodium sulfate or sodium carbonate (pH 11.5) treatments, and they do not have counterparts in the granule content. Finally, the identity among selected parotid and pancreatic radioiodinated granule membrane polypeptides has been documented using two-dimensional peptide mapping of chymotryptic and tryptic digests. These findings clearly indicate that exocrine secretory granules, irrespective of the nature of stored secretion, comprise a type of vesicular carrier with a common (and probably refined) membrane composition. Conceivably, the polypeptides identified carry out general functions related to exocrine secretion.« less

Recombinant expression of extracellular domain of mutant Epidermal Growth Factor Receptor in prokaryotic and baculovirus expression systems.

PubMed

Vettath, Sunitha Kodengil; Shivashankar, Gaganashree; Menon, Krishnakumar N; Vijayachandran, Lakshmi S

2018-04-15

Epidermal Growth Factor Receptor variant III (EGFRvIII) is a tumor specific antigen detected in various tumors including gliomas, breast cancer, lung cancer, head and neck squamous cell carcinoma (HNSCC). Screening of EGFRvIII targeting drug molecules can be accelerated by developing drug screening platforms using recombinantly expressed protein. Choice of expression system is one of the major factors deciding the success of recombinant expression of a protein. In our study, we have tried to express and purify the extracellular domain (ECD) of this highly unstable protein using bacterial and baculovirus expression systems to select the expression system suited for our purpose. Even though the protein was successfully expressed in prokaryotic system, purification could be done only under denaturing conditions. But in the baculovirus expression system, the protein was expressed in soluble form and could be purified under native conditions, with single step of purification. Based on our results, we conclude that insect cells are better choice over E. coli cells for expressing EGFRvIII ECD in soluble form. This study provides insights for other researchers involved in expression of similar unstable membrane proteins, on selecting the best expression system and challenges involved. Copyright © 2018 Elsevier B.V. All rights reserved.

Affinity-based precipitation via a bivalent peptidic hapten for the purification of monoclonal antibodies.

PubMed

Handlogten, Michael W; Stefanick, Jared F; Deak, Peter E; Bilgicer, Basar

2014-09-07

In a previous study, we demonstrated a non-chromatographic affinity-based precipitation method, using trivalent haptens, for the purification of mAbs. In this study, we significantly improved this process by using a simplified bivalent peptidic hapten (BPH) design, which enables facile and rapid purification of mAbs while overcoming the limitations of the previous trivalent design. The improved affinity-based precipitation method (ABP(BPH)) combines the simplicity of salt-induced precipitation with the selectivity of affinity chromatography for the purification of mAbs. The ABP(BPH) method involves 3 steps: (i) precipitation and separation of protein contaminants larger than immunoglobulins with ammonium sulfate; (ii) selective precipitation of the target-antibody via BPH by inducing antibody-complex formation; (iii) solubilization of the antibody pellet and removal of BPH with membrane filtration resulting in the pure antibody. The ABP(BPH) method was evaluated by purifying the pharmaceutical antibody trastuzumab from common contaminants including CHO cell conditioned media, DNA, ascites fluid, other antibodies, and denatured antibody with >85% yield and >97% purity. Importantly, the purified antibody demonstrated native binding activity to cell lines expressing the target protein, HER2. Combined, the ABP(BPH) method is a rapid and scalable process for the purification of antibodies with the potential to improve product quality while decreasing purification costs.

Differential Selectivity of the Escherichia coli Cell Membrane Shifts the Equilibrium for the Enzyme-Catalyzed Isomerization of Galactose to Tagatose▿

PubMed Central

Kim, Jin-Ha; Lim, Byung-Chul; Yeom, Soo-Jin; Kim, Yeong-Su; Kim, Hye-Jung; Lee, Jung-Kul; Lee, Sook-Hee; Kim, Seon-Won; Oh, Deok-Kun

2008-01-01

An Escherichia coli galactose kinase gene knockout (ΔgalK) strain, which contains the l-arabinose isomerase gene (araA) to isomerize d-galactose to d-tagatose, showed a high conversion yield of tagatose compared with the original galK strain because galactose was not metabolized by endogenous galactose kinase. In whole cells of the ΔgalK strain, the isomerase-catalyzed reaction exhibited an equilibrium shift toward tagatose, producing a tagatose fraction of 68% at 37°C, whereas the purified l-arabinose isomerase gave a tagatose equilibrium fraction of 36%. These equilibrium fractions are close to those predicted from the measured equilibrium constants of the isomerization reaction catalyzed in whole cells and by the purified enzyme. The equilibrium shift in these cells resulted from the higher uptake and lower release rates for galactose, which is a common sugar substrate, than for tagatose, which is a rare sugar product. A ΔmglB mutant had decreased uptake rates for galactose and tagatose, indicating that a methylgalactoside transport system, MglABC, is the primary contributing transporter for the sugars. In the present study, whole-cell conversion using differential selectivity of the cell membrane was proposed as a method for shifting the equilibrium in sugar isomerization reactions. PMID:18263746

Differential selectivity of the Escherichia coli cell membrane shifts the equilibrium for the enzyme-catalyzed isomerization of galactose to tagatose.

PubMed

Kim, Jin-Ha; Lim, Byung-Chul; Yeom, Soo-Jin; Kim, Yeong-Su; Kim, Hye-Jung; Lee, Jung-Kul; Lee, Sook-Hee; Kim, Seon-Won; Oh, Deok-Kun

2008-04-01

An Escherichia coli galactose kinase gene knockout (DeltagalK) strain, which contains the l-arabinose isomerase gene (araA) to isomerize d-galactose to d-tagatose, showed a high conversion yield of tagatose compared with the original galK strain because galactose was not metabolized by endogenous galactose kinase. In whole cells of the DeltagalK strain, the isomerase-catalyzed reaction exhibited an equilibrium shift toward tagatose, producing a tagatose fraction of 68% at 37 degrees C, whereas the purified l-arabinose isomerase gave a tagatose equilibrium fraction of 36%. These equilibrium fractions are close to those predicted from the measured equilibrium constants of the isomerization reaction catalyzed in whole cells and by the purified enzyme. The equilibrium shift in these cells resulted from the higher uptake and lower release rates for galactose, which is a common sugar substrate, than for tagatose, which is a rare sugar product. A DeltamglB mutant had decreased uptake rates for galactose and tagatose, indicating that a methylgalactoside transport system, MglABC, is the primary contributing transporter for the sugars. In the present study, whole-cell conversion using differential selectivity of the cell membrane was proposed as a method for shifting the equilibrium in sugar isomerization reactions.

Antifungal Activity of Eupolauridine and Its Action on DNA Topoisomerases

PubMed Central

Khan, Shabana I.; Nimrod, Alison C.; Mehrpooya, Mohammed; Nitiss, John L.; Walker, Larry A.; Clark, Alice M.

2002-01-01

The azafluoranthene alkaloid eupolauridine has previously been shown to have in vitro antifungal activity and selective inhibition of fungal topoisomerase I. The present study was undertaken to examine further its selectivity and mode of action. Eupolauridine completely inhibits the DNA relaxation activity of purified fungal topoisomerase I at 50 μg/ml, but it does not stabilize the cleavage complex of either human or fungal topoisomerase I. Cleavage complex stabilization is the mode of action of topoisomerase I targeting drugs of the camptothecin family. Also, unlike camptothecin, eupolauridine does not cause significant cytotoxicity in mammalian cells. To determine if the inhibition of topoisomerase I is the principal mode of antifungal action of eupolauridine, Saccharomyces cerevisiae strains with alterations in topoisomerase genes were used in clonogenic assays. The antifungal activity of eupolauridine was not diminished in the absence of topoisomerase I; rather, the cells lacking the enzyme were more sensitive to the drug. Cell-killing activity of eupolauridine was also more pronounced in cells that overexpressed topoisomerase II. In vitro assays with the purified yeast enzyme confirmed that eupolauridine stabilized topoisomerase II covalent complexes. These results indicate that a major target for fungal cell killing by eupolauridine is DNA topoisomerase II rather than topoisomerase I, but does not exclude the possibility that the drug also acts against other targets. PMID:12019091

Antifungal activity of eupolauridine and its action on DNA topoisomerases.

PubMed

Khan, Shabana I; Nimrod, Alison C; Mehrpooya, Mohammed; Nitiss, John L; Walker, Larry A; Clark, Alice M

2002-06-01

The azafluoranthene alkaloid eupolauridine has previously been shown to have in vitro antifungal activity and selective inhibition of fungal topoisomerase I. The present study was undertaken to examine further its selectivity and mode of action. Eupolauridine completely inhibits the DNA relaxation activity of purified fungal topoisomerase I at 50 microg/ml, but it does not stabilize the cleavage complex of either human or fungal topoisomerase I. Cleavage complex stabilization is the mode of action of topoisomerase I targeting drugs of the camptothecin family. Also, unlike camptothecin, eupolauridine does not cause significant cytotoxicity in mammalian cells. To determine if the inhibition of topoisomerase I is the principal mode of antifungal action of eupolauridine, Saccharomyces cerevisiae strains with alterations in topoisomerase genes were used in clonogenic assays. The antifungal activity of eupolauridine was not diminished in the absence of topoisomerase I; rather, the cells lacking the enzyme were more sensitive to the drug. Cell-killing activity of eupolauridine was also more pronounced in cells that overexpressed topoisomerase II. In vitro assays with the purified yeast enzyme confirmed that eupolauridine stabilized topoisomerase II covalent complexes. These results indicate that a major target for fungal cell killing by eupolauridine is DNA topoisomerase II rather than topoisomerase I, but does not exclude the possibility that the drug also acts against other targets.

The alpha glycerophosphate cycle in Drosophila melanogaster VI. structure and evolution of enzyme paralogs in the genus Drosophila.

PubMed

Carmon, Amber; MacIntyre, Ross

2010-01-01

The genome sequences of 12 Drosophila species contain 3 paralogs for alpha glycerophosphate dehydrogenase (GPDH) and for the mitochondrial alpha glycerophosphate oxidase (GPO). These 2 enzymes participate in the alpha glycerophosphate cycle in the adult thoracic flight muscles. The flight muscle enzymes are encoded by gpdh-1 at 26A2 and gpo-1 at 52C8. In this paper, we show that the GPDH paralogs share the same evolutionarily conserved functional domains and most intron positions, whereas the GPO paralogs share only some of the functional domains of mitochondrial oxidoreductases. The GPO paralogs not expressed in the flight muscles essentially lack introns. GPDH paralogs encoded by gpdh-2 and gpdh-3 and the GPO paralogs encoded by gpo-2 and gpo-3 are expressed only in the testes. Gene trees for the GPDH and GPO paralogs indicate that the genes expressed in the flight muscles are evolving very slowly presumably under strong purifying selection whereas the paralogs expressed in the testes are evolving more rapidly. The concordance between species and gene trees, d(N)/d(S) ratios, phylogenetic analysis by maximum likelihood-based tests, and analyses of radical and conservative substitutions all indicate that the additional GPDH and GPO paralogs are also evolving under purifying selection.

Exposure to Movie Reckless Driving in Early Adolescence Predicts Reckless, but Not Inattentive Driving.

PubMed

Kostermans, Evelien; Stoolmiller, Mike; de Leeuw, Rebecca N H; Engels, Rutger C M E; Sargent, James D

2014-01-01

We examine the association between exposure to depictions of reckless driving in movies and unsafe driving, modeling inattentive and reckless driving as separate outcomes. Data were obtained by telephone from 1,630 US adolescents aged 10 to 14 years at baseline who were drivers at a survey 6 years later. Exposure to movie reckless driving was measured based on movies seen from a randomly selected list of 50 movie titles that had been content coded for reckless driving among characters. Associations were tested with inattentive and reckless driving behaviors in the subsequent survey-controlling for baseline age, sex, socioeconomic status, parental education, school performance, extracurricular activities, daily television and video/computer game exposure, number of movies watched per week, self-regulation and sensation seeking. Exposure to movie reckless driving was common, with approximately 10% of movie characters having driven recklessly. Confirmatory factor analysis revealed a significant distinction between items tapping reckless and inattentive driving at the 6th wave. Age and exposure to movie reckless driving at baseline were directly associated with wave-6 reckless (but not inattentive) driving. Additionally, growth in sensation seeking mediated a prospective relation between the total number of movies watched per week at baseline and reckless driving, independent of exposure to movie reckless driving. Males and high sensation seekers reported lower seatbelt usage and more reckless driving, whereas lower self-regulation predicted inattentive driving. In this study, exposure to movie reckless driving during early adolescence predicted adolescents' reckless driving, suggesting a direct modeling effect. Other aspects of movies were also associated with reckless driving, with that association mediated through growth in sensation seeking. Predictors of reckless driving were different from predictors of inattentive driving, with lower self-regulation associated with the latter outcome. Making a clear distinction between interventions for reckless or inattentive driving seems crucial for accident prevention.

Exposure to Movie Reckless Driving in Early Adolescence Predicts Reckless, but Not Inattentive Driving

PubMed Central

Kostermans, Evelien; Stoolmiller, Mike; de Leeuw, Rebecca N. H.; Engels, Rutger C. M. E.; Sargent, James D.

2014-01-01

Objective We examine the association between exposure to depictions of reckless driving in movies and unsafe driving, modeling inattentive and reckless driving as separate outcomes. Methods Data were obtained by telephone from 1,630 US adolescents aged 10 to 14 years at baseline who were drivers at a survey 6 years later. Exposure to movie reckless driving was measured based on movies seen from a randomly selected list of 50 movie titles that had been content coded for reckless driving among characters. Associations were tested with inattentive and reckless driving behaviors in the subsequent survey–controlling for baseline age, sex, socioeconomic status, parental education, school performance, extracurricular activities, daily television and video/computer game exposure, number of movies watched per week, self-regulation and sensation seeking. Results Exposure to movie reckless driving was common, with approximately 10% of movie characters having driven recklessly. Confirmatory factor analysis revealed a significant distinction between items tapping reckless and inattentive driving at the 6th wave. Age and exposure to movie reckless driving at baseline were directly associated with wave-6 reckless (but not inattentive) driving. Additionally, growth in sensation seeking mediated a prospective relation between the total number of movies watched per week at baseline and reckless driving, independent of exposure to movie reckless driving. Males and high sensation seekers reported lower seatbelt usage and more reckless driving, whereas lower self-regulation predicted inattentive driving. Discussion In this study, exposure to movie reckless driving during early adolescence predicted adolescents’ reckless driving, suggesting a direct modeling effect. Other aspects of movies were also associated with reckless driving, with that association mediated through growth in sensation seeking. Predictors of reckless driving were different from predictors of inattentive driving, with lower self-regulation associated with the latter outcome. Making a clear distinction between interventions for reckless or inattentive driving seems crucial for accident prevention. PMID:25493323

A spectral power analysis of driving behavior changes during the transition from nondistraction to distraction.

