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

Evolution of CRISPs associated with toxicoferan-reptilian venom and mammalian reproduction.

PubMed

Sunagar, Kartik; Johnson, Warren E; O'Brien, Stephen J; Vasconcelos, Vítor; Antunes, Agostinho

2012-07-01

Cysteine-rich secretory proteins (CRISPs) are glycoproteins found exclusively in vertebrates and have broad diversified functions. They are hypothesized to play important roles in mammalian reproduction and in reptilian venom, where they disrupt homeostasis of the prey through several mechanisms, including among others, blockage of cyclic nucleotide-gated and voltage-gated ion channels and inhibition of smooth muscle contraction. We evaluated the molecular evolution of CRISPs in toxicoferan reptiles at both nucleotide and protein levels relative to their nonvenomous mammalian homologs. We show that the evolution of CRISP gene in these reptiles is significantly influenced by positive selection and in snakes (ω = 3.84) more than in lizards (ω = 2.33), whereas mammalian CRISPs were under strong negative selection (CRISP1 = 0.55, CRISP2 = 0.40, and CRISP3 = 0.68). The use of ancestral sequence reconstruction, mapping of mutations on the three-dimensional structure, and detailed evaluation of selection pressures suggests that the toxicoferan CRISPs underwent accelerated evolution aided by strong positive selection and directional mutagenesis, whereas their mammalian homologs are constrained by negative selection. Gene and protein-level selection analyses identified 41 positively selected sites in snakes and 14 sites in lizards. Most of these sites are located on the molecular surface (nearly 76% in snakes and 79% in lizards), whereas the backbone of the protein retains a highly conserved structural scaffold. Nearly 46% of the positively selected sites occur in the cysteine-rich domain of the protein. This directional mutagenesis, where the hotspots of mutations are found on the molecular surface and functional domains of the protein, acts as a diversifying mechanism for the exquisite biological targeting of CRISPs in toxicoferan reptiles. Finally, our analyses suggest that the evolution of toxicoferan-CRISP venoms might have been influenced by the specific predatory mechanism employed by the organism. CRISPs in Elapidae, which mostly employ neurotoxins, have experienced less positive selection pressure (ω = 2.86) compared with the "nonvenomous" colubrids (ω = 4.10) that rely on grip and constriction to capture the prey, and the Viperidae, a lineage that mostly employs haemotoxins (ω = 4.19). Relatively lower omega estimates in Anguimorph lizards (ω = 2.33) than snakes (ω = 3.84) suggests that lizards probably depend more on pace and powerful jaws for predation than venom.

Signatures of selection among sex-determining alleles of the honey bee.

PubMed

Hasselmann, Martin; Beye, Martin

2004-04-06

Patterns of DNA polymorphisms are a primary tool for dissecting signatures of selection; however, the underlying selective forces are poorly understood for most genes. A classical example of diversifying selection is the complementary sex-determining locus that is found in the very large insect order Hymenoptera (bees, wasps, ants, and sawflies). The gene responsible for sex determination, the complementary sex determiner (csd), has been most recently identified in the honey bee. Females are heterozygous at this locus. Males result when there is only one functional allele present, as a result of either homozygosity (fertilized eggs) or, more commonly, hemizygosity (unfertilized eggs). The homozygotes, diploid males, do not reproduce and have zero fitness, which implies positive selection in favor of rare alleles. Large differences in csd cDNA sequences within and between four populations were found that fall into two major groups, types I and II. Type I consists of several allelic lineages that were maintained over an extended period, an indication of balancing selection. Diversifying selection has operated on several confined parts of the protein, as shown by an excess of nonsynonymous differences. Elevated sequence differences indicate another selected part near a repeat region. These findings have general implications about the understanding of both the function of the multiallelic mechanism and the adaptive processes on the level of nucleotide sequences. Moreover, the first csd sequence data are a notable basis for the avoidance of diploid males in bee selection programs by allele-assisted breeding.

Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity

PubMed Central

Sperschneider, Jana; Gardiner, Donald M.; Thatcher, Louise F.; Lyons, Rebecca; Singh, Karam B.; Manners, John M.; Taylor, Jennifer M.

2015-01-01

Pathogens and hosts are in an ongoing arms race and genes involved in host–pathogen interactions are likely to undergo diversifying selection. Fusarium plant pathogens have evolved diverse infection strategies, but how they interact with their hosts in the biotrophic infection stage remains puzzling. To address this, we analyzed the genomes of three Fusarium plant pathogens for genes that are under diversifying selection. We found a two-speed genome structure both on the chromosome and gene group level. Diversifying selection acts strongly on the dispensable chromosomes in Fusarium oxysporum f. sp. lycopersici and on distinct core chromosome regions in Fusarium graminearum, all of which have associations with virulence. Members of two gene groups evolve rapidly, namely those that encode proteins with an N-terminal [SG]-P-C-[KR]-P sequence motif and proteins that are conserved predominantly in pathogens. Specifically, 29 F. graminearum genes are rapidly evolving, in planta induced and encode secreted proteins, strongly pointing toward effector function. In summary, diversifying selection in Fusarium is strongly reflected as genomic footprints and can be used to predict a small gene set likely to be involved in host–pathogen interactions for experimental verification. PMID:25994930

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

Evolution of Antifreeze Protein Genes in the Diatom Genus Fragilariopsis: Evidence for Horizontal Gene Transfer, Gene Duplication and Episodic Diversifying Selection

PubMed Central

Sorhannus, Ulf

2011-01-01

Hypotheses about horizontal transfer of antifreeze protein genes to ice-living diatoms were addressed using two different statistical methods available in the program Prunier. The role of diversifying selection in driving the differentiation of a set of antifreeze protein genes in the diatom genus Fragilariopsis was also investigated. Four horizontal gene transfer events were identified. Two of these took place between two major eukaryote lineages, that is from the diatom Chaetoceros neogracile to the copepod Stephos longipes and from a basidiomycete clade to a monophyletic group, consisting of the diatom species Fragilariopsis curta and Fragilariopsis cylindrus. The remaining two events included transfers from an ascomycete lineage to the proteobacterium Stigmatella aurantiaca and from the proteobacterium Polaribacter irgensii to a group composed of 4 proteobacterium species. After the Fragilariopsis lineage acquired the antifreeze protein gene from the basidiomycetes, it duplicated and went through episodic evolution, characterized by strong positive selection acting on short segments of the branches in the tree. This selection pattern suggests that the paralogs differentiated functionally over relatively short time periods. Taken together, the results obtained here indicate that the group of antifreeze protein genes considered here have a complex evolutionary history. PMID:22253534

Positive selection of digestive Cys proteases in herbivorous Coleoptera.

PubMed

Vorster, Juan; Rasoolizadeh, Asieh; Goulet, Marie-Claire; Cloutier, Conrad; Sainsbury, Frank; Michaud, Dominique

2015-10-01

Positive selection is thought to contribute to the functional diversification of insect-inducible protease inhibitors in plants in response to selective pressures exerted by the digestive proteases of their herbivorous enemies. Here we assessed whether a reciprocal evolutionary process takes place on the insect side, and whether ingestion of a positively selected plant inhibitor may translate into a measurable rebalancing of midgut proteases in vivo. Midgut Cys proteases of herbivorous Coleoptera, including the major pest Colorado potato beetle (Leptinotarsa decemlineata), were first compared using a codon-based evolutionary model to look for the occurrence of hypervariable, positively selected amino acid sites among the tested sequences. Hypervariable sites were found, distributed within -or close to- amino acid regions interacting with Cys-type inhibitors of the plant cystatin protein family. A close examination of L. decemlineata sequences indicated a link between their assignment to protease functional families and amino acid identity at positively selected sites. A function-diversifying role for positive selection was further suggested empirically by in vitro protease assays and a shotgun proteomic analysis of L. decemlineata Cys proteases showing a differential rebalancing of protease functional family complements in larvae fed single variants of a model cystatin mutated at positively selected amino acid sites. These data confirm overall the occurrence of hypervariable, positively selected amino acid sites in herbivorous Coleoptera digestive Cys proteases. They also support the idea of an adaptive role for positive selection, useful to generate functionally diverse proteases in insect herbivores ingesting functionally diverse, rapidly evolving dietary cystatins. Copyright © 2015 Elsevier Ltd. All rights reserved.

Diversified models for portfolio selection based on uncertain semivariance

NASA Astrophysics Data System (ADS)

Chen, Lin; Peng, Jin; Zhang, Bo; Rosyida, Isnaini

2017-02-01

Since the financial markets are complex, sometimes the future security returns are represented mainly based on experts' estimations due to lack of historical data. This paper proposes a semivariance method for diversified portfolio selection, in which the security returns are given subjective to experts' estimations and depicted as uncertain variables. In the paper, three properties of the semivariance of uncertain variables are verified. Based on the concept of semivariance of uncertain variables, two types of mean-semivariance diversified models for uncertain portfolio selection are proposed. Since the models are complex, a hybrid intelligent algorithm which is based on 99-method and genetic algorithm is designed to solve the models. In this hybrid intelligent algorithm, 99-method is applied to compute the expected value and semivariance of uncertain variables, and genetic algorithm is employed to seek the best allocation plan for portfolio selection. At last, several numerical examples are presented to illustrate the modelling idea and the effectiveness of the algorithm.

Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

PubMed Central

Waman, Vaishali P.; Kolekar, Pandurang; Ramtirthkar, Mukund R.; Kale, Mohan M.

2016-01-01

Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae). There are four serotypes of Dengue Virus (DENV-1 to DENV-4), each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. Methods Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. Results DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. Discussion Complete genome-based analysis revealed that the worldwide population of DENV-2 strains is subdivided into fifteen lineages. The population structure of DENV-2 is spatiotemporal and is shaped by episodic positive selection and recombination. Intra-genotype diversity was observed in four genotypes (Asian/American, Asian I, cosmopolitan and sylvatic). Episodic positive selection on envelope and non-structural genes translates into antigenic diversity and appears to be responsible for emergence of strains/lineages in DENV-2 genotypes. Understanding of the genotype diversity and emerging lineages will be useful to design strategies for epidemiological surveillance and vaccine design. PMID:27635316

Signatures of Diversifying Selection in European Pig Breeds

PubMed Central

Wilkinson, Samantha; Lu, Zen H.; Megens, Hendrik-Jan; Archibald, Alan L.; Haley, Chris; Jackson, Ian J.; Groenen, Martien A. M.; Crooijmans, Richard P. M. A.; Ogden, Rob; Wiener, Pamela

2013-01-01

Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition. PMID:23637623

Employer Interest in Child Care Growing and Diversifying.

ERIC Educational Resources Information Center

Neugebauer, Roger

1993-01-01

Continuing employer interest in child care reflects the fact that child care is still a major concern for employees. Discusses trends related to the positive results of child care; the leading role of bigger companies; employers' concerns regarding equity, liability, and cost; a more diversified response to meeting employees' child-care needs; and…

Expression of Immunoglobulin Receptors with Distinctive Features Indicating Antigen Selection by Marginal Zone B Cells from Human Spleen

PubMed Central

Colombo, Monica; Cutrona, Giovanna; Reverberi, Daniele; Bruno, Silvia; Ghiotto, Fabio; Tenca, Claudya; Stamatopoulos, Kostas; Hadzidimitriou, Anastasia; Ceccarelli, Jenny; Salvi, Sandra; Boccardo, Simona; Calevo, Maria Grazia; De Santanna, Amleto; Truini, Mauro; Fais, Franco; Ferrarini, Manlio

2013-01-01

Marginal zone (MZ) B cells, identified as surface (s)IgMhighsIgDlowCD23low/−CD21+CD38− B cells, were purified from human spleens, and the features of their V(D)J gene rearrangements were investigated and compared with those of germinal center (GC), follicular mantle (FM) and switched memory (SM) B cells. Most MZ B cells were CD27+ and exhibited somatic hypermutations (SHM), although to a lower extent than SM B cells. Moreover, among MZ B-cell rearrangements, recurrent sequences were observed, some of which displayed intraclonal diversification. The same diversifying sequences were detected in very low numbers in GC and FM B cells and only when a highly sensitive, gene-specific polymerase chain reaction was used. This result indicates that MZ B cells could expand and diversify in situ and also suggested the presence of a number of activation-induced cytidine deaminase (AID)-expressing B cells in the MZ. The notion of antigen-driven expansion/selection in situ is further supported by the VH CDR3 features of MZ B cells with highly conserved amino acids at specific positions and by the finding of shared (“stereotyped”) sequences in two different spleens. Collectively, the data are consistent with the notion that MZ B cells are a special subset selected by in situ antigenic stimuli. PMID:23877718

Computational analysis and functional expression of ancestral copepod luciferase.

PubMed

Takenaka, Yasuhiro; Noda-Ogura, Akiko; Imanishi, Tadashi; Yamaguchi, Atsushi; Gojobori, Takashi; Shigeri, Yasushi

2013-10-10

We recently reported the cDNA sequences of 11 copepod luciferases from the superfamily Augaptiloidea in the order Calanoida. They were classified into two groups, Metridinidae and Heterorhabdidae/Lucicutiidae families, by phylogenetic analyses. To elucidate the evolutionary processes, we have now further isolated 12 copepod luciferases from Augaptiloidea species (Metridia asymmetrica, Metridia curticauda, Pleuromamma scutullata, Pleuromamma xiphias, Lucicutia ovaliformis and Heterorhabdus tanneri). Codon-based synonymous/nonsynonymous tests of positive selection for 25 identified copepod luciferases suggested that positive Darwinian selection operated in the evolution of Heterorhabdidae luciferases, whereas two types of Metridinidae luciferases had diversified via neutral mechanism. By in silico analysis of the decoded amino acid sequences of 25 copepod luciferases, we inferred two protein sequences as ancestral copepod luciferases. They were expressed in HEK293 cells where they exhibited notable luciferase activity both in intracellular lysates and cultured media, indicating that the luciferase activity was established before evolutionary diversification of these copepod species. © 2013.

The Contribution of the Self-Efficacy of Curriculum Development Team and Curriculum Document Quality to the Implementation of Diversified Curriculum in Indonesia

ERIC Educational Resources Information Center

Susilana, Rudi; Asra; Herlina

2014-01-01

The aim of this study is to describe how the self-efficacy of curriculum development team (CDT) and curriculum document quality contributed to the implementation of diversified curriculum in elementary schools. This research is a survey study using descriptive method. Schools were the unit of analysis while respondents selected from the schools…

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

Genetic evidence for contribution of human dispersal to the genetic diversity of EBA-175 in Plasmodium falciparum.

PubMed

Yasukochi, Yoshiki; Naka, Izumi; Patarapotikul, Jintana; Hananantachai, Hathairad; Ohashi, Jun

2015-08-01

The 175-kDa erythrocyte binding antigen (EBA-175) of Plasmodium falciparum plays a crucial role in merozoite invasion into human erythrocytes. EBA-175 is believed to have been under diversifying selection; however, there have been no studies investigating the effect of dispersal of humans out of Africa on the genetic variation of EBA-175 in P. falciparum. The PCR-direct sequencing was performed for a part of the eba-175 gene (regions II and III) using DNA samples obtained from Thai patients infected with P. falciparum. The divergence times for the P. falciparum eba-175 alleles were estimated assuming that P. falciparum/Plasmodium reichenowi divergence occurred 6 million years ago (MYA). To examine the possibility of diversifying selection, nonsynonymous and synonymous substitution rates for Plasmodium species were also estimated. A total of 32 eba-175 alleles were identified from 131 Thai P. falciparum isolates. Their estimated divergence time was 0.13-0.14 MYA, before the exodus of humans from Africa. A phylogenetic tree for a large sequence dataset of P. falciparum eba-175 alleles from across the world showed the presence of a basal Asian-specific cluster for all P. falciparum sequences. A markedly more nonsynonymous substitutions than synonymous substitutions in region II in P. falciparum was also detected, but not within Plasmodium species parasitizing African apes, suggesting that diversifying selection has acted specifically on P. falciparum eba-175. Plasmodium falciparum eba-175 genetic diversity appeared to increase following the exodus of Asian ancestors from Africa. Diversifying selection may have played an important role in the diversification of eba-175 allelic lineages. The present results suggest that the dispersals of humans out of Africa influenced significantly the molecular evolution of P. falciparum EBA-175.

Molecular adaptation within the coat protein-encoding gene of Tunisian almond isolates of Prunus necrotic ringspot virus.

PubMed

Boulila, Moncef; Ben Tiba, Sawssen; Jilani, Saoussen

2013-04-01

The sequence alignments of five Tunisian isolates of Prunus necrotic ringspot virus (PNRSV) were searched for evidence of recombination and diversifying selection. Since failing to account for recombination can elevate the false positive error rate in positive selection inference, a genetic algorithm (GARD) was used first and led to the detection of potential recombination events in the coat protein-encoding gene of that virus. The Recco algorithm confirmed these results by identifying, additionally, the potential recombinants. For neutrality testing and evaluation of nucleotide polymorphism in PNRSV CP gene, Tajima's D, and Fu and Li's D and F statistical tests were used. About selection inference, eight algorithms (SLAC, FEL, IFEL, REL, FUBAR, MEME, PARRIS, and GA branch) incorporated in HyPhy package were utilized to assess the selection pressure exerted on the expression of PNRSV capsid. Inferred phylogenies pointed out, in addition to the three classical groups (PE-5, PV-32, and PV-96), the delineation of a fourth cluster having the new proposed designation SW6, and a fifth clade comprising four Tunisian PNRSV isolates which underwent recombination and selective pressure and to which the name Tunisian outgroup was allocated.

Transcultural nursing as a global care humanizer, diversifier, and unifier.

PubMed

Leininger, M M

1997-01-01

Three dominant themes of transcultural nursing as a global humanizer, diversifier, and unifier are discussed in relation to their meaning and uses in education, practice, research and consultation. The presenter takes the position that these three dominant themes are essential and imperative to promote, transform, and maintain desired care outcomes which are beneficial, satisfying, and healthy for people of diverse and similar cultures. The three themes are discussed within Leininger's theory of Culture Care Diversity and Universality with focus on the modes of action and decision-making. The author encourages transcultural nurses to take leadership to be an active global humanizer, diversifier, and unifier and transform nursing and health care into the 21st century.

A diversified portfolio model of adaptability.

PubMed

Chandra, Siddharth; Leong, Frederick T L

2016-12-01

A new model of adaptability, the diversified portfolio model (DPM) of adaptability, is introduced. In the 1950s, Markowitz developed the financial portfolio model by demonstrating that investors could optimize the ratio of risk and return on their portfolios through risk diversification. The DPM integrates attractive features of a variety of models of adaptability, including Linville's self-complexity model, the risk and resilience model, and Bandura's social cognitive theory. The DPM draws on the concept of portfolio diversification, positing that diversified investment in multiple life experiences, life roles, and relationships promotes positive adaptation to life's challenges. The DPM provides a new integrative model of adaptability across the biopsychosocial levels of functioning. More importantly, the DPM addresses a gap in the literature by illuminating the antecedents of adaptive processes studied in a broad array of psychological models. The DPM is described in relation to the biopsychosocial model and propositions are offered regarding its utility in increasing adaptiveness. Recommendations for future research are also offered. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Evidence of recombination and positive selection in cetacean papillomaviruses.

PubMed

Robles-Sikisaka, Refugio; Rivera, Rebecca; Nollens, Hendrik H; St Leger, Judy; Durden, Wendy N; Stolen, Megan; Burchell, Jennifer; Wellehan, James F X

2012-06-05

Papillomaviruses (PVs) are small DNA viruses that have been associated with increased epithelial proliferation. Over one hundred PV types have been identified in humans; however, only three have been identified in bottlenose dolphins (Tursiops truncatus) to date. Using rolling circle amplification and degenerate PCR, we identified four novel PV genomes of bottlenose dolphins. TtPV4, TtPV5 and TtPV6 were identified in genital lesions while TtPV7 was identified in normal genital mucosa. Bayesian analysis of the full-length L1 genes found that TtPV4 and TtPV7 group within the Upsilonpapillomavirus genus while TtPV5 and TtPV6 group with Omikronpapillomavirus. However, analysis of the E1 gene did not distinguish these genera, implying that these genes may not share a common history, consistent with recombination. Recombination analyses identified several probable events. Signals of positive selection were found mostly in the E1 and E2 genes. Recombination and diversifying selection pressures constitute important driving forces of cetacean PV evolution. Copyright © 2012 Elsevier Inc. All rights reserved.

Evidence of recombination and positive selection in cetacean papillomaviruses

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

Robles-Sikisaka, Refugio, E-mail: refugio.robles1@gmail.com; Rivera, Rebecca, E-mail: RRivera@hswri.org; Nollens, Hendrik H., E-mail: Hendrik.Nollens@SeaWorld.com

2012-06-05

Papillomaviruses (PVs) are small DNA viruses that have been associated with increased epithelial proliferation. Over one hundred PV types have been identified in humans; however, only three have been identified in bottlenose dolphins (Tursiops truncatus) to date. Using rolling circle amplification and degenerate PCR, we identified four novel PV genomes of bottlenose dolphins. TtPV4, TtPV5 and TtPV6 were identified in genital lesions while TtPV7 was identified in normal genital mucosa. Bayesian analysis of the full-length L1 genes found that TtPV4 and TtPV7 group within the Upsilonpapillomavirus genus while TtPV5 and TtPV6 group with Omikronpapillomavirus. However, analysis of the E1 genemore » did not distinguish these genera, implying that these genes may not share a common history, consistent with recombination. Recombination analyses identified several probable events. Signals of positive selection were found mostly in the E1 and E2 genes. Recombination and diversifying selection pressures constitute important driving forces of cetacean PV evolution.« less

Diversifying selection and host adaptation in two endosymbiont genomes

PubMed Central

Brownlie, Jeremy C; Adamski, Marcin; Slatko, Barton; McGraw, Elizabeth A

2007-01-01

Background The endosymbiont Wolbachia pipientis infects a broad range of arthropod and filarial nematode hosts. These diverse associations form an attractive model for understanding host:symbiont coevolution. Wolbachia's ubiquity and ability to dramatically alter host reproductive biology also form the foundation of research strategies aimed at controlling insect pests and vector-borne disease. The Wolbachia strains that infect nematodes are phylogenetically distinct, strictly vertically transmitted, and required by their hosts for growth and reproduction. Insects in contrast form more fluid associations with Wolbachia. In these taxa, host populations are most often polymorphic for infection, horizontal transmission occurs between distantly related hosts, and direct fitness effects on hosts are mild. Despite extensive interest in the Wolbachia system for many years, relatively little is known about the molecular mechanisms that mediate its varied interactions with different hosts. We have compared the genomes of the Wolbachia that infect Drosophila melanogaster, wMel and the nematode Brugia malayi, wBm to that of an outgroup Anaplasma marginale to identify genes that have experienced diversifying selection in the Wolbachia lineages. The goal of the study was to identify likely molecular mechanisms of the symbiosis and to understand the nature of the diverse association across different hosts. Results The prevalence of selection was far greater in wMel than wBm. Genes contributing to DNA metabolism, cofactor biosynthesis, and secretion were positively selected in both lineages. In wMel there was a greater emphasis on DNA repair, cell division, protein stability, and cell envelope synthesis. Conclusion Secretion pathways and outer surface protein encoding genes are highly affected by selection in keeping with host:parasite theory. If evidence of selection on various cofactor molecules reflects possible provisioning, then both insect as well as nematode Wolbachia may be providing substances to hosts. Selection on cell envelope synthesis, DNA replication and repair machinery, heat shock, and two component switching suggest strategies insect Wolbachia may employ to cope with diverse host and intra-host environments. PMID:17470297

Studying the genetic basis of speciation in high gene flow marine invertebrates

PubMed Central

2016-01-01

A growing number of genes responsible for reproductive incompatibilities between species (barrier loci) exhibit the signals of positive selection. However, the possibility that genes experiencing positive selection diverge early in speciation and commonly cause reproductive incompatibilities has not been systematically investigated on a genome-wide scale. Here, I outline a research program for studying the genetic basis of speciation in broadcast spawning marine invertebrates that uses a priori genome-wide information on a large, unbiased sample of genes tested for positive selection. A targeted sequence capture approach is proposed that scores single-nucleotide polymorphisms (SNPs) in widely separated species populations at an early stage of allopatric divergence. The targeted capture of both coding and non-coding sequences enables SNPs to be characterized at known locations across the genome and at genes with known selective or neutral histories. The neutral coding and non-coding SNPs provide robust background distributions for identifying FST-outliers within genes that can, in principle, identify specific mutations experiencing diversifying selection. If natural hybridization occurs between species, the neutral coding and non-coding SNPs can provide a neutral admixture model for genomic clines analyses aimed at finding genes exhibiting strong blocks to introgression. Strongylocentrotid sea urchins are used as a model system to outline the approach but it can be used for any group that has a complete reference genome available. PMID:29491951

77 FR 35953 - Arts in Education National Program; Final Priority, Requirements, Definitions, and Selection...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-15

... diversified approaches to teaching and learning through the arts. Discussion: The funds available for this..., educational programming, and supporting systemic school reform. Final Selection Criteria: The Assistant Deputy... cumulative regulations; (3) In choosing among alternative regulatory approaches, select those approaches that...

The glycoprotein TRP36 of Ehrlichia sp. UFMG-EV and related cattle pathogen Ehrlichia sp. UFMT-BV evolved from a highly variable clade of E. canis under adaptive diversifying selection.

PubMed

Cabezas-Cruz, Alejandro; Valdés, James J; de la Fuente, José

2014-12-10

A new species of Ehrlichia, phylogenetically distant from E. ruminantium, was found in 2010 infecting cattle in Canada. In 2012 and 2013, we reported the in vitro propagation, molecular and ultrastructural characterization of Ehrlichia sp. UFMG-EV (E. mineirensis), a new species of Ehrlichia isolated from the haemolymph of Brazilian Rhipicephalus (Boophilus) microplus ticks. A new organism, named Ehrlichia sp. UFMT-BV, closely related to Ehrlichia sp. UFMG-EV, was recently described in Brazil and after experimental infection it was shown to be pathogenic for cattle. This new emerging clade of cattle Ehrlichia pathogens is closely related to E. canis. The major immunogenic Tandem Repeat Protein (TRP36; also known as gp36) is extensively used to characterize the genetic diversity of E. canis. Homologs of TRP36 were found in both Ehrlichia sp. UFMG-EV and Ehrlichia sp. UFMT-BV. Herein, we characterized the evolution of this new Ehrlichia clade using TRP36 sequences. Our working hypothesis is that Ehrlichia sp. UFMG-EV and related microorganisms evolved from a highly variable E. canis clade. In support of our hypothesis we found that Ehrlichia sp. UFMG-EV and Ehrlichia sp. UFMT-BV TRP36 evolved from a highly divergent and variable clade within E. canis and this clade evolved under episodic diversifying selection with a high proportion of sites under positive selection. Our results suggest that Ehrlichia sp. UFMG-EV and Ehrlichia sp. UFMT-BV evolved from a variable clade within E. canis.

Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans.

PubMed

Lee, Alexandra J; Das, Suman R; Wang, Wei; Fitzgerald, Theresa; Pickett, Brett E; Aevermann, Brian D; Topham, David J; Falsey, Ann R; Scheuermann, Richard H

2015-05-01

Although a large number of immune epitopes have been identified in the influenza A virus (IAV) hemagglutinin (HA) protein using various experimental systems, it is unclear which are involved in protective immunity to natural infection in humans. We developed a data mining approach analyzing natural H1N1 human isolates to identify HA protein regions that may be targeted by the human immune system and can predict the evolution of IAV. We identified 16 amino acid sites experiencing diversifying selection during the evolution of prepandemic seasonal H1N1 strains and found that 11 sites were located in experimentally determined B-cell/antibody (Ab) epitopes, including three distinct neutralizing Caton epitopes: Sa, Sb, and Ca2 [A. J. Caton, G. G. Brownlee, J. W. Yewdell, and W. Gerhard, Cell 31:417-427, 1982, http://dx.doi.org/10.1016/0092-8674(82)90135-0]. We predicted that these diversified epitope regions would be the targets of mutation as the 2009 H1N1 pandemic (pH1N1) lineage evolves in response to the development of population-level protective immunity in humans. Using a chi-squared goodness-of-fit test, we identified 10 amino acid sites that significantly differed between the pH1N1 isolates and isolates from the recent 2012-2013 and 2013-2014 influenza seasons. Three of these sites were located in the same diversified B-cell/Ab epitope regions as identified in the analysis of prepandemic sequences, including Sa and Sb. As predicted, hemagglutination inhibition (HI) assays using human sera from subjects vaccinated with the initial pH1N1 isolate demonstrated reduced reactivity against 2013-2014 isolates. Taken together, these results suggest that diversifying selection analysis can identify key immune epitopes responsible for protective immunity to influenza virus in humans and thereby predict virus evolution. The WHO estimates that approximately 5 to 10% of adults and 20 to 30% of children in the world are infected by influenza virus each year. While an adaptive immune response helps eliminate the virus following acute infection, the virus rapidly evolves to evade the established protective memory immune response, thus allowing for the regular seasonal cycles of influenza virus infection. The analytical approach described here, which combines an analysis of diversifying selection with an integration of immune epitope data, has allowed us to identify antigenic regions that contribute to protective immunity and are therefore the key targets of immune evasion by the virus. This information can be used to determine when sequence variations in seasonal influenza virus strains have affected regions responsible for protective immunity in order to decide when new vaccine formulations are warranted. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Gene conversion and positive selection driving the evolution of the Caenorhabditis ssp. ZIM/HIM-8 protein family.

PubMed

Liu, Qingpo

2009-03-01

In C. elegans, four C2H2 zinc-finger proteins (ZIM-1, ZIM-2, ZIM-3, and HIM-8), which are arranged in tandem, mediate chromosome-specific pairing and synapsis during meiosis. The zim/him-8 genes from three Caenorhabditis species were contrasted in an effort to investigate the mechanisms driving their evolution. Here it is shown that the preservation of higher degree of sequence similarity in the N-terminal portion, particularly in several regions within the second exon between paralogous zim genes (especially between zim-1 and zim-3), is due to independent interparalogue gene conversions. However, the evolutionary force is not uniformly strong across species. The present data reveal that more frequent gene conversion events have occurred in C. elegans, whereas only gene conversions between zim-1 and zim-3 are detected in C. remanei. Although gene conversions are predicted to be present among zim-1, zim-2, and zim-3 in C. briggsae, the conversion tracts between zim-1/zim-2 and zim-2/zim-3 are very short. Moreover, positive selection analysis was performed on the basis of the significantly discordant phylogenies reconstructed using the N- and C-terminal sequences, respectively. Several codon sites located in the regions that are supposed not to have experienced gene conversions are predicted to be under the influence of positive selection. In comparison, stronger positive selection has acted on the C-terminal region relative to the N-terminal region. Thus, the zim/him-8 genes that evolve concertedly have also been shown to undergo adaptive diversifying selection.

Short human occupations in the Middle Palaeolithic level i of the Abric Romani rock-shelter (Capellades, Barcelona, Spain)

USGS Publications Warehouse

Vallerdu, J.; Allue, E.; Bischoff, J.L.; Caceres, I.; Carbonell, E.; Cebria, A.; Garcia-Anton, D.; Huguet, R.; Ibanez, N.; Martinez, K.; Pasto, I.; Rosell, J.; Saladie, P.; Vaquero, Manola

2005-01-01

The small occupation surfaces and restricted provisioning strategies suggest short settlements in the Abric Romani. This shorter occupation model complements the longer diversified provisioning strategy recorded in both small and medium-sized occupied surfaces. The selection of precise elements for transport and the possible deferred consumption in the diversified provision strategy suggest an individual supply. In this respect, Neanderthal occupations in the Romani rock-shelter show a direct relation to: 1) hunting strategic resources; 2) high, linear mobility.

TEACHING TECHNIQUES--SELECTED READINGS.

ERIC Educational Resources Information Center

Modern Language Association of America, New York, NY.

A DIVERSIFIED SELECTION OF ARTICLES CONTAINING DESCRIPTIONS AND EXPLANATIONS OF TEACHING TECHNIQUES, PUBLISHED FROM 1961 TO 1967, IS PROVIDED IN THIS PACKET. INCLUDED ARE--(1) "TOWARD BETTER CLASSROOM TEACHING" (GREW), (2) "GOOD TEACHING PRACTICES--A SURVEY OF HIGH SCHOOL FL CLASSES" (HAMLIN AND OTHERS), (3) "LISTENING COMPREHENSION" (RIVERS), (4)…

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.

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.

Proposing a Comprehensive Model for Identifying Teaching Candidates

ERIC Educational Resources Information Center

Bowles, Terry; Hattie, John; Dinham, Stephen; Scull, Janet; Clinton, Janet

2014-01-01

Teacher education in universities continues to diversify in the twenty-first century. Just as course offerings, course delivery, staffing and the teaching/research mix varies extensively from university to university so does the procedure for pre-service teacher selection. Various factors bear on selection procedures and practices however few…

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

PubMed Central

Pilot, M; Greco, C; vonHoldt, B M; Jędrzejewska, B; Randi, E; Jędrzejewski, W; Sidorovich, V E; Ostrander, E A; Wayne, R K

2014-01-01

Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability. PMID:24346500

Stags, Hawks, and Doves: Social Evolution Theory and Individual Variation in Cooperation.

PubMed

Van Cleve, Jeremy

2017-09-01

One of the triumphs of evolutionary biology is the discovery of robust mechanisms that promote the evolution of cooperative behaviors even when cooperation reduces the fertility or survival of cooperators. These mechanisms include, kin selection, reciprocity, and direct benefits to cooperation that are often nonlinear. Though they have been extensively studied separately, investigating the joint action of these mechanisms has been more difficult. Moreover, how these mechanisms shape variation in cooperation is not well known. Such variation is crucial for understanding the evolution of behavioral syndromes and animal personality. Here, I use the tools of kin selection and evolutionary game theory to build a framework that integrates these mechanisms for pairwise social interactions. Using relatedness as a measure of the strength of kin selection, responsiveness as a measure of reciprocity, and synergy as a measure of payoff nonlinearity, I show how different combinations of these three parameters produce directional selection for or against cooperation or variation in levels of cooperation via stabilizing or diversifying selection. Moreover, each of these outcomes maps uniquely to one of four classic games from evolutionary game theory, which means that modulating relatedness, responsiveness, and synergy effectively transforms the payoff matrix from one the evolutionary game to another. Assuming that cooperation exacts a fertility cost on cooperators and provides a fertility benefit to social partners, a prisoner's dilemma game and directional selection against cooperation occur when relatedness and responsiveness are low and synergy is not too positive. Enough positive synergy in these conditions generates a stag-hunt game and diversifying selection. High levels of relatedness or responsiveness turn cooperation from a fitness cost into a fitness benefit, which produces a mutualism game and directional selection for cooperation when synergy is not too negative. Sufficiently negative synergy in this case creates a hawk-dove game and stabilizing selection for cooperation. I extend the results with relatedness and synergy to social groups and show that how group size changes the effect of relatedness and synergy on selection for cooperation depends on how the per capita benefit of cooperation changes with group size. Together, these results provide a general framework with which to generate comparative predictions that can be tested using quantitative genetic techniques and experimental techniques that manipulate investment in cooperation. These predictions will help us understand both interspecific variation in cooperation as well as within-population and within-group variation in cooperation related to behavioral syndromes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Evolutionary divergence of mitochondrial genomes in two Tetranychus species distributed across different climates.