PubMed

Wang, Yuan; Bao, Shan; Du, Wenjun; Ye, Zhirui; Sayer, James R

2017-11-17

This article investigated and compared frequency domain and time domain characteristics of drivers' behaviors before and after the start of distracted driving. Data from an existing naturalistic driving study were used. Fast Fourier transform (FFT) was applied for the frequency domain analysis to explore drivers' behavior pattern changes between nondistracted (prestarting of visual-manual task) and distracted (poststarting of visual-manual task) driving periods. Average relative spectral power in a low frequency range (0-0.5 Hz) and the standard deviation in a 10-s time window of vehicle control variables (i.e., lane offset, yaw rate, and acceleration) were calculated and further compared. Sensitivity analyses were also applied to examine the reliability of the time and frequency domain analyses. Results of the mixed model analyses from the time and frequency domain analyses all showed significant degradation in lateral control performance after engaging in visual-manual tasks while driving. Results of the sensitivity analyses suggested that the frequency domain analysis was less sensitive to the frequency bandwidth, whereas the time domain analysis was more sensitive to the time intervals selected for variation calculations. Different time interval selections can result in significantly different standard deviation values, whereas average spectral power analysis on yaw rate in both low and high frequency bandwidths showed consistent results, that higher variation values were observed during distracted driving when compared to nondistracted driving. This study suggests that driver state detection needs to consider the behavior changes during the prestarting periods, instead of only focusing on periods with physical presence of distraction, such as cell phone use. Lateral control measures can be a better indicator of distraction detection than longitudinal controls. In addition, frequency domain analyses proved to be a more robust and consistent method in assessing driving performance compared to time domain analyses.

Testing the niche variation hypothesis with a measure of body condition

EPA Science Inventory

Individual variation and fitness are cornerstones of evolution by natural selection. The niche variation hypothesis (NVH) posits that when interspecific competition is relaxed, intraspecific competition should drive niche expansion by selection favoring use of novel resources. Po...

Mine Winder Drives in Integrated Copper Complex

NASA Astrophysics Data System (ADS)

Dey, Pranab Kumar

2018-04-01

This paper describes various features required to be evaluated before selecting mine winder drives. In handling such project, the selection of proper equipments is necessary at the initial design stage of planning and how the electrical system design considers all aspects to protect the grid from unwarranted influence of the connected loads and minimize the generation of harmonics due to network configurations adopted to keep it within the stipulated value dictated by the supply authorities has been discussed. The design should cover all aspects to provide quality power with effective braking system required as per the mining statute for operational safety. It also emphasizes on the requirement of quality maintenance.

Relaxation of herbivore-mediated selection drives the evolution of genetic covariances between plant competitive and defense traits.

PubMed

Uesugi, Akane; Connallon, Tim; Kessler, André; Monro, Keyne

2017-06-01

Insect herbivores are important mediators of selection on traits that impact plant defense against herbivory and competitive ability. Although recent experiments demonstrate a central role for herbivory in driving rapid evolution of defense and competition-mediating traits, whether and how herbivory shapes heritable variation in these traits remains poorly understood. Here, we evaluate the structure and evolutionary stability of the G matrix for plant metabolites that are involved in defense and allelopathy in the tall goldenrod, Solidago altissima. We show that G has evolutionarily diverged between experimentally replicated populations that evolved in the presence versus the absence of ambient herbivory, providing direct evidence for the evolution of G by natural selection. Specifically, evolution in an herbivore-free habitat altered the orientation of G, revealing a negative genetic covariation between defense- and competition-related metabolites that is typically masked in herbivore-exposed populations. Our results may be explained by predictions of classical quantitative genetic theory, as well as the theory of acquisition-allocation trade-offs. The study provides compelling evidence that herbivory drives the evolution of plant genetic architecture. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Drinking and Driving among College Students: The Influence of Alcohol-Control Policies

ERIC Educational Resources Information Center

Journal of American College Health, 2005

2005-01-01

Randomly selected full-time college students attending four-year colleges in 39 states completed a questionnaire about alcohol consumption and driving. The results revealed that 29 percent of the students drove after drinking some amount of alcohol 10 percent drove after drinking five or more drinks, and 23 percent rode with a driver who was high…

Adaptive Driving Equipment: Selection and Major Considerations [and] Battery Powered Scooters and 3-Wheelers. Information Support Packets #1 and #2.

ERIC Educational Resources Information Center

Stevens, John H.

Two brief guides offer suggestions for persons with physical disabilities who are considering the purchase of adaptive driving equipment, battery-powered scooters, or three wheelers. The first guide offers guidelines for individuals considering purchase of special hand controls or other modifications or a van lift to enhance their independence in…

49 CFR 571.126 - Standard No. 126; Electronic stability control systems.

Code of Federal Regulations, 2013 CFR

2013-10-01

... cycle that is designed for low-speed, off-road driving, or (b) the vehicle is in a four-wheel drive configuration selected by the driver on the previous ignition cycle that is designed for operation at higher.... Light outriggers are designed with a maximum weight of 27 kg (59.5 lb) and a maximum roll moment of...

Mirage events & driver haptic steering alerts in a motion-base driving simulator: A method for selecting an optimal HMI.

PubMed

Talamonti, Walter; Tijerina, Louis; Blommer, Mike; Swaminathan, Radhakrishnan; Curry, Reates; Ellis, R Darin

2017-11-01

This paper describes a new method, a 'mirage scenario,' to support formative evaluation of driver alerting or warning displays for manual and automated driving. This method provides driving contexts (e.g., various Times-To-Collision (TTCs) to a lead vehicle) briefly presented and then removed. In the present study, during each mirage event, a haptic steering display was evaluated. This haptic display indicated a steering response may be initiated to drive around an obstacle ahead. A motion-base simulator was used in a 32-participant study to present vehicle motion cues similar to the actual application. Surprise was neither present nor of concern, as it would be for a summative evaluation of a forward collision warning system. Furthermore, no collision avoidance maneuvers were performed, thereby reducing the risk of simulator sickness. This paper illustrates the mirage scenario procedures, the rating methods and definitions used with the mirage scenario, and analysis of the ratings obtained, together with a multi-attribute utility theory (MAUT) approach to evaluate and select among alternative designs for future summative evaluation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of road infrastructure and traffic complexity in speed adaptation behaviour of distracted drivers.

PubMed

Oviedo-Trespalacios, Oscar; Haque, Md Mazharul; King, Mark; Washington, Simon

2017-04-01

The use of mobile phones while driving remains a major human factors issue in the transport system. A significant safety concern is that driving while distracted by a mobile phone potentially modifies the driving speed leading to conflicts with other road users and consequently increases crash risk. However, the lack of systematic knowledge of the mechanisms involved in speed adaptation of distracted drivers constrains the explanation and modelling of the extent of this phenomenon. The objective of this study was to investigate speed adaptation of distracted drivers under varying road infrastructure and traffic complexity conditions. The CARRS-Q Advanced Driving Simulator was used to test participants on a simulated road with different traffic conditions, such as free flow traffic along straight roads, driving in urbanized areas, and driving in heavy traffic along suburban roads. Thirty-two licensed young drivers drove the simulator under three phone conditions: baseline (no phone conversation), hands-free and handheld phone conversations. To understand the relationships between distraction, road infrastructure and traffic complexity, speed adaptation calculated as the deviation of driving speed from the posted speed limit was modelled using a decision tree. The identified groups of road infrastructure and traffic characteristics from the decision tree were then modelled with a Generalized Linear Mixed Model (GLMM) with repeated measures to develop inferences about speed adaptation behaviour of distracted drivers. The GLMM also included driver characteristics and secondary task demands as predictors of speed adaptation. Results indicated that complex road environments like urbanization, car-following situations along suburban roads, and curved road alignment significantly influenced speed adaptation behaviour. Distracted drivers selected a lower speed while driving along a curved road or during car-following situations, but speed adaptation was negligible in the presence of high visual cutter, indicating the prioritization of the driving task over the secondary task. Additionally, drivers who scored high on self-reported safe attitudes towards mobile phone usage, and who reported prior involvement in a road traffic crash, selected a lower driving speed in the distracted condition than in the baseline. The results aid in understanding how driving task demands influence speed adaptation of distracted drivers under various road infrastructure and traffic complexity conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Measurand transient signal suppressor

NASA Technical Reports Server (NTRS)

Bozeman, Richard J., Jr. (Inventor)

1994-01-01

A transient signal suppressor for use in a controls system which is adapted to respond to a change in a physical parameter whenever it crosses a predetermined threshold value in a selected direction of increasing or decreasing values with respect to the threshold value and is sustained for a selected discrete time interval is presented. The suppressor includes a sensor transducer for sensing the physical parameter and generating an electrical input signal whenever the sensed physical parameter crosses the threshold level in the selected direction. A manually operated switch is provided for adapting the suppressor to produce an output drive signal whenever the physical parameter crosses the threshold value in the selected direction of increasing or decreasing values. A time delay circuit is selectively adjustable for suppressing the transducer input signal for a preselected one of a plurality of available discrete suppression time and producing an output signal only if the input signal is sustained for a time greater than the selected suppression time. An electronic gate is coupled to receive the transducer input signal and the timer output signal and produce an output drive signal for energizing a control relay whenever the transducer input is a non-transient signal which is sustained beyond the selected time interval.

Computational Modeling of Distinct Neocortical Oscillations Driven by Cell-Type Selective Optogenetic Drive: Separable Resonant Circuits Controlled by Low-Threshold Spiking and Fast-Spiking Interneurons

PubMed Central

Vierling-Claassen, Dorea; Cardin, Jessica A.; Moore, Christopher I.; Jones, Stephanie R.

2010-01-01

Selective optogenetic drive of fast-spiking (FS) interneurons (INs) leads to enhanced local field potential (LFP) power across the traditional “gamma” frequency band (20–80 Hz; Cardin et al., 2009). In contrast, drive to regular-spiking (RS) pyramidal cells enhances power at lower frequencies, with a peak at 8 Hz. The first result is consistent with previous computational studies emphasizing the role of FS and the time constant of GABAA synaptic inhibition in gamma rhythmicity. However, the same theoretical models do not typically predict low-frequency LFP enhancement with RS drive. To develop hypotheses as to how the same network can support these contrasting behaviors, we constructed a biophysically principled network model of primary somatosensory neocortex containing FS, RS, and low-threshold spiking (LTS) INs. Cells were modeled with detailed cell anatomy and physiology, multiple dendritic compartments, and included active somatic and dendritic ionic currents. Consistent with prior studies, the model demonstrated gamma resonance during FS drive, dependent on the time constant of GABAA inhibition induced by synchronous FS activity. Lower-frequency enhancement during RS drive was replicated only on inclusion of an inhibitory LTS population, whose activation was critically dependent on RS synchrony and evoked longer-lasting inhibition. Our results predict that differential recruitment of FS and LTS inhibitory populations is essential to the observed cortical dynamics and may provide a means for amplifying the natural expression of distinct oscillations in normal cortical processing. PMID:21152338

Driving behavior recognition using EEG data from a simulated car-following experiment.

PubMed

Yang, Liu; Ma, Rui; Zhang, H Michael; Guan, Wei; Jiang, Shixiong

2018-07-01

Driving behavior recognition is the foundation of driver assistance systems, with potential applications in automated driving systems. Most prevailing studies have used subjective questionnaire data and objective driving data to classify driving behaviors, while few studies have used physiological signals such as electroencephalography (EEG) to gather data. To bridge this gap, this paper proposes a two-layer learning method for driving behavior recognition using EEG data. A simulated car-following driving experiment was designed and conducted to simultaneously collect data on the driving behaviors and EEG data of drivers. The proposed learning method consists of two layers. In Layer I, two-dimensional driving behavior features representing driving style and stability were selected and extracted from raw driving behavior data using K-means and support vector machine recursive feature elimination. Five groups of driving behaviors were classified based on these two-dimensional driving behavior features. In Layer II, the classification results from Layer I were utilized as inputs to generate a k-Nearest-Neighbor classifier identifying driving behavior groups using EEG data. Using independent component analysis, a fast Fourier transformation, and linear discriminant analysis sequentially, the raw EEG signals were processed to extract two core EEG features. Classifier performance was enhanced using the adaptive synthetic sampling approach. A leave-one-subject-out cross validation was conducted. The results showed that the average classification accuracy for all tested traffic states was 69.5% and the highest accuracy reached 83.5%, suggesting a significant correlation between EEG patterns and car-following behavior. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mechanical design of walking machines.

PubMed

Arikawa, Keisuke; Hirose, Shigeo

2007-01-15

The performance of existing actuators, such as electric motors, is very limited, be it power-weight ratio or energy efficiency. In this paper, we discuss the method to design a practical walking machine under this severe constraint with focus on two concepts, the gravitationally decoupled actuation (GDA) and the coupled drive. The GDA decouples the driving system against the gravitational field to suppress generation of negative power and improve energy efficiency. On the other hand, the coupled drive couples the driving system to distribute the output power equally among actuators and maximize the utilization of installed actuator power. First, we depict the GDA and coupled drive in detail. Then, we present actual machines, TITAN-III and VIII, quadruped walking machines designed on the basis of the GDA, and NINJA-I and II, quadruped wall walking machines designed on the basis of the coupled drive. Finally, we discuss walking machines that travel on three-dimensional terrain (3D terrain), which includes the ground, walls and ceiling. Then, we demonstrate with computer simulation that we can selectively leverage GDA and coupled drive by walking posture control.

Driving and Patients With Dementia

PubMed Central

Hamdy, R. C.; Kinser, A.; Kendall-Wilson, T.; Depelteau, A.; Whalen, K.; Culp, J.

2018-01-01

Driving is a symbol of autonomy and independence, eagerly awaited during adolescence, cherished during adulthood and reluctantly rescinded during old age. It is nevertheless an individual’s privilege, not right, especially as driving may affect other drivers and pedestrians on the road. It is therefore not only the individual patient who is at stake but essentially the entire community. In this case scenario, we describe the situation that arose when a patient with multi-infarct dementia wanted to go for a drive and his son and grandson tried to convince him that he could no longer drive. What went wrong in the caregivers/patient interaction is presented. The futility of arguing with patients who have dementia is highlighted as well as the suspiciousness it may generate. Alternate actions that can be useful to avoid/avert the situation from escalating and having a catastrophic ending are discussed. Testing/evaluating patients with dementia for fitness to drive is also reviewed and a list of select resources is included. PMID:29900187

The relationship between attentional bias toward safety and driving behavior.

PubMed

Zheng, Tingting; Qu, Weina; Zhang, Kan; Ge, Yan

2016-11-01

As implicit cognitive processes garner more and more importance, studies in the fields of healthy psychology and organizational safety research have focused on attentional bias, a kind of selective allocation of attentional resources in the early stage of cognitive processing. However, few studies have explored the role of attentional bias on driving behavior. This study assessed drivers' attentional bias towards safety-related words (ABS) using the dot-probe paradigm and self-reported daily driving behaviors. The results revealed significant negative correlations between attentional bias scores and several indicators of dangerous driving. Drivers with fewer dangerous driving behaviors showed greater ABS. We also built a significant linear regression model between ABS and the total DDDI score, as well as ABS and the number of accidents. Finally, we discussed the possible mechanism underlying these associations and several limitations of our study. This study opens up a new topic for the exploration of implicit processes in driving safety research. Copyright © 2016 Elsevier Ltd. All rights reserved.

An evaluation of thirteen local selective enforcement projects designed to reduce drunken driving in Virginia.

DOT National Transportation Integrated Search

1985-01-01

In accordance with federal requirements, the effectiveness of thirteen locally based DUI selective enforcement projects funded with grants from the National Highway Traffic Safety Administration was evaluated. The grants were awarded in the FY 1982 g...

A versatile expression vector for the growth and amplification of unmodified phage display polypeptides.

PubMed

Winton, Alexander J; Baptiste, Janae L; Allen, Mark A

2018-09-01

Proteins and polypeptides represent nature's most complex and versatile polymer. They provide complicated shapes, diverse chemical functionalities, and tightly regulated and controlled sizes. Several disease states are related to the misfolding or overproduction of polypeptides and yet polypeptides are present in several therapeutic molecules. In addition to biological roles; short chain polypeptides have been shown to interact with and drive the bio-inspired synthesis or modification of inorganic materials. This paper outlines the development of a versatile cloning vector which allows for the expression of a short polypeptide by controlling the incorporation of a desired DNA coding insert. As a demonstration of the efficacy of the expression system, a solid binding polypeptide identified from M13 phage display was expressed and purified. The solid binding polypeptide was expressed as a soluble 6xHis-SUMO tagged construct. Expression was performed in E. coli using auto-induction followed by Ni-NTA affinity chromatography and ULP1 protease cleavage. Methodology demonstrates the production of greater than 8 mg of purified polypeptide per liter of E. coli culture. Isotopic labeling of the peptide is also demonstrated. The versatility of the designed cloning vector, use of the 6xHis-SUMO solubility partner, bacterial expression in auto-inducing media and the purification methodology make this expressionun vector a readily scalable and user-friendly system for the creation of desired peptide domains. Copyright © 2018. Published by Elsevier Inc.

Mechanized fluid connector and assembly tool system with ball detents

NASA Technical Reports Server (NTRS)

Zentner, Ronald C. (Inventor); Smith, Steven A. (Inventor)

1991-01-01

A fluid connector system is disclosed which includes a modified plumbing union having a rotatable member for drawing said union into a fluid tight condition. A drive tool is electric motor actuated and includes a reduction gear train providing an output gear engaging an integral peripheral spur gear on the rotatable member. Coaxial alignment means are attached to both the connector assembly and the drive tool. A hand lever actuated latching system includes a plurality of circumferentially spaced latching balls selectively wedged against the alignment means attached to the connector assembly or to secure the drive tool with its output gear in mesh with the integral peripheral spur gear. The drive motor is torque, speed, and direction controllable.

Near-term hybrid vehicle program, phase 1. Appendix B: Design trade-off studies. [various hybrid/electric power train configurations and electrical and mechanical drive-line components

NASA Technical Reports Server (NTRS)

1979-01-01

The relative attractiveness of various hybrid/electric power train configurations and electrical and mechanical drive-line components was studied. The initial screening was concerned primarily with total vehicle weight and economic factors and identified the hybrid power train combinations which warranted detailed evaluation over various driving cycles. This was done using a second-by-second vehicle simulation program which permitted the calculations of fuel economy, electricity usage, and emissions as a function of distance traveled in urban and highway driving. Power train arrangement possibilities were examined in terms of their effect on vehicle handling, safety, serviceability, and passenger comfort. A dc electric drive system utilizing a separately excited motor with field control and battery switching was selected for the near term hybrid vehicle. Hybrid vehicle simulations showed that for the first 30 mi (the electric range of the vehicle) in urban driving, the fuel economy was 80 mpg using a gasoline engine and 100 mpg using a diesel engine. In urban driving the hybrid would save about 75% of the fuel used by the conventional vehicle and in combined urban/highway driving the fuel saving is about 50%.

Cerebral oscillatory activity during simulated driving using MEG.

PubMed

Sakihara, Kotoe; Hirata, Masayuki; Ebe, Kazutoshi; Kimura, Kenji; Yi Ryu, Seong; Kono, Yoshiyuki; Muto, Nozomi; Yoshioka, Masako; Yoshimine, Toshiki; Yorifuji, Shiro

2014-01-01

We aimed to examine cerebral oscillatory differences associated with psychological processes during simulated car driving. We recorded neuromagnetic signals in 14 healthy volunteers using magnetoencephalography (MEG) during simulated driving. MEG data were analyzed using synthetic aperture magnetometry to detect the spatial distribution of cerebral oscillations. Group effects between subjects were analyzed statistically using a non-parametric permutation test. Oscillatory differences were calculated by comparison between "passive viewing" and "active driving." "Passive viewing" was the baseline, and oscillatory differences during "active driving" showed an increase or decrease in comparison with a baseline. Power increase in the theta band was detected in the superior frontal gyrus (SFG) during active driving. Power decreases in the alpha, beta, and low gamma bands were detected in the right inferior parietal lobe (IPL), left postcentral gyrus (PoCG), middle temporal gyrus (MTG), and posterior cingulate gyrus (PCiG) during active driving. Power increase in the theta band in the SFG may play a role in attention. Power decrease in the right IPL may reflect selectively divided attention and visuospatial processing, whereas that in the left PoCG reflects sensorimotor activation related to driving manipulation. Power decreases in the MTG and PCiG may be associated with object recognition.

The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences

PubMed Central

Touchon, Marie; Cury, Jean; Yoon, Eun-Jeong; Krizova, Lenka; Cerqueira, Gustavo C.; Murphy, Cheryl; Feldgarden, Michael; Wortman, Jennifer; Clermont, Dominique; Lambert, Thierry; Grillot-Courvalin, Catherine; Nemec, Alexandr; Courvalin, Patrice; Rocha, Eduardo P.C.

2014-01-01

Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise of pathogens in a genus. We have sampled, sequenced, and assessed the diversity of genomes of validly named and tentative species of the Acinetobacter genus, a clade including major nosocomial pathogens and biotechnologically important species. We inferred a robust global phylogeny and delimited several new putative species. The genus is very ancient and extremely diverse: Genomes of highly divergent species share more orthologs than certain strains within a species. We systematically characterized elements and mechanisms driving genome diversification, such as conjugative elements, insertion sequences, and natural transformation. We found many error-prone polymerases that may play a role in resistance to toxins, antibiotics, and in the generation of genetic variation. Surprisingly, temperate phages, poorly studied in Acinetobacter, were found to account for a significant fraction of most genomes. Accordingly, many genomes encode clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems with some of the largest CRISPR-arrays found so far in bacteria. Integrons are strongly overrepresented in Acinetobacter baumannii, which correlates with its frequent resistance to antibiotics. Our data suggest that A. baumannii arose from an ancient population bottleneck followed by population expansion under strong purifying selection. The outstanding diversification of the species occurred largely by horizontal transfer, including some allelic recombination, at specific hotspots preferentially located close to the replication terminus. Our work sets a quantitative basis to understand the diversification of Acinetobacter into emerging resistant and versatile pathogens. PMID:25313016

Structure and Dynamics of the Liver Receptor Homolog 1-PGC1α Complex.

PubMed

Mays, Suzanne G; Okafor, C Denise; Tuntland, Micheal L; Whitby, Richard J; Dharmarajan, Venkatasubramanian; Stec, Józef; Griffin, Patrick R; Ortlund, Eric A

2017-07-01

Peroxisome proliferator-activated gamma coactivator 1- α (PGC1 α ) regulates energy metabolism by directly interacting with transcription factors to modulate gene expression. Among the PGC1 α binding partners is liver receptor homolog 1 (LRH-1; NR5A2), an orphan nuclear hormone receptor that controls lipid and glucose homeostasis. Although PGC1 α is known to bind and activate LRH-1, mechanisms through which PGC1 α changes LRH-1 conformation to drive transcription are unknown. Here, we used biochemical and structural methods to interrogate the LRH-1-PGC1 α complex. Purified, full-length LRH-1, as well as isolated ligand binding domain, bound to PGC1 α with higher affinity than to the coactivator, nuclear receptor coactivator-2 (Tif2), in coregulator peptide recruitment assays. We present the first crystal structure of the LRH-1-PGC1 α complex, which depicts several hydrophobic contacts and a strong charge clamp at the interface between these partners. In molecular dynamics simulations, PGC1 α induced correlated atomic motion throughout the entire LRH-1 activation function surface, which was dependent on charge-clamp formation. In contrast, Tif2 induced weaker signaling at the activation function surface than PGC1 α but promoted allosteric signaling from the helix 6/ β -sheet region of LRH-1 to the activation function surface. These studies are the first to probe mechanisms underlying the LRH-1-PGC1 α interaction and may illuminate strategies for selective therapeutic targeting of PGC1 α -dependent LRH-1 signaling pathways. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

Age and visual impairment decrease driving performance as measured on a closed-road circuit.

PubMed

Wood, Joanne M

2002-01-01

In this study the effects of visual impairment and age on driving were investigated and related to visual function. Participants were 139 licensed drivers (young, middle-aged, and older participants with normal vision, and older participants with ocular disease). Driving performance was assessed during the daytime on a closed-road driving circuit. Visual performance was assessed using a vision testing battery. Age and visual impairment had a significant detrimental effect on recognition tasks (detection and recognition of signs and hazards), time to complete driving tasks (overall course time, reversing, and maneuvering), maneuvering ability, divided attention, and an overall driving performance index. All vision measures were significantly affected by group membership. A combination of motion sensitivity, useful field of view (UFOV), Pelli-Robson letter contrast sensitivity, and dynamic acuity could predict 50% of the variance in overall driving scores. These results indicate that older drivers with either normal vision or visual impairment had poorer driving performance compared with younger or middle-aged drivers with normal vision. The inclusion of tests such as motion sensitivity and the UFOV significantly improve the predictive power of vision tests for driving performance. Although such measures may not be practical for widespread screening, their application in selected cases should be considered.

Spatial gene drives and pushed genetic waves

PubMed Central

Tanaka, Hidenori; Stone, Howard A.; Nelson, David R.

2017-01-01

Gene drives have the potential to rapidly replace a harmful wild-type allele with a gene drive allele engineered to have desired functionalities. However, an accidental or premature release of a gene drive construct to the natural environment could damage an ecosystem irreversibly. Thus, it is important to understand the spatiotemporal consequences of the super-Mendelian population genetics before potential applications. Here, we use a reaction–diffusion model for sexually reproducing diploid organisms to study how a locally introduced gene drive allele spreads to replace the wild-type allele, although it possesses a selective disadvantage s > 0. Using methods developed by Barton and collaborators, we show that socially responsible gene drives require 0.5 < s < 0.697, a rather narrow range. In this “pushed wave” regime, the spatial spreading of gene drives will be initiated only when the initial frequency distribution is above a threshold profile called “critical propagule,” which acts as a safeguard against accidental release. We also study how the spatial spread of the pushed wave can be stopped by making gene drives uniquely vulnerable (“sensitizing drive”) in a way that is harmless for a wild-type allele. Finally, we show that appropriately sensitized drives in two dimensions can be stopped, even by imperfect barriers perforated by a series of gaps. PMID:28743753

The impact of personality on driving safety among Chinese high-speed railway drivers.

PubMed

Guo, Ming; Wei, Wei; Liao, Ganli; Chu, Fulei

2016-07-01

This study explored the impact of personality traits on driving safety in high-speed railway drivers. A sample of high-speed railway drivers in Beijing (N=214) completed a questionnaire, including information on personality traits and background variables. The NEO Five Factor Inventory (NEO-FFI) was administered to characterize participants based on five personality traits: Neuroticism, Extraversion, Agreeableness, Openness to Experience, and Conscientiousness. The survey data were combined with naturalistic data of accident involvement and risky driving behavior in China. Poisson regression results show that drivers with high Conscientiousness and Extraversion caused fewer accidents. Higher Conscientiousness and lower Agreeableness were related to less frequent risky driving behavior. Education level and age negatively moderated the relation between certain personality traits and driving safety. The findings suggest that personality traits should be considered when selecting and training high-speed railway drivers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides.

PubMed

Hopwood, Paul E; Head, Megan L; Jordan, Eleanor J; Carter, Mauricio J; Davey, Emma; Moore, Allen J; Royle, Nick J

2016-06-01

Male and female genital morphology varies widely across many taxa, and even among populations. Disentangling potential sources of selection on genital morphology is problematic because each sex is predicted to respond to adaptations in the other due to reproductive conflicts of interest. To test how variation in this sexual conflict trait relates to variation in genital morphology we used our previously developed artificial selection lines for high and low repeated mating rates. We selected for high and low repeated mating rates using monogamous pairings to eliminate contemporaneous female choice and male-male competition. Male and female genital shape responded rapidly to selection on repeated mating rate. High and low mating rate lines diverged from control lines after only 10 generations of selection. We also detected significant patterns of male and female genital shape coevolution among selection regimes. We argue that because our selection lines differ in sexual conflict, these results support the hypothesis that sexually antagonistic coevolution can drive the rapid divergence of genital morphology. The greatest divergence in morphology corresponded with lines in which the resolution of sexual conflict over mating rate was biased in favor of male interests. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Comparison of single-step and two-step purified coagulants from Moringa oleifera seed for turbidity and DOC removal.