PubMed

Sun, J-T; Jin, P-Y; Hoffmann, A A; Duan, X-Z; Dai, J; Hu, G; Xue, X-F; Hong, X-Y

2018-05-24

There is increasing evidence that mitochondrial genomes (mitogenomes) can be under selection, whereas the selective regimes shaping mitogenome evolution remain largely unclear. To test for mitochondrial genome evolution in relation to the climate adaptation, we explored mtDNA variation in two spider mite (Tetranychus) species, which distribute across different climates. We sequenced 26 complete mitogenomes of T. truncatus which occurs in both warm and cold regions, and 9 complete mitogenomes of T. pueraricola which is only restricted in warm regions. Patterns of evolution in the two species mitogenomes were compared through a series of d N /d S methods and physicochemical profiles of amino acid replacements. We found that (1) the mitogenomes of both species were under widespread purifying selection. (2) Elevated directional adaptive selection was observed in the T. truncatus mitogenome, perhaps linked to the cold climates adaptation of T. truncatus. (3) The strength of selection varied across genes, and diversifying positive selection detected on ND4 and ATP6 pointed to their crucial roles during adaptation to different climatic conditions. This study gained insight into the mitogenome evolution in relation to the climate adaptation. This article is protected by copyright. All rights reserved. © 2018 The Royal Entomological Society.

Both Epistasis and Diversifying Selection Drive the Structural Evolution of the Ebola Virus Glycoprotein Mucin-Like Domain.

PubMed

Ibeh, Neke; Nshogozabahizi, Jean Claude; Aris-Brosou, Stéphane

2016-06-01

Throughout the last 3 decades, Ebola virus (EBOV) outbreaks have been confined to isolated areas within Central Africa; however, the 2014 variant reached unprecedented transmission and mortality rates. While the outbreak was still under way, it was reported that the variant leading up to this outbreak evolved faster than previous EBOV variants, but evidence for diversifying selection was undetermined. Here, we test this selection hypothesis and show that while previous EBOV outbreaks were preceded by bursts of diversification, evidence for site-specific diversifying selection during the emergence of the 2014 EBOV clade is weak. However, we show strong evidence supporting an interplay between selection and correlated evolution (epistasis), particularly in the mucin-like domain (MLD) of the EBOV glycoprotein. By reconstructing ancestral structures of the MLD, we further propose a structural mechanism explaining how the substitutions that accumulated between 1918 and 1969 distorted the MLD, while more recent epistatic substitutions restored part of the structure, with the most recent substitution being adaptive. We suggest that it is this complex interplay between weak selection, epistasis, and structural constraints that has shaped the evolution of the 2014 EBOV variant. The role that selection plays in the emergence of viral epidemics remains debated, particularly in the context of the 2014 EBOV outbreak. Most critically, should such evidence exist, it is generally unclear how this relates to function and increased virulence. Here, we show that the viral lineage leading up to the 2014 outbreak underwent a complex interplay between selection and correlated evolution (epistasis) in a protein region that is critical for immune evasion. We then reconstructed the three-dimensional structure of this domain and showed that the initial mutations in this lineage deformed the structure, while subsequent mutations restored part of the structure. Along this mutational path, the first and last mutations were adaptive, while the intervening ones were epistatic. Altogether, we provide a mechanistic model that explains how selection and epistasis acted on the structural constraints that materialized during the 2014 EBOV outbreak. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Plasmodium relictum infection and MHC diversity in the house sparrow (Passer domesticus)

PubMed Central

Loiseau, Claire; Zoorob, Rima; Robert, Alexandre; Chastel, Olivier; Julliard, Romain; Sorci, Gabriele

2011-01-01

Antagonistic coevolution between hosts and parasites has been proposed as a mechanism maintaining genetic diversity in both host and parasite populations. In particular, the high level of genetic diversity usually observed at the major histocompatibility complex (MHC) is generally thought to be maintained by parasite-driven selection. Among the possible ways through which parasites can maintain MHC diversity, diversifying selection has received relatively less attention. This hypothesis is based on the idea that parasites exert spatially variable selection pressures because of heterogeneity in parasite genetic structure, abundance or virulence. Variable selection pressures should select for different host allelic lineages resulting in population-specific associations between MHC alleles and risk of infection. In this study, we took advantage of a large survey of avian malaria in 13 populations of the house sparrow (Passer domesticus) to test this hypothesis. We found that (i) several MHC alleles were either associated with increased or decreased risk to be infected with Plasmodium relictum, (ii) the effects were population specific, and (iii) some alleles had antagonistic effects across populations. Overall, these results support the hypothesis that diversifying selection in space can maintain MHC variation and suggest a pattern of local adaptation where MHC alleles are selected at the local host population level. PMID:20943698

Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast.

PubMed

Herrera, C M; Pozo, M I; Bazaga, P

2011-11-01

Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights into the ecological and genetic correlates of clonality, and into the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using amplified fragment length polymorphism (AFLP) markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by amova (Φ(st)  = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparts to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality. © 2011 Blackwell Publishing Ltd.

The future of discovery chemistry: quo vadis? Academic to industrial--the maturation of medicinal chemistry to chemical biology.

PubMed

Hoffmann, Torsten; Bishop, Cheryl

2010-04-01

At Roche, we set out to think about the future role of medicinal chemistry in drug discovery in a project involving both Roche internal stakeholders and external experts in drug discovery chemistry. To derive a coherent strategy, selected scientists were asked to take extreme positions and to derive two orthogonal strategic options: chemistry as the traditional mainstream science and chemistry as the central entrepreneurial science. We believe today's role of medicinal chemistry in industry has remained too narrow. To provide the innovation that industry requires, medicinal chemistry must play its part and diversify at pace with our increasing understanding of chemical biology and network pharmacology. 2010 Elsevier Ltd. All rights reserved.

Variation and evolution of male sex combs in Drosophila: nature of selection response and theories of genetic variation for sexual traits.

PubMed

Ahuja, Abha; Singh, Rama S

2008-05-01

We investigated the genetic architecture of variation in male sex comb bristle number, a rapidly evolving secondary sexual character of Drosophila. Twenty-four generations of divergent artificial selection for sex comb bristle number in a heterogeneous population of Drosophila melanogaster resulted in a significant response that was more pronounced in the direction of low bristle numbers. We observed a strong positive correlated response to selection in the corresponding female transverse bristle row. The correlated response in male abdominal and sternopleural bristle numbers, on the other hand, did not follow the same pattern as sex comb bristle number differences between selection lines. Relaxation-of-selection experiments along with mate choice and fecundity assays using the selection lines developed demonstrated the action of stabilizing selection on sex comb bristle number. Our results show (1) substantial genetic variation underlying sex comb bristle number variation; (2) a weak relationship between the sex comb and developmentally related, non-sex bristle systems; and (3) that sexual selection may be a driving force in sex comb evolution, indicating the potential of sex combs to diversify rapidly during population differentiation and speciation. We discuss the implications of these results for theories of genetic variation in display and nondisplay male sex traits.

Iodine(III)-Mediated Selective Intermolecular C-H Amination for the Chemical Diversification of Tryptamines.

PubMed

Bosnidou, Alexandra E; Millán, Alba; Ceballos, Javier; Martínez, Claudio; Muñiz, Kilian

2016-08-05

Defined hypervalent iodine reagents of the general structure PhI[N(SO2R)(SO2R')]2 promote the selective direct C-H-amination of the indole core of various tryptamines. Starting from a general C2-amination strategy, subsequent transformations enable a variety of site-selective functionalizations, which proceed with noteworthy high chemoselectivity and provide an overall access to structurally diversified products.

Selection and optimization of hits from a high-throughput phenotypic screen against Trypanosoma cruzi.

PubMed

Keenan, Martine; Alexander, Paul W; Chaplin, Jason H; Abbott, Michael J; Diao, Hugo; Wang, Zhisen; Best, Wayne M; Perez, Catherine J; Cornwall, Scott M J; Keatley, Sarah K; Thompson, R C Andrew; Charman, Susan A; White, Karen L; Ryan, Eileen; Chen, Gong; Ioset, Jean-Robert; von Geldern, Thomas W; Chatelain, Eric

2013-10-01

Inhibitors of Trypanosoma cruzi with novel mechanisms of action are urgently required to diversify the current clinical and preclinical pipelines. Increasing the number and diversity of hits available for assessment at the beginning of the discovery process will help to achieve this aim. We report the evaluation of multiple hits generated from a high-throughput screen to identify inhibitors of T. cruzi and from these studies the discovery of two novel series currently in lead optimization. Lead compounds from these series potently and selectively inhibit growth of T. cruzi in vitro and the most advanced compound is orally active in a subchronic mouse model of T. cruzi infection. High-throughput screening of novel compound collections has an important role to play in diversifying the trypanosomatid drug discovery portfolio. A new T. cruzi inhibitor series with good drug-like properties and promising in vivo efficacy has been identified through this process.

Contrasting evolutionary histories of MHC class I and class II loci in grouse—Effects of selection and gene conversion

USGS Publications Warehouse

Minias, Piotr; Bateson, Zachary W.; Whittingham, Linda A.; Johnson, Jeff A.; Oyler-McCance, Sara J.; Dunn, Peter O.

2016-01-01

Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.