PubMed

Sánchez-Martín, J; Ghebremichael, K; Beltrán-Heredia, J

2010-08-01

The coagulant proteins from Moringa oleifera purified with single-step and two-step ion-exchange processes were used for the coagulation of surface water from Meuse river in The Netherlands. The performances of the two purified coagulants and the crude extract were assessed in terms of turbidity and DOC removal. The results indicated that the optimum dosage of the single-step purified coagulant was more than two times higher compared to the two-step purified coagulant in terms of turbidity removal. And the residual DOC in the two-step purified coagulant was lower than in single-step purified coagulant or crude extract. (c) 2010 Elsevier Ltd. All rights reserved.

Contrasted evolutionary histories of two Toll-like receptors (Tlr4 and Tlr7) in wild rodents (MURINAE)

PubMed Central

2013-01-01

Background In vertebrates, it has been repeatedly demonstrated that genes encoding proteins involved in pathogen-recognition by adaptive immunity (e.g. MHC) are subject to intensive diversifying selection. On the other hand, the role and the type of selection processes shaping the evolution of innate-immunity genes are currently far less clear. In this study we analysed the natural variation and the evolutionary processes acting on two genes involved in the innate-immunity recognition of Microbe-Associated Molecular Patterns (MAMPs). Results We sequenced genes encoding Toll-like receptor 4 (Tlr4) and 7 (Tlr7), two of the key bacterial- and viral-sensing receptors of innate immunity, across 23 species within the subfamily Murinae. Although we have shown that the phylogeny of both Tlr genes is largely congruent with the phylogeny of rodents based on a comparably sized non-immune sequence dataset, we also identified several potentially important discrepancies. The sequence analyses revealed that major parts of both Tlrs are evolving under strong purifying selection, likely due to functional constraints. Yet, also several signatures of positive selection have been found in both genes, with more intense signal in the bacterial-sensing Tlr4 than in the viral-sensing Tlr7. 92% and 100% of sites evolving under positive selection in Tlr4 and Tlr7, respectively, were located in the extracellular domain. Directly in the Ligand-Binding Region (LBR) of TLR4 we identified two rapidly evolving amino acid residues and one site under positive selection, all three likely involved in species-specific recognition of lipopolysaccharide of gram-negative bacteria. In contrast, all putative sites of LBRTLR7 involved in the detection of viral nucleic acids were highly conserved across rodents. Interspecific differences in the predicted 3D-structure of the LBR of both Tlrs were not related to phylogenetic history, while analyses of protein charges clearly discriminated Rattini and Murini clades. Conclusions In consequence of the constraints given by the receptor protein function purifying selection has been a dominant force in evolution of Tlrs. Nevertheless, our results show that episodic diversifying parasite-mediated selection has shaped the present species-specific variability in rodent Tlrs. The intensity of diversifying selection was higher in Tlr4 than in Tlr7, presumably due to structural properties of their ligands. PMID:24028551

40 CFR 1065.845 - Response factor determination.

Code of Federal Regulations, 2014 CFR

2014-07-01

... that FID zero and span balance gases may be any combination of purified air or purified nitrogen that... and span balance gases may be any combination of purified air or purified nitrogen that meets the...

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

Li, Yongjun; Yang, Lingyun

We report an efficient dynamic aperture (DA) optimization approach using multiobjective genetic algorithm (MOGA), which is driven by nonlinear driving terms computation. It was found that having small low order driving terms is a necessary but insufficient condition of having a decent DA. Then direct DA tracking simulation is implemented among the last generation candidates to select the best solutions. The approach was demonstrated successfully in optimizing NSLS-II storage ring DA.

Selection for Social Signalling Drives the Evolution of Chameleon Colour Change

PubMed Central

Stuart-Fox, Devi; Moussalli, Adnan

2008-01-01

Rapid colour change is a remarkable natural phenomenon that has evolved in several vertebrate and invertebrate lineages. The two principal explanations for the evolution of this adaptive strategy are (1) natural selection for crypsis (camouflage) against a range of different backgrounds and (2) selection for conspicuous social signals that maximise detectability to conspecifics, yet minimise exposure to predators because they are only briefly displayed. Here we show that evolutionary shifts in capacity for colour change in southern African dwarf chameleons (Bradypodion spp.) are associated with increasingly conspicuous signals used in male contests and courtship. To the chameleon visual system, species showing the most dramatic colour change display social signals that contrast most against the environmental background and amongst adjacent body regions. We found no evidence for the crypsis hypothesis, a finding reinforced by visual models of how both chameleons and their avian predators perceive chameleon colour variation. Instead, our results suggest that selection for conspicuous social signals drives the evolution of colour change in this system, supporting the view that transitory display traits should be under strong selection for signal detectability. PMID:18232740

Signal design and perception in Hypocnemis antbirds: evidence for convergent evolution via social selection.

PubMed

Tobias, Joseph A; Seddon, Nathalie

2009-12-01

Natural selection is known to produce convergent phenotypes through mimicry or ecological adaptation. It has also been proposed that social selection--i.e., selection exerted by social competition--may drive convergent evolution in signals mediating interspecific communication, yet this idea remains controversial. Here, we use color spectrophotometry, acoustic analyses, and playback experiments to assess the hypothesis of adaptive signal convergence in two competing nonsister taxa, Hypocnemis peruviana and H. subflava (Aves: Thamnophilidae). We show that the structure of territorial songs in males overlaps in sympatry, with some evidence of convergent character displacement. Conversely, nonterritorial vocal and visual signals in males are strikingly diagnostic, in line with 6.8% divergence in mtDNA sequences. The same pattern of variation applies to females. Finally, we show that songs in both sexes elicit strong territorial responses within and between species, whereas songs of a third, allopatric and more closely related species (H. striata) are structurally divergent and elicit weaker responses. Taken together, our results provide compelling evidence that social selection can act across species boundaries to drive convergent or parallel evolution in taxa competing for space and resources.

Chromosome segregation drives division site selection in Streptococcus pneumoniae.

PubMed

van Raaphorst, Renske; Kjos, Morten; Veening, Jan-Willem

2017-07-18

Accurate spatial and temporal positioning of the tubulin-like protein FtsZ is key for proper bacterial cell division. Streptococcus pneumoniae (pneumococcus) is an oval-shaped, symmetrically dividing opportunistic human pathogen lacking the canonical systems for division site control (nucleoid occlusion and the Min-system). Recently, the early division protein MapZ was identified and implicated in pneumococcal division site selection. We show that MapZ is important for proper division plane selection; thus, the question remains as to what drives pneumococcal division site selection. By mapping the cell cycle in detail, we show that directly after replication both chromosomal origin regions localize to the future cell division sites, before FtsZ. Interestingly, Z-ring formation occurs coincidently with initiation of DNA replication. Perturbing the longitudinal chromosomal organization by mutating the condensin SMC, by CRISPR/Cas9-mediated chromosome cutting, or by poisoning DNA decatenation resulted in mistiming of MapZ and FtsZ positioning and subsequent cell elongation. Together, we demonstrate an intimate relationship between DNA replication, chromosome segregation, and division site selection in the pneumococcus, providing a simple way to ensure equally sized daughter cells.

Adsorption of lead onto smectite from aqueous solution.

PubMed

Mhamdi, M; Galai, H; Mnasri, N; Elaloui, E; Trabelsi-Ayadi, M

2013-03-01

The purpose of this research is to study the effect of a new method of adsorption using membrane filtration to determine the maximum amount of lead adsorbed by clay and investigate the behavior of the clay after adsorption of the said metal. Treatment of wastewater contaminated with heavy metals depends on the characteristics of the effluent, the amount of final discharge, the cost of treatment, and the compatibility of the treatment process. The process of adsorption of heavy metals by clays may be a simple, selective, and economically viable alternative to the conventional physical-chemical treatment. This is justified by the importance of the surface developed by this material, the presence of negative charges on the said surface, the possibility of ion exchange taking place, and its wide availability in nature. The removal of lead from wastewater was studied by using the adsorption technique and using clay as the adsorbent. A method was optimized for adsorption through a membrane approaching natural adsorption. This new method is simple, selective, and the lead adsorption time is about 3 days. The various properties of clay were determined. It was observed that the cation exchange capacity of the clay was 56 meq/100 g of hydrated clay for the raw sample and 82 meq/100 g for the purified sample. The total surface area determined by the methylene blue method was equal to 556 and 783 m(2)/g for the raw and purified samples, respectively. The adsorption kinetics depends on several parameters. The Pb(II) clay, obeys the Langmuir, Freundlich, and the Elovich adsorption isotherms with high regression coefficients. The use of this adsorbent notably decreases the cost of treatment. It was concluded that clay shows a strong adsorption capacity on Pb(II), the maximum interaction occurring with purified clay treated at high concentration of lead. It is proposed that this adsorption through a membrane be extended for the treatment of effluents containing other metals.

Widespread Positive Selection Drives Differentiation of Centromeric Proteins in the Drosophila melanogaster subgroup.

PubMed

Beck, Emily A; Llopart, Ana

2015-11-25

Rapid evolution of centromeric satellite repeats is thought to cause compensatory amino acid evolution in interacting centromere-associated kinetochore proteins. Cid, a protein that mediates kinetochore/centromere interactions, displays particularly high amino acid turnover. Rapid evolution of both Cid and centromeric satellite repeats led us to hypothesize that the apparent compensatory evolution may extend to interacting partners in the Condensin I complex (i.e., SMC2, SMC4, Cap-H, Cap-D2, and Cap-G) and HP1s. Missense mutations in these proteins often result in improper centromere formation and aberrant chromosome segregation, thus selection for maintained function and coevolution among proteins of the complex is likely strong. Here, we report evidence of rapid evolution and recurrent positive selection in seven centromere-associated proteins in species of the Drosophila melanogaster subgroup, and further postulate that positive selection on these proteins could be a result of centromere drive and compensatory changes, with kinetochore proteins competing for optimal spindle attachment.

Facially Selective Cu-catalyzed Carbozincation of Cyclopropenes Using Arylzinc Reagents Formed by Sequential I/Mg/Zn exchange

PubMed Central

Tarwade, Vinod; Selvaraj, Ramajeyam; Fox, Joseph M.

2012-01-01

Described is a Cu-catalyzed directed carbozincation of cyclopropenes with organozinc reagents prepared by I/Mg/Zn exchange. This protocol broadens the scope with respect to functional group tolerance and enables use of aryl iodide precursors, rather than purified diorganozinc precursors. Critical to diastereoselectivity of the carbozincation step is the removal of magnesium halide salts after transmetallation with ZnCl2. PMID:23035947

Method for producing silicon thin-film transistors with enhanced forward current drive

DOEpatents

Weiner, K.H.

1998-06-30

A method is disclosed for fabricating amorphous silicon thin film transistors (TFTs) with a polycrystalline silicon surface channel region for enhanced forward current drive. The method is particularly adapted for producing top-gate silicon TFTs which have the advantages of both amorphous and polycrystalline silicon TFTs, but without problem of leakage current of polycrystalline silicon TFTs. This is accomplished by selectively crystallizing a selected region of the amorphous silicon, using a pulsed excimer laser, to create a thin polycrystalline silicon layer at the silicon/gate-insulator surface. The thus created polysilicon layer has an increased mobility compared to the amorphous silicon during forward device operation so that increased drive currents are achieved. In reverse operation the polysilicon layer is relatively thin compared to the amorphous silicon, so that the transistor exhibits the low leakage currents inherent to amorphous silicon. A device made by this method can be used, for example, as a pixel switch in an active-matrix liquid crystal display to improve display refresh rates. 1 fig.

Method for producing silicon thin-film transistors with enhanced forward current drive

DOEpatents

Weiner, Kurt H.

1998-01-01

A method for fabricating amorphous silicon thin film transistors (TFTs) with a polycrystalline silicon surface channel region for enhanced forward current drive. The method is particularly adapted for producing top-gate silicon TFTs which have the advantages of both amorphous and polycrystalline silicon TFTs, but without problem of leakage current of polycrystalline silicon TFTs. This is accomplished by selectively crystallizing a selected region of the amorphous silicon, using a pulsed excimer laser, to create a thin polycrystalline silicon layer at the silicon/gate-insulator surface. The thus created polysilicon layer has an increased mobility compared to the amorphous silicon during forward device operation so that increased drive currents are achieved. In reverse operation the polysilicon layer is relatively thin compared to the amorphous silicon, so that the transistor exhibits the low leakage currents inherent to amorphous silicon. A device made by this method can be used, for example, as a pixel switch in an active-matrix liquid crystal display to improve display refresh rates.

Functional architecture of an optic flow-responsive area that drives horizontal eye movements in zebrafish.

PubMed

Kubo, Fumi; Hablitzel, Bastian; Dal Maschio, Marco; Driever, Wolfgang; Baier, Herwig; Arrenberg, Aristides B

2014-03-19

Animals respond to whole-field visual motion with compensatory eye and body movements in order to stabilize both their gaze and position with respect to their surroundings. In zebrafish, rotational stimuli need to be distinguished from translational stimuli to drive the optokinetic and the optomotor responses, respectively. Here, we systematically characterize the neural circuits responsible for these operations using a combination of optogenetic manipulation and in vivo calcium imaging during optic flow stimulation. By recording the activity of thousands of neurons within the area pretectalis (APT), we find four bilateral pairs of clusters that process horizontal whole-field motion and functionally classify eleven prominent neuron types with highly selective response profiles. APT neurons are prevalently direction selective, either monocularly or binocularly driven, and hierarchically organized to distinguish between rotational and translational optic flow. Our data predict a wiring diagram of a neural circuit tailored to drive behavior that compensates for self-motion. Copyright © 2014 Elsevier Inc. All rights reserved.

The Microanatomic Segregation of Selection by Apoptosis in the Germinal Center

PubMed Central

Mayer, Christian T.; Gazumyan, Anna; Kara, Ervin E.; Gitlin, Alexander D.; Golijanin, Jovana; Viant, Charlotte; Pai, Joy; Oliveira, Thiago Y.; Wang, Qiao; Escolano, Amelia; Medina-Ramirez, Max; Sanders, Rogier W.; Nussenzweig, Michel C.

2018-01-01

B cells undergo rapid cell division and affinity maturation in anatomically distinct sites in lymphoid organs called germinal centers (GCs). Homeostasis is maintained in part by B-cell apoptosis. However, the precise contribution of apoptosis to GC biology and selection is not well defined. We developed apoptosis-indicator mice and used them to visualize, purify, and characterize dying GC B cells. Apoptosis is prevalent in the GC with up to half of all GC B cells dying every 6h. Moreover, programmed cell death is differentially regulated in the light zone (LZ) and the dark zone (DZ): LZ B cells die by default if they are not positively selected, whereas DZ cells die when their antigen receptors are damaged by activation-induced cytidine deaminase (AID). PMID:28935768

Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development

PubMed Central

Mahmoudi Saber, Morteza

2017-01-01

Abstract Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes. We discovered 679 such HCNSs from human, chimpanzee, gorilla, orangutan and gibbon genomes. These HCNSs were demonstrated to be under purifying selection but with lineage-restricted characteristics different from old CNSs. A significant proportion of their ancestral sequences had accelerated rates of nucleotide substitutions, insertions and deletions during the evolution of common ancestor of Hominoidea, suggesting the intervention of positive Darwinian selection for creating those HCNSs. In contrary to enhancer elements and similar to silencer sequences, these Hominoidea-restricted HCNSs are located in close proximity of transcription start sites. Their target genes are enriched in the nervous system, development and transcription, and they tend to be remotely located from the nearest coding gene. Chip-seq signals and gene expression patterns suggest that Hominoidea-restricted HCNSs are likely to be functional regulatory elements by imposing silencing effects on their target genes in a tissue-restricted manner during fetal brain development. These HCNSs, emerged through adaptive evolution and conserved through purifying selection, represent a set of promising targets for future functional studies of the evolution of Hominoidea-restricted phenotypes. PMID:28633494

Genome Evolution in the Obligate but Environmentally Active Luminous Symbionts of Flashlight Fish

PubMed Central

Hendry, Tory A.; de Wet, Jeffrey R.; Dougan, Katherine E.; Dunlap, Paul V.

2016-01-01

The luminous bacterial symbionts of anomalopid flashlight fish are thought to be obligately dependent on their hosts for growth and share several aspects of genome evolution with unrelated obligate symbionts, including genome reduction. However, in contrast to most obligate bacteria, anomalopid symbionts have an active environmental phase that may be important for symbiont transmission. Here we investigated patterns of evolution between anomalopid symbionts compared with patterns in free-living relatives and unrelated obligate symbionts to determine if trends common to obligate symbionts are also found in anomalopid symbionts. Two symbionts, “Candidatus Photodesmus katoptron” and “Candidatus Photodesmus blepharus,” have genomes that are highly similar in gene content and order, suggesting genome stasis similar to ancient obligate symbionts present in insect lineages. This genome stasis exists in spite of the symbiont’s inferred ability to recombine, which is frequently lacking in obligate symbionts with stable genomes. Additionally, we used genome comparisons and tests of selection to infer which genes may be particularly important for the symbiont’s ecology compared with relatives. In keeping with obligate dependence, substitution patterns suggest that most symbiont genes are experiencing relaxed purifying selection compared with relatives. However, genes involved in motility and carbon storage, which are likely to be used outside the host, appear to be under increased purifying selection. Two chemoreceptor chemotaxis genes are retained by both species and show high conservation with amino acid sensing genes, suggesting that the bacteria may actively seek out hosts using chemotaxis toward amino acids, which the symbionts are not able to synthesize. PMID:27389687

ACP5 (Uteroferrin): Phylogeny of an Ancient and Conserved Gene Expressed in the Endometrium of Mammals1

PubMed Central

Padua, Maria B.; Lynch, Vincent J.; Alvarez, Natalia V.; Garthwaite, Mark A.; Golos, Thaddeus G.; Bazer, Fuller W.; Kalkunte, Satyan; Sharma, Surendra; Wagner, Gunter P.; Hansen, Peter J.

2012-01-01

ABSTRACT Type 5 acid phosphatase (ACP5; also known as tartrate-resistant acid phosphatase or uteroferrin) is a metalloprotein secreted by the endometrial glandular epithelium of pigs, mares, sheep, and water buffalo. In this paper, we describe the phylogenetic distribution of endometrial expression of ACP5 and demonstrate that endometrial expression arose early in evolution (i.e., before divergence of prototherian and therian mammals ∼166 million years ago). To determine expression of ACP5 in the pregnant endometrium, RNA was isolated from rhesus, mouse, rat, dog, sheep, cow, horse, armadillo, opossum, and duck-billed platypus. Results from RT-PCR and RNA-Seq experiments confirmed that ACP5 is expressed in all species examined. ACP5 was also demonstrated immunochemically in endometrium of rhesus, marmoset, sheep, cow, goat, and opossum. Alignment of inferred amino acid sequences shows a high conservation of ACP5 throughout speciation, with species-specific differences most extensive in the N-terminal and C-terminal regions of the protein. Analysis by Selecton indicated that most of the sites in ACP5 are undergoing purifying selection, and no sites undergoing positive selection were found. In conclusion, endometrial expression of ACP5 is a common feature in all orders of mammals and has been subjected to purifying selection. Expression of ACP5 in the uterus predates the divergence of therians and prototherians. ACP5 is an evolutionary conserved gene that likely exerts a common function important for pregnancy in mammals using a wide range of reproductive strategies. PMID:22278982

The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes.

PubMed

Tchigvintsev, Anatoli; Tran, Hai; Popovic, Ana; Kovacic, Filip; Brown, Greg; Flick, Robert; Hajighasemi, Mahbod; Egorova, Olga; Somody, Joseph C; Tchigvintsev, Dmitri; Khusnutdinova, Anna; Chernikova, Tatyana N; Golyshina, Olga V; Yakimov, Michail M; Savchenko, Alexei; Golyshin, Peter N; Jaeger, Karl-Erich; Yakunin, Alexander F

2015-03-01

Most of the Earth's biosphere is cold and is populated by cold-adapted microorganisms. To explore the natural enzyme diversity of these environments and identify new carboxylesterases, we have screened three marine metagenome gene libraries for esterase activity. The screens identified 23 unique active clones, from which five highly active esterases were selected for biochemical characterization. The purified metagenomic esterases exhibited high activity against α-naphthyl and p-nitrophenyl esters with different chain lengths. All five esterases retained high activity at 5 °C indicating that they are cold-adapted enzymes. The activity of MGS0010 increased more than two times in the presence of up to 3.5 M NaCl or KCl, whereas the other four metagenomic esterases were inhibited to various degrees by these salts. The purified enzymes showed different sensitivities to inhibition by solvents and detergents, and the activities of MGS0010, MGS0105 and MGS0109 were stimulated three to five times by the addition of glycerol. Screening of purified esterases against 89 monoester substrates revealed broad substrate profiles with a preference for different esters. The metagenomic esterases also hydrolyzed several polyester substrates including polylactic acid suggesting that they can be used for polyester depolymerization. Thus, esterases from marine metagenomes are cold-adapted enzymes exhibiting broad biochemical diversity reflecting the environmental conditions where they evolved.

Purification of influenza deoxyribonucleic acid-based vaccine using agmatine monolith.

PubMed

Bicho, D; Caramelo-Nunes, C; Sousa, A; Sousa, F; Queiroz, J A; Tomaz, C T

2016-02-15

Lately, researchers have made several efforts to improve vaccine production to fight highly contagious respiratory diseases like influenza. One of the most promising options for reducing the impact of this virus is DNA vaccination. However, a large quantity of highly pure plasmid DNA (pDNA) is necessary to attain this goal. The present work describes the production and purification of the plasmid NTC7482-41H-VA2HA expressing influenza virus hemagglutinin using an agmatine monolith. This ligand was chosen to purify supercoiled (sc) pDNA from complex lysates because of its versatile multimodal character. Its natural intervention in several biological systems together with its similarity with the highly studied arginine ligand allowed the development of a simpler and more specific purification process. Agmatine works under two strategies: descending ammonium sulfate gradient and ascending sodium chloride gradient. Furthermore, pH manipulation revealed an important role in pDNA isoforms selectivity. Dynamic binding capacity (DBC) experiments were performed varying different parameters and showed an increase with pDNA concentration, while high flow rate and high pH had the opposite effect. Sc pDNA was purified with high yield and was efficient with respect to cell transfection and cell viability. This monolith showed to be appropriate to purify the plasmid NTC7482-41H-VA2HA, providing a valuable tool for pDNA influenza vaccines preparation. Copyright © 2016. Published by Elsevier B.V.

[Partial purification of peptides present in the Tityus macrochirus (Buthidae) scorpion venom and preliminary assessment of their cytotoxicity].

PubMed

Rincón-Cortés, Clara Andrea; Reyes-Montaño, Edgar Antonio; Vega-Castro, Nohora Angélica

2017-06-01

Scorpion venom contains peptides with neurotoxic action primarily active on ion channels in the nervous system of insects and mammals. They are also characterized as cytolytic and anticancer, biological characteristics that have not yet been reported for the Tityus macrochirus venom. To assess if the total T. macrochirus venom and the fraction of partially purified peptides decrease the viability of various tumor-derived cell lines. The scorpion venom was collected by electrical stimulation and, subsequently, subjected to chromatography, electrophoresis, and ultrafiltration with Amicon Ultra 0.5® membranes for the partial identification and purification of its peptides. The cytotoxic activity of the venom and the peptides fraction trials on tumor-derived cell lines were carried out by the MTT method. The T. macrochirus scorpion venom has peptides with molecular weights ranging between 3 and 10 kDa. They were partially purified using the ultrafiltration technique, and assessed by the RP-HPLC method. Cytotoxicity trials with the whole T. macrochirus venom showed a higher viability decrease on the PC3 cell line compared to the other cell lines assessed, while the partially purified peptides decreased the HeLa cell line viability. Peptides in the T. macrochirus scorpion venom showed cytotoxic activity on some tumorderived cell lines. We observed some degree of selectivity against other cell lines assessed.

Molecular approaches towards development of purified natural products and their structurally known derivatives as efficient anti-cancer drugs: current trends.

PubMed

Saha, Santu Kumar; Khuda-Bukhsh, Anisur Rahman

2013-08-15

Several natural products and their derivatives, either in purified or structurally identified form, exhibit immense pharmacological and biological properties, some of them showing considerable anticancer potential. Although the molecular mechanisms of action of some of these products are yet to be elucidated, extensive research in this area continues to generate new data that are clinically exploitable. Recent advancement in molecular biology, high throughput screening, biomarker identifications, target selection and genomic approaches have enabled us to understand salient interactions of natural products and their derivatives with cancer cells vis-à-vis normal cells. In this review we highlight the recent approaches and application of innovative technologies made to improve quality as well as efficiency of structurally identified natural products and their derivatives, particularly in small molecular forms capable of being used in "targeted therapies" in oncology. These products preferentially involve multiple mechanistic pathways and overcome chemo-resistance in tumor types with cumulative action. We also mention briefly a few physico-chemical features that compare natural products with drugs in recent natural product discovery approaches. We further report here a few purified natural products as examples that provide molecular interventions in cancer therapeutics to give the reader a glimpse of the current trends of approach for discovering useful anticancer drugs. © 2013 Elsevier B.V. All rights reserved.

Exopolysaccharide produced by Pediococcus acidilactici M76 isolated from the Korean traditional rice wine, makgeolli.

PubMed

Song, Young-Ran; Jeong, Do-Youn; Cha, Youn-Soo; Baik, Sang-Ho

2013-05-01

This work is aimed to increase knowledge of the functional exopolysaccharide (EPS) from lactic acid bacteria (LAB) in makgeolli, a Korean fermented rice wine. Among LAB strains isolated from makgeolli, strain M76 was selected as a functional strain producing a bioactive EPS, based on its antioxidative activity on the DPPH radical. The 16S rRNA gene sequencing analysis showed a high sequence similarity (99.0%) with P. acidilactici, but had different biochemical properties with the already known P. acidilactici type strains in the aspect of carbohydrates utilization. The obtained P. acidilactici M76 produced a soluble EPS above 2 g/l. One-step chromatography using gel filtration after ethanol precipitation from the supernatant of P. acidilactici M76 was enough to obtain purified EPS with a single peak, showing a molecular mass of approximately 67 kDa. Componential and structural analyses of EPS by TLC, HPLC, and FT-IR indicated that the EPS is a glucan, consisting of glucose units. The purified EPS had antioxidant activity on the DPPH radical of 45.8% at a concentration of 1 mg/ml. The purified EPS also showed proliferative effect on the pancreatic RIN-m5F cell line and remarkable protection activity on alloxan-induced cytotoxicity. This potent antioxidant and antidiabetic EPS by LAB in makgeolli may contribute to understanding the functionality of makgeolli.

Novel Coprinopsis cinerea Polyesterase That Hydrolyzes Cutin and Suberin▿ †

PubMed Central

Kontkanen, Hanna; Westerholm-Parvinen, Ann; Saloheimo, Markku; Bailey, Michael; Rättö, Marjaana; Mattila, Ismo; Mohsina, Marzia; Kalkkinen, Nisse; Nakari-Setälä, Tiina; Buchert, Johanna

2009-01-01

Three cutinase gene-like genes from the basidiomycete Coprinopsis cinerea (Coprinus cinereus) found with a similarity search were cloned and expressed in Trichoderma reesei under the control of an inducible cbh1 promoter. The selected transformants of all three polyesterase constructs showed activity with p-nitrophenylbutyrate, used as a model substrate. The most promising transformant of the cutinase CC1G_09668.1 gene construct was cultivated in a laboratory fermentor, with a production yield of 1.4 g liter−l purified protein. The expressed cutinase (CcCUT1) was purified to homogeneity by immobilized metal affinity chromatography exploiting a C-terminal His tag. The N terminus of the enzyme was found to be blocked. The molecular mass of the purified enzyme was determined to be around 18.8 kDa by mass spectrometry. CcCUT1 had higher activity on shorter (C2 to C10) fatty acid esters of p-nitrophenol than on longer ones, and it also exhibited lipase activity. CcCUT1 had optimal activity between pH 7 and 8 but retained activity over a wide pH range. The enzyme retained 80% of its activity after 20 h of incubation at 50°C, but residual activity decreased sharply at 60°C. Microscopic analyses and determination of released hydrolysis products showed that the enzyme was able to depolymerize apple cutin and birch outer bark suberin. PMID:19201950

Novel Coprinopsis cinerea polyesterase that hydrolyzes cutin and suberin.