Contrasting evolutionary histories of MHC class I and class II loci in grouse—effects of selection and gene conversion

PubMed Central

Minias, P; Bateson, Z W; Whittingham, L A; Johnson, J A; Oyler-McCance, S; Dunn, P O

2016-01-01

Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens. PMID:26860199

A Comprehensive Systems Biology Approach to Studying Zika Virus.

PubMed

May, Meghan; Relich, Ryan F

2016-01-01

Zika virus (ZIKV) is responsible for an ongoing and intensifying epidemic in the Western Hemisphere. We examined the complete predicted proteomes, glycomes, and selectomes of 33 ZIKV strains representing temporally diverse members of the African lineage, the Asian lineage, and the current outbreak in the Americas. Derivation of the complete selectome is an 'omics' approach to identify distinct evolutionary pressures acting on different features of an organism. Employment of the M8 model did not show evidence of global diversifying selection acting on the ZIKV polyprotein; however, a mixed effect model of evolution showed strong evidence (P<0.05) for episodic diversifying selection acting on specific sites. Single nucleotide polymorphisms (SNPs) were predictably frequent across strains relative to the derived consensus sequence. None of the 9 published detection procedures utilize targets that share 100% identity across the 33 strains examined, indicating that ZIKV escape from molecular detection is predictable. The predicted O-linked glycome showed marked diversity across strains; however, the N-linked glycome was highly stable. All Asian and American strains examined were predicted to include glycosylation of E protein ASN154, a modification proposed to mediate neurotropism, whereas the modification was not predicted for African strains. SNP diversity, episodic diversifying selection, and differential glycosylation, particularly of ASN154, may have major biological implications for ZIKV disease. Taken together, the systems biology perspective of ZIKV indicates: a.) The recently emergent Asian/American N-glycotype is mediating the new and emerging neuropathogenic potential of ZIKV; and b.) further divergence at specific sites is predictable as endemnicity is established in the Americas.

Discovery of melanocortin ligands via a double simultaneous substitution strategy based on the Ac-His-DPhe-Arg-Trp-NH2 template.

PubMed

Todorovic, Aleksandar; Lensing, Cody J; Holder, Jerry Ryan; Scott, Joseph W; Sorensen, Nicholas B; Haskell-Luevano, Carrie

2018-05-21

The melanocortin system regulates an array of diverse physiological functions including pigmentation, feeding behavior, energy homeostasis, cardiovascular regulation, sexual function, and steroidogenesis. Endogenous melanocortin agonist ligands all possess the minimal messaging tetrapeptide sequence His-Phe-Arg-Trp. Based on this endogenous sequence, the Ac-His1-DPhe2-Arg3-Trp4-NH 2 tetrapeptide has previously been shown to be a useful scaffold when utilizing traditional positional scanning approaches to modify activity at the various melanocortin receptors (MC1-5R). The study reported herein was undertaken to evaluate a double simultaneous substitution strategy as an approach to further diversify the Ac-His1-DPhe2-Arg3-Trp4-NH 2 tetrapeptide with concurrent introduction of natural and unnatural amino acids at positions 1, 2, or 4 as well as an octanoyl residue at the N-terminus. The designed library includes the following combinations: (A) double simultaneous substitution at capping group position (Ac) together with position 1, 2, or 4, (B) double simultaneous substitution at position 1 and 2, (C) double simultaneous substitution at position 1 and 4, and (D) double simultaneous substitution at position 2 and 4. Several lead ligands with unique pharmacologies were discovered in the current study including antagonists targeting the neuronal mMC3R with minimal agonist activity and ligands with selective profiles for the various melanocortin subtypes. The results suggest that the double simultaneous substitution strategy is a suitable approach in altering melanocortin receptor potency, selectivity, or converting agonists into antagonists and vice versa.

Capsid coding region diversity of re-emerging lineage C foot-and-mouth disease virus serotype Asia1 from India.

PubMed

Subramaniam, Saravanan; Mohapatra, Jajati K; Das, Biswajit; Sharma, Gaurav K; Biswal, Jitendra K; Mahajan, Sonalika; Misri, Jyoti; Dash, Bana B; Pattnaik, Bramhadev

2015-07-01

Foot-and-mouth disease virus (FMDV) serotype Asia1 was first reported in India in 1951, where three major genetic lineages (B, C and D) of this serotype have been described until now. In this study, the capsid protein coding region of serotype Asia1 viruses (n = 99) from India were analyzed, giving importance to the viruses circulating since 2007. All of the isolates (n = 50) recovered during 2007-2013 were found to group within the re-emerging cluster of lineage C (designated as sublineage C(R)). The evolutionary rate of sublineage C(R) was estimated to be slightly higher than that of the serotype as a whole, and the time of the most recent common ancestor for this cluster was estimated to be approximately 2001. In comparison to the older isolates of lineage C (1993-2001), the re-emerging viruses showed variation at eight amino acid positions, including substitutions at the antigenically critical residues VP279 and VP2131. However, no direct correlation was found between sequence variations and antigenic relationships. The number of codons under positive selection and the nature of the selection pressure varied widely among the structural proteins, implying a heterogeneous pattern of evolution in serotype Asia1. While episodic diversifying selection appears to play a major role in shaping the evolution of VP1 and VP3, selection pressure acting on codons of VP2 is largely pervasive. Further, episodic positive selection appears to be responsible for the early diversification of lineage C. Recombination events identified in the structural protein coding region indicates its probable role in adaptive evolution of serotype Asia1 viruses.

Genomic data for 78 chickens from 14 populations

PubMed Central

Li, Diyan; Che, Tiandong; Chen, Binlong; Tian, Shilin; Zhou, Xuming; Zhang, Guolong; Li, Miao; Gaur, Uma; Li, Yan; Luo, Majing; Zhang, Long; Xu, Zhongxian; Zhao, Xiaoling; Yin, Huadong; Wang, Yan; Jin, Long; Tang, Qianzi; Xu, Huailiang; Yang, Mingyao; Zhou, Rongjia; Li, Ruiqiang

2017-01-01

Abstract Background: Since the domestication of the red jungle fowls (Gallus gallus; dating back to ∼10 000 B.P.) in Asia, domestic chickens (Gallus gallus domesticus) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production, and skin color. Population genomic variations through diversifying selection have not been fully investigated. Findings: The whole genomes of 78 domestic chickens were sequenced to an average of 18-fold coverage for each bird. By combining this data with publicly available genomes of five wild red jungle fowls and eight Xishuangbanna game fowls, we conducted a comprehensive comparative genomics analysis of 91 chickens from 17 populations. After aligning ∼21.30 gigabases (Gb) of high-quality data from each individual to the reference chicken genome, we identified ∼6.44 million (M) single nucleotide polymorphisms (SNPs) for each population. These SNPs included 1.10 M novel SNPs in 17 populations that were absent in the current chicken dbSNP (Build 145) entries. Conclusions: The current data is important for population genetics and further studies in chickens and will serve as a valuable resource for investigating diversifying selection and candidate genes for selective breeding in chickens. PMID:28431039

Grumman Takes Initiative

ERIC Educational Resources Information Center

Gilmore, A. W.

1970-01-01

Grumman Company has attempted to counter their acute shortage of engineers with diversified experience by establishing the Engineering Professional Development Program (EPDP). Selected engineers participate in an evening scholarship program, assignments to various sections within the company, and in-house seminars and programs to prepare them for…

Improving dietary diversity of school adolescents through school based nutrition education and home gardening in Jimma Zone: Quasi-experimental design.

PubMed

Tamiru, Dessalegn; Argaw, Alemayehu; Gerbaba, Mulusew; Nigussie, Aderajew; Ayana, Girmay; Belachew, Tefera

2016-12-01

The purpose of this operational study was to assess the effectiveness school-based health and nutrition intervention supported with backyard gardening on the dietary diversity among school adolescents. A total of 1000 school adolescents from 10 to 19years were selected randomly. The intervention involved peer-led behavior change communication and health promotion through school media and health clubs. Data were collected at baseline, midline and end-line using structured questionnaires. Multivariable logistic regression analyses were used to determine the independent effect of interventions. There was a significant increment of proportion of school children consuming diversified diet among the intervention group from 34.8% at baseline through 65.6% at midline to 74.7% at the end-line (p<0.001). Among control group, there was no change from midline (49.4%) to endline (48.8%), though there was a change from baseline (32.1%) to midline (49.4%). A significant difference of dietary diversity intake was observed between intervention and control groups at midline (F=5.64, p=0.042) and endline (F=5.85, p<0.001) survey. Being in the intervention school (OR=2.55 [1.55, 3.50]), being a boy (OR=1.75 [1.91, 2.56]) and having farmer mothers (OR=2.58 [1.01, 6.87]) were independent positive predictors of a diversified diet intake. However, having a mother who attended secondary schools were inversely associated (OR=0.25 [0.06, 0.97]) with consuming a diversified diet. Findings of this study demonstrated that there was a significant improvement in dietary diversity of adolescents in intervention schools. The results imply that school based nutrition education should be a part of comprehensive school health programs to reach students and potentially their families. Copyright © 2016 Elsevier Ltd. All rights reserved.