PubMed

Kontkanen, Hanna; Westerholm-Parvinen, Ann; Saloheimo, Markku; Bailey, Michael; Rättö, Marjaana; Mattila, Ismo; Mohsina, Marzia; Kalkkinen, Nisse; Nakari-Setälä, Tiina; Buchert, Johanna

2009-04-01

Three cutinase gene-like genes from the basidiomycete Coprinopsis cinerea (Coprinus cinereus) found with a similarity search were cloned and expressed in Trichoderma reesei under the control of an inducible cbh1 promoter. The selected transformants of all three polyesterase constructs showed activity with p-nitrophenylbutyrate, used as a model substrate. The most promising transformant of the cutinase CC1G_09668.1 gene construct was cultivated in a laboratory fermentor, with a production yield of 1.4 g liter(-l) purified protein. The expressed cutinase (CcCUT1) was purified to homogeneity by immobilized metal affinity chromatography exploiting a C-terminal His tag. The N terminus of the enzyme was found to be blocked. The molecular mass of the purified enzyme was determined to be around 18.8 kDa by mass spectrometry. CcCUT1 had higher activity on shorter (C(2) to C(10)) fatty acid esters of p-nitrophenol than on longer ones, and it also exhibited lipase activity. CcCUT1 had optimal activity between pH 7 and 8 but retained activity over a wide pH range. The enzyme retained 80% of its activity after 20 h of incubation at 50 degrees C, but residual activity decreased sharply at 60 degrees C. Microscopic analyses and determination of released hydrolysis products showed that the enzyme was able to depolymerize apple cutin and birch outer bark suberin.

Ball Screw Actuator Including an Axial Soft Stop

NASA Technical Reports Server (NTRS)

Forrest, Steven Talbert (Inventor); Woessner, George (Inventor); Abel, Steve (Inventor); Wingett, Paul T. (Inventor); Hanlon, Casey (Inventor)

2016-01-01

An actuator includes an actuator housing, a ball screw, and an axial soft stop assembly. The ball screw extends through the actuator housing and has a first end and a second end. The ball screw is coupled to receive a drive force and is configured, upon receipt of the drive force, to selectively move in a retract direction and an extend direction. The axial soft stop assembly is disposed within the actuator housing. The axial soft stop assembly is configured to be selectively engaged by the ball screw and, upon being engaged thereby, to translate, with compliance, a predetermined distance in the extend direction, and to prevent further movement of the ball screw upon translating the predetermined distance.

Proteome Comparisons between Hemolymph of Two Honeybee Strains (Apis mellifera ligustica) Reveal Divergent Molecular Basis in Driving Hemolymph Function and High Royal Jelly Secretion.

PubMed

Ararso, Zewdu; Ma, Chuan; Qi, Yuping; Feng, Mao; Han, Bin; Hu, Han; Meng, Lifeng; Li, Jianke

2018-01-05

Hemolymph is vital for the immunity of honeybees and offers a way to investigate their physiological status. To gain novel insight into the functionality and molecular details of the hemolymph in driving increased Royal Jelly (RJ) production, we characterized and compared hemolymph proteomes across the larval and adult ages of Italian bees (ITbs) and Royal Jelly bees (RJbs), a stock selected from ITbs for increasing RJ output. Unprecedented in-depth proteome was attained with the identification of 3394 hemolymph proteins in both bee lines. The changes in proteome support the general function of hemolymph to drive development and immunity across different ages. However, age-specific proteome settings have adapted to prime the distinct physiology for larvae and adult bees. In larvae, the proteome is thought to drive temporal immunity, rapid organogenesis, and reorganization of larval structures. In adults, the proteome plays key roles in prompting tissue development and immune defense in newly emerged bees, in gland maturity in nurse bees, and in carbohydrate energy production in forager bees. Between larval and adult samples of the same age, RJbs and ITbs have tailored distinct hemolymph proteome programs to drive their physiology. In particular, in day 4 larvae and nurse bees, a large number of highly abundant proteins are enriched in protein synthesis and energy metabolism in RJbs. This implies that they have adapted their proteome to initiate different developmental trajectories and high RJ secretion in response to selection for enhanced RJ production. Our hitherto unexplored in-depth proteome coverage provides novel insight into molecular details that drive hemolymph function and high RJ production by RJbs.

Recent demography drives changes in linked selection across the maize genome

USDA-ARS?s Scientific Manuscript database

The interaction between genetic drift and selection in shaping genetic diversity is not fully understood. In particular, a population's propensity to drift is typically summarized by its long-term e_ective population size (Ne), but rapidly changing population demographics may complicate this relatio...

Age-related carbonylation of fibrocartilage structural proteins drives tissue degenerative modification.

PubMed

Scharf, Brian; Clement, Cristina C; Yodmuang, Supansa; Urbanska, Aleksandra M; Suadicani, Sylvia O; Aphkhazava, David; Thi, Mia M; Perino, Giorgio; Hardin, John A; Cobelli, Neil; Vunjak-Novakovic, Gordana; Santambrogio, Laura

2013-07-25

Aging-related oxidative stress has been linked to degenerative modifications in different organs and tissues. Using redox proteomic analysis and illustrative tandem mass spectrometry mapping, we demonstrate oxidative posttranslational modifications in structural proteins of intervertebral discs (IVDs) isolated from aging mice. Increased protein carbonylation was associated with protein fragmentation and aggregation. Complementing these findings, a significant loss of elasticity and increased stiffness was measured in fibrocartilage from aging mice. Studies using circular dichroism and intrinsic tryptophan fluorescence revealed a significant loss of secondary and tertiary structures of purified collagens following oxidation. Collagen unfolding and oxidation promoted both nonenzymatic and enzymatic degradation. Importantly, induction of oxidative modification in healthy fibrocartilage recapitulated the biochemical and biophysical modifications observed in the aging IVD. Together, these results suggest that protein carbonylation, glycation, and lipoxidation could be early events in promoting IVD degenerative changes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Ionomer-Membrane Water Processing Methods

NASA Technical Reports Server (NTRS)

MacCallum, Taber K. (Inventor); Kelsey, Laura (Inventor)

2016-01-01

This disclosure provides water processing apparatuses, systems, and methods for recovering water from wastewater such as urine. The water processing apparatuses, systems, and methods can utilize membrane technology for extracting purified water in a single step. A containment unit can include an ionomer membrane, such as Nafion(TradeMark) over a hydrophobic microporous membrane, such as polytetrafluoroethylene (PTFE). The containment unit can be filled with wastewater, and the hydrophobic microporous membrane can be impermeable to liquids and solids of the wastewater but permeable to gases and vapors of the wastewater, and the ionomer membrane can be permeable to water vapor but impermeable to one or more contaminants of the gases and vapors. The containment unit can be exposed to a dry purge gas to maintain a water vapor partial pressure differential to drive permeation of the water vapor, and the water vapor can be collected and processed into potable water.

Ionomer-Membrane Water Processing Apparatus

NASA Technical Reports Server (NTRS)

MacCallum, Taber K. (Inventor); Kelsey, Laura (Inventor)

2016-01-01

This disclosure provides water processing apparatuses, systems, and methods for recovering water from wastewater such as urine. The water processing apparatuses, systems, and methods can utilize membrane technology for extracting purified water in a single step. A containment unit can include an ionomer membrane, such as Nafion(Registered Trademark), over a hydrophobic microporous membrane, such as polytetrafluoroethylene (PTFE). The containment unit can be filled with wastewater, and the hydrophobic microporous membrane can be impermeable to liquids and solids of the wastewater but permeable to gases and vapors of the wastewater, and the ionomer membrane can be permeable to water vapor but impermeable to one or more contaminants of the gases and vapors. The containment unit can be exposed to a dry purge gas to maintain a water vapor partial pressure differential to drive permeation of the water vapor, and the water vapor can be collected and processed into potable water.

Ionomer-Membrane Water Processing Apparatus

NASA Technical Reports Server (NTRS)

MacCallum, Taber K. (Inventor); Kelsey, Laura Katrina (Inventor)

2017-01-01

This disclosure provides water processing apparatuses, systems, and methods for recovering water from wastewater such as urine. The water processing apparatuses, systems, and methods can utilize membrane technology for extracting purified water in a single step. A containment unit can include an ionomer membrane, such as Nafion.RTM., over a hydrophobic microporous membrane, such as polytetrafluoroethylene (PTFE). The containment unit can be filled with wastewater, and the hydrophobic microporous membrane can be impermeable to liquids and solids of the wastewater but permeable to gases and vapors of the wastewater, and the ionomer membrane can be permeable to water vapor but impermeable to one or more contaminants of the gases and vapors. The containment unit can be exposed to a dry purge gas to maintain a water vapor partial pressure differential to drive permeation of the water vapor, and the water vapor can be collected and processed into potable water.

The effects of aniline impurities on monopropellant hydrazine thruster performance

NASA Technical Reports Server (NTRS)

Holcomb, L.; Mattson, L.; Oshiro, R.

1976-01-01

Both a 0.45-N and a 0.9-N thruster representative of the designs being flown on 3-axis stabilized spacecraft were used in testing various grades of hydrazine for the phenomenon of monopropellant hydrazine thruster catalyst bed poisoning. Both designs employed Shell 405 ABSG spontaneous catalyst. It is found that pulse shape distortion can be minimized, if not eliminated, by using aniline-free hydrazine. The mechanisms for both steady-state and pulse-mode performance loss are associated with the formation of a catalyst coke similar to the polycyclic aromatic poisons encountered in the petroleum industry. These poisoning mechanisms are reversible, with high-temperature operation being required to drive off the aniline coke deposits. It is recommended that a purified-grade hydrazine be considered for any mission that imposes operational conditions on a thruster which can result in aniline-induced poisoning of the catalyst bed.

Amorphous and nanocrystalline luminescent Si and Ge obtained via a solid-state chemical metathesis synthesis route

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

McMillan, Paul F.; Gryko, Jan; Bull, Craig

A new solid-state metathesis synthesis route was applied to obtain bulk samples of amorphous or microcrystalline Si and Ge. The method involves reaction of Zintl phases such as NaSi or NaGe, with ammonium or metal (e.g., CuCl, CoBr{sub 2}) halides. The driving force for the solid-state reaction is provided by the formation of alkali halides and the transition metals or metal silicides, or gaseous ammonia and hydrogen. The semiconductors were purified by washing to remove other solid products. The amorphous semiconductors were obtained in bulk form from reactions carried out at 200-300{sup o}C. Syntheses at higher temperatures gave rise tomore » microcrystalline semiconductors, or to micro-/nanocrystalline particles contained within the amorphous material. Similar crystalline/amorphous composites were obtained after heat treatment of bulk amorphous materials.« less

Effects of Malignant Melanoma Initiating Cells on T-Cell Activation

PubMed Central

Schatton, Tobias; Schütte, Ute; Frank, Markus H.

2016-01-01

Although human malignant melanoma is a highly immunogenic cancer, both the endogenous antitumor immune response and melanoma immunotherapy often fail to control neoplastic progression. Accordingly, characterizing melanoma cell subsets capable of evading antitumor immunity could unravel optimized treatment strategies that might reduce morbidity and mortality from melanoma. By virtue of their preferential capacity to modulate antitumor immune responses and drive inexorable tumor growth and progression, malignant melanoma-initiating cells (MMICs) warrant closer investigation to further elucidate the cellular and molecular mechanisms underlying melanoma immune evasion and immunotherapy resistance. Here we describe methodologies that enable the characterization of immunoregulatory effects of purified MMICs versus melanoma bulk populations in coculture with syngeneic or allogeneic lymphocytes, using [3H] thymidine incorporation, enzyme-linked immunosorbent spot (ELISPOT), or ELISA assays. These assays were traditionally developed to analyze alloimmune processes and we successfully adapted them for the study of tumor-mediated immunomodulatory functions. PMID:26786883

A single-domain antibody-linked Fab bispecific antibody Her2-S-Fab has potent cytotoxicity against Her2-expressing tumor cells.

PubMed

Li, Aifen; Xing, Jieyu; Li, Li; Zhou, Changhua; Dong, Bin; He, Ping; Li, Qing; Wang, Zhong

2016-12-01

Her2, which is frequently overexpressed in breast cancer, is one of the most studied tumor-associated antigens for cancer therapy. Anti-HER2 monoclonal antibody, trastuzumab, has achieved significant clinical benefits in metastatic breast cancer. In this study, we describe a novel bispecific antibody Her2-S-Fab targeting Her2 by linking a single domain anti-CD16 VHH to the trastuzumab Fab. The Her2-S-Fab antibody can be efficiently expressed and purified from Escherichia coli, and drive potent cancer cell killing in HER2-overexpressing cancer cells. In xenograft model, the Her2-S-Fab suppresses tumor growth in the presence of human immune cells. Our results suggest that the bispecific Her2-S-Fab may provide a valid alternative to Her2 positive cancer therapy.

Feedback between environment and traits under selection in a seasonal environment: consequences for experimental evolution.

PubMed

Collot, Dorian; Nidelet, Thibault; Ramsayer, Johan; Martin, Olivier C; Méléard, Sylvie; Dillmann, Christine; Sicard, Delphine; Legrand, Judith

2018-04-11

Batch cultures are frequently used in experimental evolution to study the dynamics of adaptation. Although they are generally considered to simply drive a growth rate increase, other fitness components can also be selected for. Indeed, recurrent batches form a seasonal environment where different phases repeat periodically and different traits can be under selection in the different seasons. Moreover, the system being closed, organisms may have a strong impact on the environment. Thus, the study of adaptation should take into account the environment and eco-evolutionary feedbacks. Using data from an experimental evolution on yeast Saccharomyces cerevisiae , we developed a mathematical model to understand which traits are under selection, and what is the impact of the environment for selection in a batch culture. We showed that two kinds of traits are under selection in seasonal environments: life-history traits, related to growth and mortality, but also transition traits, related to the ability to react to environmental changes. The impact of environmental conditions can be summarized by the length of the different seasons which weight selection on each trait: the longer a season is, the higher the selection on associated traits. Since phenotypes drive season length, eco-evolutionary feedbacks emerge. Our results show how evolution in successive batches can affect season lengths and strength of selection on different traits. © 2018 The Author(s).

Teens' distracted driving behavior: Prevalence and predictors.

PubMed

Gershon, Pnina; Zhu, Chunming; Klauer, Sheila G; Dingus, Tom; Simons-Morton, Bruce

2017-12-01

Teen drivers' over-involvement in crashes has been attributed to a variety of factors, including distracted driving. With the rapid development of in-vehicle systems and portable electronic devices, the burden associated with distracted driving is expected to increase. The current study identifies predictors of secondary task engagement among teenage drivers and provides basis for interventions to reduce distracted driving behavior. We described the prevalence of secondary tasks by type and driving conditions and evaluated the associations between the prevalence of secondary task engagement, driving conditions, and selected psychosocial factors. The private vehicles of 83 newly-licensed teenage drivers were equipped with Data Acquisition Systems (DAS), which documented driving performance measures, including secondary task engagement and driving environment characteristics. Surveys administered at licensure provided psychosocial measures. Overall, teens engaged in a potentially distracting secondary task in 58% of sampled road clips. The most prevalent types of secondary tasks were interaction with a passenger, talking/singing (no passenger), external distraction, and texting/dialing the cell phone. Secondary task engagement was more prevalent among those with primary vehicle access and when driving alone. Social norms, friends' risky driving behaviors, and parental limitations were significantly associated with secondary task prevalence. In contrast, environmental attributes, including lighting and road surface conditions, were not associated with teens' engagement in secondary tasks. Our findings indicated that teens engaged in secondary tasks frequently and poorly regulate their driving behavior relative to environmental conditions. Practical applications: Peer and parent influences on secondary task engagement provide valuable objectives for countermeasures to reduce distracted driving among teenage drivers. Copyright © 2017 National Safety Council and Elsevier Ltd. All rights reserved.

Laser particle sorter

DOEpatents

Martin, J.C.; Buican, T.N.

1987-11-30

Method and apparatus are provided for sorting particles, such as biological particles. A first laser is used to define an optical path having an intensity gradient which is effective to propel the particles along the path but which is sufficiently weak that the particles are not trapped in an axial direction. A probe laser beam is provided for interrogating the particles to identify predetermined phenotypical characteristics of the particles. A second laser beam is provided to intersect the driving first laser beam, wherein the second laser beam is activated by an output signal indicative of a predetermined characteristic. The second laser beam is switchable between a first intensity and a second intensity, where the first intensity is effective to displace selected particles from the driving laser beam and the second intensity is effective to propel selected particles along the deflection laser beam. The selected particles may then be propelled by the deflection beam to a location effective for further analysis. 2 figs.

The change of steel surface chemistry regarding oxygen partial pressure and dew point

NASA Astrophysics Data System (ADS)

Norden, Martin; Blumenau, Marc; Wuttke, Thiemo; Peters, Klaus-Josef

2013-04-01

By investigating the surface state of a Ti-IF, TiNb-IF and a MnCr-DP after several series of intercritical annealing, the impact of the annealing gas composition on the selective oxidation process is discussed. On behalf of the presented results, it can be concluded that not the general oxygen partial pressure in the annealing furnace, which is a result of the equilibrium reaction of water and hydrogen, is the main driving force for the selective oxidation process. It is shown that the amounts of adsorbed gases at the strip surface and the effective oxygen partial pressure resulting from the adsorbed gases, which is mainly dependent on the water content of the annealing furnace, is driving the selective oxidation processes occurring during intercritical annealing. Thus it is concluded, that for industrial applications the dew point must be the key parameter value for process control.

Laser particle sorter

DOEpatents

Martin, John C.; Buican, Tudor N.

1989-01-01

Method and apparatus for sorting particles, such as biological particles. A first laser defines an optical path having an intensity gradient which is effective to propel the particles along the path but which is sufficiently weak that the particles are not trapped in an axial direction. A probe laser beam interrogates the particles to identify predetermined phenotypical characteristics of the particles. A second laser beam intersects the driving first laser beam, wherein the second laser beam is activated by an output signal indicative of a predetermined characteristic. The second laser beam is switchable between a first intensity and a second intensity, where the first intensity is effective to displace selected particles from the driving laser beam and the second intensity is effective to propel selected particles along the deflection laser beam. The selected particles may then be propelled by the deflection beam to a location effective for further analysis.

Family feuds: social competition and sexual conflict in complex societies

PubMed Central

Rubenstein, Dustin R.

2012-01-01

Darwin was initially puzzled by the processes that led to ornamentation in males—what he termed sexual selection—and those that led to extreme cooperation and altruism in complex animal societies—what was later termed kin selection. Here, I explore the relationships between sexual and kin selection theory by examining how social competition for reproductive opportunities—particularly in females—and sexual conflict over mating partners are inherent and critical parts of complex altruistic societies. I argue that (i) patterns of reproductive sharing within complex societies can drive levels of social competition and reproductive conflict not only in males but also in females living in social groups, and ultimately the evolution of female traits such as ornaments and armaments; (ii) mating conflict over female choice of sexual partners can influence kin structure within groups and drive the evolution of complex societies; and (iii) patterns of reproductive sharing and conflict among females may also drive the evolution of complex societies by influencing kin structure within groups. Ultimately, complex societies exhibiting altruistic behaviour appear to have only arisen in taxa where social competition over reproductive opportunities and sexual conflict over mating partners were low. Once such societies evolved, there were important selective feedbacks on traits used to regulate and mediate intra-sexual competition over reproductive opportunities, particularly in females. PMID:22777018

Androgen deprivation treatment of sexual behavior.

PubMed

Houts, Frederick W; Taller, Inna; Tucker, Douglas E; Berlin, Fred S

2011-01-01

Gonadotropin-releasing hormone agonists are underutilized in patients seeking diminution of problematic sexual drives. This chapter reviews the literature on surgical castration of sex offenders, anti-androgen use and the rationale for providing androgen deprivation therapy, rather than selective serotonin reuptake inhibitors or more conservative interventions, for patients with paraphilias and excessive sexual drive. Discussions of informed consent, side effects, contraindications and case examples are provided. Copyright © 2011 S. Karger AG, Basel.

Characterization of a monoclonal antibody against P57, the C3/C3b-cleaving proteinase expressed in human erythrocyte membranes.

PubMed

Fiandino-Tirel, A; Barel, M; Lyamani, F; Gauffre, A; Hermann, J; Frade, R

1991-08-01

A monoclonal antibody was raised against p57, a serine proteinase, characterized by an apparent molecular weight of 57 kDa, and purified from human erythrocyte membranes. P57 proteinase cleaves the human third component of complement, C3. The antibody selected, MP1, of IgG2a isotype, precipitated specifically the p57 antigen which carried the C3/C3b-cleaving activity present in membrane crude extract of human erythrocytes. P57 proteinase eluted from MP1-sepharose was inhibited by 5 x 10(-4) M PMSF, enhanced by 0.5% SDS and generated C3 fragments identical to those generated by membrane crude extract of human erythrocytes. All these properties were identical to those of the p57 previously purified by biochemical procedures. In addition, 5000 binding sites were detected on cell surface. This MP1 monoclonal antibody will be helpful to analyse the role of p57 in human erythrocytes.

A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy antigen receptor for chemokines.

PubMed

Smolarek, Dorota; Hattab, Claude; Hassanzadeh-Ghassabeh, Gholamreza; Cochet, Sylvie; Gutiérrez, Carlos; de Brevern, Alexandre G; Udomsangpetch, Rachanee; Picot, Julien; Grodecka, Magdalena; Wasniowska, Kazimiera; Muyldermans, Serge; Colin, Yves; Le Van Kim, Caroline; Czerwinski, Marcin; Bertrand, Olivier

2010-10-01

Fy blood group antigens are carried by the Duffy antigen receptor for chemokines (DARC), a red cells receptor for Plasmodium vivax broadly implicated in human health and diseases. Recombinant VHHs, or nanobodies, the smallest intact antigen binding fragment derivative from the heavy chain-only antibodies present in camelids, were prepared from a dromedary immunized against DARC N-terminal extracellular domain and selected for DARC binding. A described VHH, CA52, does recognize native DARC on cells. It inhibits P. vivax invasion of erythrocytes and displaces interleukin-8 bound to DARC. The targeted epitope overlaps the well-defined DARC Fy6 epitope. K (D) of CA52-DARC equilibrium is sub-nanomolar, hence ideal to develop diagnostic or therapeutic compounds. Immunocapture by immobilized CA52 yielded highly purified DARC from engineered K562 cells. This first report on a VHH with specificity for a red blood cell protein exemplifies VHHs' potentialities to target, to purify, and to modulate the function of cellular markers.

Purification and characterization of enantioselective N-acetyl-β-Phe acylases from Burkholderia sp. AJ110349.

PubMed

Imabayashi, Yuki; Suzuki, Shun'ichi; Kawasaki, Hisashi; Nakamatsu, Tsuyoshi

2016-01-01

For the production of enantiopure β-amino acids, enantioselective resolution of N-acyl β-amino acids using acylases, especially those recognizing N-acetyl-β-amino acids, is one of the most attractive methods. Burkholderia sp. AJ110349 had been reported to exhibit either (R)- or (S)-enantiomer selective N-acetyl-β-Phe amidohydrolyzing activity, and in this study, both (R)- and (S)-enantioselective N-acetyl-β-Phe acylases were purified to be electrophoretically pure and determined the sequences, respectively. They were quite different in terms of enantioselectivities and in their amino acids sequences and molecular weights. Although both the purified acylases were confirmed to catalyze N-acetyl hydrolyzing activities, neither of them show sequence similarities to the N-acetyl-α-amino acid acylases reported thus far. Both (R)- and (S)-enantioselective N-acetyl-β-Phe acylase were expressed in Escherichia coli. Using these recombinant strains, enantiomerically pure (R)-β-Phe (>99% ee) and (S)-β-Phe (>99% ee) were obtained from the racemic substrate.

Cloning, expression, and purification of the virulence-associated protein D from Xylella fastidiosa.

PubMed

Catani, Cleide Ferreira; Azzoni, Adriano Rodrigues; Paula, Débora Pires; Tada, Susely Ferraz Siqueira; Rosselli, Luciana Kauer; de Souza, Anete Pereira; Yano, Tomomasa

2004-10-01

In this study, an efficient expression system, based on the pET32Xa/LIC vector, for producing a Xylella fastidiosa virulence-associated protein D, found to have a strong similarity to Riemerella anatipestifer and Actinobacillus actinomycetencomitans VapD protein, is presented. The protein has a molecular mass of 17.637 Da and a calculated pI of 5.49. The selected XFa0052 gene was cloned in the pET32Xa/LIC vector and the plasmid was transformed into Escherichia coli BL21 (DE3) strain at 37 degrees C, with an induction time of 2 h and 1 mM IPTG concentration. The protein present in the soluble fraction was purified by immobilized metal affinity chromatography (IMAC), and had its identity determined by mass spectrometry (MALDI-TOF) and N-terminal sequencing. The purified protein was found as a single band on SDS-PAGE and its correct folding was verified by circular dichroism spectroscopy.

Recombinant scFv antibodies against infectious pancreatic necrosis virus isolated by flow cytometry.

PubMed

Xu, Li-Ming; Zhao, Jing-Zhuang; Liu, Miao; Cao, Yong-Sheng; Yin, Jia-Sheng; Liu, Hong-Bai; Lu, Tongyan

2016-11-01

Infectious pancreatic necrosis is a significant disease of farmed salmonids in China. In this study, a single chain variable fragment (scFv) antibody library derived from rainbow trout (Oncorhynchus mykiss) and viral protein VP2 of a Chinese infectious pancreatic necrosis virus (IPNV) isolate ChRtm213 were co-expressed by a bacterial display technology. The library was subjected to three rounds of screening by flow cytometry (FCM) to select IPNV specific antibodies. Six antibody clones with different mean fluorescence intensities (MFI) were obtained by picking colonies at random. The antibody clones were expressed and purified. The purified IPNV-specific scFv antibodies were used successfully in Western blotting, enzyme linked immunosorbent assay (ELISA) and an immunofluorescence antibody test (IFAT). This method provides a high throughput means to screen an antibody library by flow cytometry, and isolate a panel of antibody that can be used as potential reagents for the detection and study of IPNV that are prevalent in China. Copyright © 2016 Elsevier B.V. All rights reserved.

Development of Metal-impregnated Single Walled Carbon Nanotubes for Toxic Gas Contaminant Control in Advanced Life Support Systems

NASA Technical Reports Server (NTRS)

Pisharody, Suresh A.; Fisher, John W.; Wignarajah, K.

2002-01-01

The success of physico-chemical waste processing and resource recovery technologies for life support application depends partly on the ability of gas clean-up systems to efficiently remove trace contaminants generated during the process with minimal use of expendables. Carbon nanotubes promise superior performance over conventional approaches to gas clean-up due to their ability to direct the selective uptake of gaseous species based on their controlled pore size, high surface area, ordered chemical structure that allows functionalization and their effectiveness also as catalyst support materials for toxic gas conversion. We present results and findings from a preliminary study on the effectiveness of metal impregnated single walled nanotubes as catalyst/catalyst support materials for toxic gas contaminate control. The study included the purification of single walled nanotubes, the catalyst impregnation of the purified nanotubes, the experimental characterization of the surface properties of purified single walled nanotubes and the characterization of physisorption and chemisorption of uptake molecules.

Purification, crystallization and preliminary X-ray diffraction analysis of the glyoxalase II from Leishmania infantum

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

Trincão, José; Sousa Silva, Marta; Barata, Lídia

2006-08-01

A glyoxalase II from L. infantum was cloned, purified and crystallized and its structure was solved by X-ray crystallography. In trypanosomatids, trypanothione replaces glutathione in all glutathione-dependent processes. Of the two enzymes involved in the glyoxalase pathway, glyoxalase I and glyoxalase II, the latter shows absolute specificity towards trypanothione thioester, making this enzyme an excellent model to understand the molecular basis of trypanothione binding. Cloned glyoxalase II from Leishmania infantum was overexpressed in Escherichia coli, purified and crystallized. Crystals belong to space group C222{sub 1} (unit-cell parameters a = 65.6, b = 88.3, c = 85.2 Å) and diffract beyondmore » 2.15 Å using synchrotron radiation. The structure was solved by molecular replacement using the human glyoxalase II structure as a search model. These results, together with future detailed kinetic characterization using lactoyltrypanothione, should shed light on the evolutionary selection of trypanothione instead of glutathione by trypano-somatids.« less

A high-throughput differential filtration assay to screen and select detergents for membrane proteins

PubMed Central

Vergis, James M.; Purdy, Michael D.; Wiener, Michael C.