Probing a 2-aminobenzimidazole library for binding to RNA internal loops via two-dimensional combinatorial screening.

PubMed

Velagapudi, Sai Pradeep; Pushechnikov, Alexei; Labuda, Lucas P; French, Jonathan M; Disney, Matthew D

2012-11-16

There are many potential RNA drug targets in bacterial, viral, and human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA-ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. In an effort to better understand RNA-ligand interactions, we diversified the 2-aminobenzimidazole core (2AB) and probed the resulting library for binding to a library of RNA internal loops. We chose the 2AB core for these studies because it is a privileged scaffold for binding RNA based on previous reports. These studies identified that N-methyl pyrrolidine, imidazole, and propylamine diversity elements at the R1 position increase binding to internal loops; variability at the R2 position is well tolerated. The preferred RNA loop space was also determined for five ligands using a statistical approach and identified trends that lead to selective recognition.

Diversifying and correlational selection on behavior toward conspecific and heterospecific competitors in brook stickleback (Culaea inconstans)

PubMed Central

Peiman, Kathryn S; Robinson, Beren W

2012-01-01

Behaviors toward heterospecifics and conspecifics may be correlated because of shared mechanisms of expression in both social contexts (nonadaptive covariation) or because correlational selection favors adaptive covariation. We evaluated these hypotheses by comparing behavior toward conspecifics and heterospecifics in brook stickleback (Culaea inconstans) from three populations sympatric with and three allopatric from a competitor, the ninespine stickleback (Pungitius pungitius). Behavioral traits were classified into three multivariate components: overt aggression, sociability, and activity. The correlation of behavior between social contexts for both overt aggression and activity varied among populations in a way unrelated to sympatry with ninespine stickleback, while mean aggression was reduced in sympatry. Correlations in allopatric populations suggest that overt aggression and activity may genetically covary between social contexts for nonadaptive reasons. Sociability was rarely correlated in allopatry but was consistently correlated in sympatry despite reduced mean sociability, suggesting that correlational selection may favor a sociability syndrome in brook stickleback when they coexist with ninespine stickleback. Thus, interspecific competition may impose diversifying selection on behavior among populations, although the causes of correlated behavior toward conspecifics and heterospecifics and whether it can evolve in one social context independent of the other may depend on the type of behavior. PMID:23139874

5 CFR 2634.1003 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... means: (1) An obligation of the United States; or (2) A diversified investment fund. A diversified investment fund is a diversified mutual fund or diversified unit investment trust, as defined in 5 CFR 2640...

5 CFR 2634.1003 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... means: (1) An obligation of the United States; or (2) A diversified investment fund. A diversified investment fund is a diversified mutual fund or diversified unit investment trust, as defined in 5 CFR 2640...

An Interview with David Florio.

ERIC Educational Resources Information Center

Educational Evaluation and Policy Analysis, 1981

1981-01-01

American Educational Research Association's (AERA) lobbyist in Washington promotes educational research as a positive resource for educators. He acts to influence governmental policies which affect research. AERA represents a diversified membership by supporting a broad portfolio of government investments in educational research. AERA never takes…

How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes.

PubMed

Chen, Shanyuan; Gomes, Rui; Costa, Vânia; Santos, Pedro; Charneca, Rui; Zhang, Ya-ping; Liu, Xue-hong; Wang, Shao-qing; Bento, Pedro; Nunes, Jose-Luis; Buzgó, József; Varga, Gyula; Anton, István; Zsolnai, Attila; Beja-Pereira, Albano

2013-10-01

The coexistence of wild boars and domestic pigs across Eurasia makes it feasible to conduct comparative genetic or genomic analyses for addressing how genetically different a domestic species is from its wild ancestor. To test whether there are differences in patterns of genetic variability between wild and domestic pigs at immunity-related genes and to detect outlier loci putatively under selection that may underlie differences in immune responses, here we analyzed 54 single-nucleotide polymorphisms (SNPs) of 19 immunity-related candidate genes on 11 autosomes in three pairs of wild boar and domestic pig populations from China, Iberian Peninsula, and Hungary. Our results showed no statistically significant differences in allele frequency and heterozygosity across SNPs between three pairs of wild and domestic populations. This observation was more likely due to the widespread and long-lasting gene flow between wild boars and domestic pigs across Eurasia. In addition, we detected eight coding SNPs from six genes as outliers being under selection consistently by three outlier tests (BayeScan2.1, FDIST2, and Arlequin3.5). Among four non-synonymous outlier SNPs, one from TLR4 gene was identified as being subject to positive (diversifying) selection and three each from CD36, IFNW1, and IL1B genes were suggested as under balancing selection. All of these four non-synonymous variants were predicted as being benign by PolyPhen-2. Our results were supported by other independent lines of evidence for positive selection or balancing selection acting on these four immune genes (CD36, IFNW1, IL1B, and TLR4). Our study showed an example applying a candidate gene approach to identify functionally important mutations (i.e., outlier loci) in wild and domestic pigs for subsequent functional experiments.

The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus.

PubMed

Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne

2014-01-01

Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a QST/FST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (QST) was compared with divergence at eight neutral microsatellite loci (FST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had QST values significantly lower than FST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (QST>FST). Estimates of heritability were high for all traits (means ranging between 0.55-0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits.

Preparing Future Professors: A Cross-Institution Mentoring Program

ERIC Educational Resources Information Center

Reis, Richard; Strage, Amy; Summit, Jennifer

2014-01-01

According to these authors, special effort is required to diversify the professional perspectives and experiences of graduate students from highly selective private institutions, who may be seen as having less commitment to teaching than their counterparts from public institutions and little experience of students with a wide range of backgrounds,…

5 CFR 6801.103 - Prohibited financial interests.

Code of Federal Regulations, 2011 CFR

2011-01-01

... ownership or operation of banks, thrifts or securities firms. (2) Mutual funds. A publicly traded or publicly available mutual fund or other collective investment fund if: (i) The fund does not have a stated... fund or their selection. (3) Pension plans. A widely held, diversified pension or other retirement fund...

5 CFR 6801.103 - Prohibited financial interests.

Code of Federal Regulations, 2010 CFR

2010-01-01

... ownership or operation of banks, thrifts or securities firms. (2) Mutual funds. A publicly traded or publicly available mutual fund or other collective investment fund if: (i) The fund does not have a stated... fund or their selection. (3) Pension plans. A widely held, diversified pension or other retirement fund...

Detection of genetic diversity and selection at the coding region of the melanocortin receptor 1 (MC1R) gene in Tibetan pigs and Landrace pigs.

PubMed

Liu, Rui; Jin, Long; Long, Keren; Chai, Jie; Ma, Jideng; Tang, Qianzi; Tian, Shilin; Hu, Yaodong; Lin, Ling; Wang, Xun; Jiang, Anan; Li, Xuewei; Li, Mingzhou

2016-01-10

Domestication and subsequent selective pressures have produced a large variety of pig coat colors in different regions and breeds. The melanocortin 1 receptor (MC1R) gene plays a crucial role in determining coat color of mammals. Here, we investigated genetic diversity and selection at the coding region of the porcine melanocortin receptor 1 (MC1R) in Tibetan pigs and Landrace pigs. By contrast, genetic variability was much lower in Landrace pigs than in Tibetan pigs. Meanwhile, haplotype analysis showed that Tibetan pigs possessed shared haplotypes, suggesting a possibility of recent introgression event by way of crossbreeding with neighboring domestic pigs or shared ancestral polymorphism. Additionally, we detected positive selection at the MC1R in both Tibetan pigs and Landrace pigs through the dN/dS analysis. These findings suggested that novel phenotypic change (dark coat color) caused by novel mutations may help Tibetan pigs against intensive solar ultraviolet (UV) radiation and camouflage in wild environment, whereas white coat color in Landrace were intentionally selected by human after domestication. Furthermore, both the phylogenetic analysis and the network analysis provided clues that MC1R in Asian and European wild boars may have initially experienced different selective pressures, and MC1R alleles diversified in modern domesticated pigs. Copyright © 2015 Elsevier B.V. All rights reserved.

Rapid evolution of PARP genes suggests a broad role for ADP-ribosylation in host-virus conflicts.