2015-01-01

Structural studies on integral membrane proteins are routinely performed on protein–detergent complexes (PDCs) consisting of purified protein solubilized in a particular detergent. Of all the membrane protein crystal structures solved to date, a subset of only four detergents has been used in more than half of these structures. Unfortunately, many membrane proteins are not well behaved in these four detergents and/or fail to yield well-diffracting crystals. Identification of detergents that maintain the solubility and stability of a membrane protein is a critical step and can be a lengthy and “protein-expensive” process. We have developed an assay that characterizes the stability and size of membrane proteins exchanged into a panel of 94 commercially available and chemically diverse detergents. This differential filtration assay (DFA), using a set of filtered microplates, requires sub-milligram quantities of purified protein and small quantities of detergents and other reagents and is performed in its entirety in several hours. PMID:20667442

Substitution rate and natural selection in parvovirus B19

PubMed Central

Stamenković, Gorana G.; Ćirković, Valentina S.; Šiljić, Marina M.; Blagojević, Jelena V.; Knežević, Aleksandra M.; Joksić, Ivana D.; Stanojević, Maja P.

2016-01-01

The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection analyses in open reading frames ORF1 and ORF2, respectively, collected 1973–2012 and including 9 newly sequenced isolates from Serbia. Phylogenetic clustering assigned majority of studied isolates to G1A. Nucleotide substitution rate for total coding DNA was 1.03 (0.6–1.27) x 10−4 substitutions/site/year, with higher values for analyzed genome partitions. In spite of the highest evolutionary rate, VP2 codons were found to be under purifying selection with rare episodic positive selection, whereas codons under diversifying selection were found in the unique part of VP1, known to contain B19 immune epitopes important in persistent infection. Analyses of overlapping gene regions identified nucleotide positions under opposite selective pressure in different ORFs, suggesting complex evolutionary mechanisms of nucleotide changes in B19 viral genomes. PMID:27775080

Capture-SELEX: Selection of DNA Aptamers for Aminoglycoside Antibiotics

PubMed Central

2012-01-01

Small organic molecules are challenging targets for an aptamer selection using the SELEX technology (SELEX—Systematic Evolution of Ligans by EXponential enrichment). Often they are not suitable for immobilization on solid surfaces, which is a common procedure in known aptamer selection methods. The Capture-SELEX procedure allows the selection of DNA aptamers for solute targets. A special SELEX library was constructed with the aim to immobilize this library on magnetic beads or other surfaces. For this purpose a docking sequence was incorporated into the random region of the library enabling hybridization to a complementary oligo fixed on magnetic beads. Oligonucleotides of the library which exhibit high affinity to the target and a secondary structure fitting to the target are released from the beads for binding to the target during the aptamer selection process. The oligonucleotides of these binding complexes were amplified, purified, and immobilized via the docking sequence to the magnetic beads as the starting point of the following selection round. Based on this Capture-SELEX procedure, the successful DNA aptamer selection for the aminoglycoside antibiotic kanamycin A as a small molecule target is described. PMID:23326761

Parallel shifts in ecology and natural selection in an island lizard

PubMed Central

Calsbeek, Ryan; Buermann, Wolfgang; Smith, Thomas B

2009-01-01

Background Natural selection is a potent evolutionary force that shapes phenotypic variation to match ecological conditions. However, we know little about the year-to-year consistency of selection, or how inter-annual variation in ecology shapes adaptive landscapes and ultimately adaptive radiations. Here we combine remote sensing data, field experiments, and a four-year study of natural selection to show that changes in vegetation structure associated with a severe drought altered both habitat use and natural selection in the brown anole, Anolis sagrei. Results In natural populations, lizards increased their use of vegetation in wet years and this was correlated with selection on limb length but not body size. By contrast, a die-back of vegetation caused by drought was followed by reduced arboreality, selection on body size, and relaxed selection on limb length. With the return of the rains and recovery of vegetation, selection reverted back to pre-drought pattern of selection acting on limb length but not body size. To test for the impact of vegetation loss on natural selection during the drought, we experimentally removed vegetation on a separate study island in a naturally wet year. The experiment revealed similar inter-annual changes in selection on body size but not limb length. Conclusion Our results illustrate the dynamic nature of ecology driving natural selection on Anolis morphology and emphasize the importance of inter-annual environmental variation in shaping adaptive variation. In addition, results illustrate the utility of using remote sensing data to examine ecology's role in driving natural selection. PMID:19126226

Using music to change mood while driving.

PubMed

van der Zwaag, Marjolein D; Janssen, Joris H; Nass, Clifford; Westerink, Joyce H D M; Chowdhury, Shrestha; de Waard, Dick

2013-01-01

This study investigated whether gradual or abrupt music change towards more calming music is most effective in calming drivers during high-demand driving situations. Twenty-eight participants were subjected to two types of music change (gradual, abrupt) in a within-subject design. First, a relatively happy mood was induced with personally selected music during an eight-minute simulated high-demand drive. The drive then continued and the mood was changed either gradually or abruptly. Subjective results showed successful music mood induction irrespective of gradual or abrupt changes. The results further showed lower skin conductance (less arousal) and more facial corrugator muscle tension (more sadness) during the abrupt music change. Fewer accidents occurred during the abrupt music mood change. To conclude, the results support the abrupt way of changing music type to down-regulate one's mood: during high-demand driving, abrupt changes in music led to more physiological calmness and improved driving performance, and were thus safer and more effective. The current study shows that during high-demand drives, drivers are calmed more effectively using abrupt music changes compared to gradual music changes. This is illustrated by reductions in physiological arousal and improved driving behaviour. Hence, in-car music presentation can be used as a tool to improve driver's mood and behaviour.

Factors Influencing the Clinical Stratification of Suitability to Drive after Stroke: A Qualitative Study.

PubMed

Stapleton, Tadhg; Connolly, Deirdre; O'Neill, Desmond

2015-01-01

While a clinical pre-selection screening process for a stroke patient's suitability for driving has been acknowledged, little is known about the factors or processes influencing this screening typically conducted by clinicians practicing at a generalist level. This study explored this clinical stratification process through the use of semi-structured interviews with senior occupational therapists (n = 17) and stroke physicians (n = 7) using qualitative description methodology. The findings revealed a trichotomy stratification of stroke patients for driving in the clinical setting; those who are fit to drive, unfit to drive, and a "maybe" group who need more detailed assessment and observation. Factors that had a major influence on this clinical-based stratification of driving suitability were client's levels of awareness, insight, and impulsivity. A period of prolonged contact with the client was preferential to guide the stratification decision in order for clinicians to build a comprehensive picture of the person. A mix of assessment approaches including standardized assessment but with increased emphasis on naturalistic observation of functional performance underpinned the clinical stratification process. This study uncovers some of the factors and processes influencing the early clinical-based stratification of driving suitability after stroke, and highlights the contribution of the generalist practitioner in the assessment of fitness to drive continuum.

Drive Cycle Analysis, Measurement of Emissions and Fuel Consumption of a PHEV School Bus: Preprint

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

Barnitt, R.; Gonder, J.

The National Renewable Energy Laboratory (NREL) collected and analyzed real-world school bus drive cycle data and selected similar standard drive cycles for testing on a chassis dynamometer. NREL tested a first-generation plug-in hybrid electric vehicle (PHEV) school bus equipped with a 6.4L engine and an Enova PHEV drive system comprising a 25-kW/80 kW (continuous/peak) motor and a 370-volt lithium ion battery pack. A Bluebird 7.2L conventional school bus was also tested. Both vehicles were tested over three different drive cycles to capture a range of driving activity. PHEV fuel savings in charge-depleting (CD) mode ranged from slightly more than 30%more » to a little over 50%. However, the larger fuel savings lasted over a shorter driving distance, as the fully charged PHEV school bus would initially operate in CD mode for some distance, then in a transitional mode, and finally in a charge-sustaining (CS) mode for continued driving. The test results indicate that a PHEV school bus can achieve significant fuel savings during CD operation relative to a conventional bus. In CS mode, the tested bus showed small fuel savings and somewhat higher nitrogen oxide (NOx) emissions than the baseline comparison bus.« less

The impact of self-driving cars on existing transportation networks

NASA Astrophysics Data System (ADS)

Ji, Xiang

2018-04-01

In this paper, considering the usage of self-driving, I research the congestion problems of traffic networks from both macro and micro levels. Firstly, the macroscopic mathematical model is established using the Greenshields function, analytic hierarchy process and Monte Carlo simulation, where the congestion level is divided into five levels according to the average vehicle speed. The roads with an obvious congestion situation is investigated mainly and the traffic flow and topology of the roads are analyzed firstly. By processing the data, I propose a traffic congestion model. In the model, I assume that half of the non-self-driving cars only take the shortest route and the other half can choose the path randomly. While self-driving cars can obtain vehicle density data of each road and choose the path more reasonable. When the path traffic density exceeds specific value, it cannot be selected. To overcome the dimensional differences of data, I rate the paths by BORDA sorting. The Monte Carlo simulation of Cellular Automaton is used to obtain the negative feedback information of the density of the traffic network, where the vehicles are added into the road network one by one. I then analyze the influence of negative feedback information on path selection of intelligent cars. The conclusion is that the increase of the proportion of intelligent vehicles will make the road load more balanced, and the self-driving cars can avoid the peak and reduce the degree of road congestion. Combined with other models, the optimal self-driving ratio is about sixty-two percent. From the microscopic aspect, by using the single-lane traffic NS rule, another model is established to analyze the road Partition scheme. The self-driving traffic is more intelligent, and their cooperation can reduce the random deceleration probability. By the model, I get the different self-driving ratio of space-time distribution. I also simulate the case of making a lane separately for self-driving, compared to the former model. It is concluded that a single lane is more efficient in a certain interval. However, it is not recommended to offer a lane separately. However, the self-driving also faces the problem of hacker attacks and greater damage after fault. So, when self-driving ratio is higher than a certain value, the increase of traffic flow rate is small. In this article, that value is discussed, and the optimal proportion is determined. Finally, I give a nontechnical explanation of the problem.

Naturally occurring variation in tadpole morphology and performance linked to predator regime

Treesearch

James B. Johnson; Daniel Saenz; Cory K. Adams; Toby J. Hibbitts

2015-01-01

Divergent natural selection drives a considerable amount of the phenotypic and genetic variation observed in natural populations. For example, variation in the predator community can generate conflicting selection on behavioral, life-history, morphological, and performance traits. Differences in predator regime can subsequently increase phenotypic and genetic...

In vitro Fab display: a cell-free system for IgG discovery

PubMed Central

Stafford, Ryan L.; Matsumoto, Marissa L.; Yin, Gang; Cai, Qi; Fung, Juan Jose; Stephenson, Heather; Gill, Avinash; You, Monica; Lin, Shwu-Hwa; Wang, Willie D.; Masikat, Mary Rose; Li, Xiaofan; Penta, Kalyani; Steiner, Alex R.; Baliga, Ramesh; Murray, Christopher J.; Thanos, Christopher D.; Hallam, Trevor J.; Sato, Aaron K.

2014-01-01

Selection technologies such as ribosome display enable the rapid discovery of novel antibody fragments entirely in vitro. It has been assumed that the open nature of the cell-free reactions used in these technologies limits selections to single-chain protein fragments. We present a simple approach for the selection of multi-chain proteins, such as antibody Fab fragments, using ribosome display. Specifically, we show that a two-chain trastuzumab (Herceptin) Fab domain can be displayed in a format which tethers either the heavy or light chain to the ribosome while retaining functional antigen binding. Then, we constructed synthetic Fab HC and LC libraries and performed test selections against carcinoembryonic antigen (CEA) and vascular endothelial growth factor (VEGF). The Fab selection output was reformatted into full-length immunoglobulin Gs (IgGs) and directly expressed at high levels in an optimized cell-free system for immediate screening, purification and characterization. Several novel IgGs were identified using this cell-free platform that bind to purified CEA, CEA positive cells and VEGF. PMID:24586053

Isolation, purification and characterization of antimicrobial protein from seedlings of Bauhinia purpurea L.

PubMed

Sakthivel, Muthu; Palani, Perumal

2016-05-01

A novel antimicrobial protein was purified from the seedlings of Bauhinia purpurea by sequential procedures entailing ammonium sulfate precipitation, cation exchange chromatography, preparative native-PAGE and a yield of 2.7% was obtained from the crude extract. The purified antimicrobial protein appeared as a single protein band on SDS-PAGE with the molecular mass of 20.9 kDa. Purified antimicrobial protein exhibited a potent antimicrobial activity against both Gram-positive and Gram-negative bacteria. Analysis of the trypsin digested peptides of purified protein using the MALDI-TOF MS/MS resulted in the identification of 174 amino acids. The purified protein had an optimum of pH of 5.5 and was stable at 35 °C for exhibiting its maximal antibacterial activity. The addition of metal ions such as Mn(2+) and Ca(2+) to the purified protein enhanced the antimicrobial activity of purified protein. The MIC of purified protein against Bacillus cereus and Escherichia coli were 13 μg/ml and 15 μg/ml, respectively. The purified protein digested the peptidoglycan layer of bacteria which was visualized by TEM analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Human health and the water environment: using the DPSEEA framework to identify the driving forces of disease.

PubMed

Gentry-Shields, Jennifer; Bartram, Jamie

2014-01-15

There is a growing awareness of global forces that threaten human health via the water environment. A better understanding of the dynamic between human health and the water environment would enable prediction of the significant driving forces and effective strategies for coping with or preventing them. This report details the use of the Driving Force-Pressure-State-Exposure-Effect-Action (DPSEEA) framework to explore the linkage between water-related diseases and their significant driving forces. The DPSEEA frameworks indicate that a select group of driving forces, including population growth, agriculture, infrastructure (dams and irrigation), and climate change, is at the root cause of key global disease burdens. Construction of the DPSEEA frameworks also allows for the evaluation of public health interventions. Sanitation was found to be a widely applicable and effective intervention, targeting the driver/pressure linkage of most of the water-related diseases examined. Ultimately, the DPSEEA frameworks offer a platform for constituents in both the health and environmental fields to collaborate and commit to a common goal targeting the same driving forces. © 2013.

Distillation Brine Purification for Resource Recovery Applications

NASA Technical Reports Server (NTRS)

Wheeler, Raymond M.

2014-01-01

Wastewater processing systems for space generate residual brine that contains water and salts that could be recovered to life support consumables. The project assessed the use of ion-exchange resins to selectively remove salts from wastewater treatment brines. The resins were then regenerated for additional use. The intention would be to generate a Na/K and CI rich or purified brine that would then be processed into high value chemicals, such as acids, bases, and/or bleach.