PubMed

Daugherty, Matthew D; Young, Janet M; Kerns, Julie A; Malik, Harmit S

2014-01-01

Post-translational protein modifications such as phosphorylation and ubiquitinylation are common molecular targets of conflict between viruses and their hosts. However, the role of other post-translational modifications, such as ADP-ribosylation, in host-virus interactions is less well characterized. ADP-ribosylation is carried out by proteins encoded by the PARP (also called ARTD) gene family. The majority of the 17 human PARP genes are poorly characterized. However, one PARP protein, PARP13/ZAP, has broad antiviral activity and has evolved under positive (diversifying) selection in primates. Such evolution is typical of domains that are locked in antagonistic 'arms races' with viral factors. To identify additional PARP genes that may be involved in host-virus interactions, we performed evolutionary analyses on all primate PARP genes to search for signatures of rapid evolution. Contrary to expectations that most PARP genes are involved in 'housekeeping' functions, we found that nearly one-third of PARP genes are evolving under strong recurrent positive selection. We identified a >300 amino acid disordered region of PARP4, a component of cytoplasmic vault structures, to be rapidly evolving in several mammalian lineages, suggesting this region serves as an important host-pathogen specificity interface. We also found positive selection of PARP9, 14 and 15, the only three human genes that contain both PARP domains and macrodomains. Macrodomains uniquely recognize, and in some cases can reverse, protein mono-ADP-ribosylation, and we observed strong signatures of recurrent positive selection throughout the macro-PARP macrodomains. Furthermore, PARP14 and PARP15 have undergone repeated rounds of gene birth and loss during vertebrate evolution, consistent with recurrent gene innovation. Together with previous studies that implicated several PARPs in immunity, as well as those that demonstrated a role for virally encoded macrodomains in host immune evasion, our evolutionary analyses suggest that addition, recognition and removal of ADP-ribosylation is a critical, underappreciated currency in host-virus conflicts.

Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts

PubMed Central

Daugherty, Matthew D.; Young, Janet M.; Kerns, Julie A.; Malik, Harmit S.

2014-01-01

Post-translational protein modifications such as phosphorylation and ubiquitinylation are common molecular targets of conflict between viruses and their hosts. However, the role of other post-translational modifications, such as ADP-ribosylation, in host-virus interactions is less well characterized. ADP-ribosylation is carried out by proteins encoded by the PARP (also called ARTD) gene family. The majority of the 17 human PARP genes are poorly characterized. However, one PARP protein, PARP13/ZAP, has broad antiviral activity and has evolved under positive (diversifying) selection in primates. Such evolution is typical of domains that are locked in antagonistic ‘arms races’ with viral factors. To identify additional PARP genes that may be involved in host-virus interactions, we performed evolutionary analyses on all primate PARP genes to search for signatures of rapid evolution. Contrary to expectations that most PARP genes are involved in ‘housekeeping’ functions, we found that nearly one-third of PARP genes are evolving under strong recurrent positive selection. We identified a >300 amino acid disordered region of PARP4, a component of cytoplasmic vault structures, to be rapidly evolving in several mammalian lineages, suggesting this region serves as an important host-pathogen specificity interface. We also found positive selection of PARP9, 14 and 15, the only three human genes that contain both PARP domains and macrodomains. Macrodomains uniquely recognize, and in some cases can reverse, protein mono-ADP-ribosylation, and we observed strong signatures of recurrent positive selection throughout the macro-PARP macrodomains. Furthermore, PARP14 and PARP15 have undergone repeated rounds of gene birth and loss during vertebrate evolution, consistent with recurrent gene innovation. Together with previous studies that implicated several PARPs in immunity, as well as those that demonstrated a role for virally encoded macrodomains in host immune evasion, our evolutionary analyses suggest that addition, recognition and removal of ADP-ribosylation is a critical, underappreciated currency in host-virus conflicts. PMID:24875882

Eukaryotic ribosome display with in situ DNA recovery.

PubMed

He, Mingyue; Edwards, Bryan M; Kastelic, Damjana; Taussig, Michael J

2012-01-01

Ribosome display is a cell-free display technology for in vitro selection and optimisation of proteins from large diversified libraries. It operates through the formation of stable protein-ribosome-mRNA (PRM) complexes and selection of ligand-binding proteins, followed by DNA recovery from the selected genetic information. Both prokaryotic and eukaryotic ribosome display systems have been developed. In this chapter, we describe the eukaryotic rabbit reticulocyte method in which a distinct in situ single-primer RT-PCR procedure is used to recover DNA from the selected PRM complexes without the need for prior disruption of the ribosome.

Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian.

PubMed

Cortázar-Chinarro, Maria; Lattenkamp, Ella Z; Meyer-Lucht, Yvonne; Luquet, Emilien; Laurila, Anssi; Höglund, Jacob

2017-08-14

Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. Using outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.

Diversifying mechanisms in the on-farm evolution of crop mixtures.

PubMed

Thomas, Mathieu; Thépot, Stéphanie; Galic, Nathalie; Jouanne-Pin, Sophie; Remoué, Carine; Goldringer, Isabelle

2015-06-01

While modern agriculture relies on genetic homogeneity, diversifying practices associated with seed exchange and seed recycling may allow crops to adapt to their environment. This socio-genetic model is an original experimental evolution design referred to as on-farm dynamic management of crop diversity. Investigating such model can help in understanding how evolutionary mechanisms shape crop diversity submitted to diverse agro-environments. We studied a French farmer-led initiative where a mixture of four wheat landraces called 'Mélange de Touselles' (MDT) was created and circulated within a farmers' network. The 15 sampled MDT subpopulations were simultaneously submitted to diverse environments (e.g. altitude, rainfall) and diverse farmers' practices (e.g. field size, sowing and harvesting date). Twenty-one space-time samples of 80 individuals each were genotyped using 17 microsatellite markers and characterized for their heading date in a 'common-garden' experiment. Gene polymorphism was studied using four markers located in earliness genes. An original network-based approach was developed to depict the particular and complex genetic structure of the landraces composing the mixture. Rapid differentiation among populations within the mixture was detected, larger at the phenotypic and gene levels than at the neutral genetic level, indicating potential divergent selection. We identified two interacting selection processes: variation in the mixture component frequencies, and evolution of within-variety diversity, that shaped the standing variability available within the mixture. These results confirmed that diversifying practices and environments maintain genetic diversity and allow for crop evolution in the context of global change. Including concrete measurements of farmers' practices is critical to disentangle crop evolution processes. © 2015 John Wiley & Sons Ltd.

Three-Fingered RAVERs: Rapid Accumulation of Variations in Exposed Residues of Snake Venom Toxins

PubMed Central

Sunagar, Kartik; Jackson, Timothy N. W.; Undheim, Eivind A. B.; Ali, Syed. A.; Antunes, Agostinho; Fry, Bryan G.

2013-01-01

Three-finger toxins (3FTx) represent one of the most abundantly secreted and potently toxic components of colubrid (Colubridae), elapid (Elapidae) and psammophid (Psammophiinae subfamily of the Lamprophidae) snake venom arsenal. Despite their conserved structural similarity, they perform a diversity of biological functions. Although they are theorised to undergo adaptive evolution, the underlying diversification mechanisms remain elusive. Here, we report the molecular evolution of different 3FTx functional forms and show that positively selected point mutations have driven the rapid evolution and diversification of 3FTx. These diversification events not only correlate with the evolution of advanced venom delivery systems (VDS) in Caenophidia, but in particular the explosive diversification of the clade subsequent to the evolution of a high pressure, hollow-fanged VDS in elapids, highlighting the significant role of these toxins in the evolution of advanced snakes. We show that Type I, II and III α-neurotoxins have evolved with extreme rapidity under the influence of positive selection. We also show that novel Oxyuranus/Pseudonaja Type II forms lacking the apotypic loop-2 stabilising cysteine doublet characteristic of Type II forms are not phylogenetically basal in relation to other Type IIs as previously thought, but are the result of secondary loss of these apotypic cysteines on at least three separate occasions. Not all 3FTxs have evolved rapidly: κ-neurotoxins, which form non-covalently associated heterodimers, have experienced a relatively weaker influence of diversifying selection; while cytotoxic 3FTx, with their functional sites, dispersed over 40% of the molecular surface, have been extremely constrained by negative selection. We show that the a previous theory of 3FTx molecular evolution (termed ASSET) is evolutionarily implausible and cannot account for the considerable variation observed in very short segments of 3FTx. Instead, we propose a theory of Rapid Accumulation of Variations in Exposed Residues (RAVER) to illustrate the significance of point mutations, guided by focal mutagenesis and positive selection in the evolution and diversification of 3FTx. PMID:24253238

Co-evolutionary interactions between host resistance and pathogen avirulence genes in rice-Magnaporthe oryzae pathosystem.

PubMed

Singh, Pankaj Kumar; Ray, Soham; Thakur, Shallu; Rathour, Rajeev; Sharma, Vinay; Sharma, Tilak Raj

2018-06-01

Rice and Magnaporthe oryzae constitutes an ideal pathosystem for studying host-pathogen interaction in cereals crops. There are two alternative hypotheses, viz. Arms race and Trench warfare, which explain the co-evolutionary dynamics of hosts and pathogens which are under continuous confrontation. Arms race proposes that both R- and Avr- genes of host and pathogen, respectively, undergo positive selection. Alternatively, trench warfare suggests that either R- or Avr- gene in the pathosystem is under balanced selection intending to stabilize the genetic advantage gained over the opposition. Here, we made an attempt to test the above-stated hypotheses in rice-M. oryzae pathosystem at loci of three R-Avr gene pairs, Piz-t-AvrPiz-t, Pi54-AvrPi54 and Pita-AvrPita using allele mining approach. Allele mining is an efficient way to capture allelic variants existing in the population and to study the selective forces imposed on the variants during evolution. Results of nucleotide diversity, neutrality statistics and phylogenetic analyses reveal that Piz-t, Pi54 and AvrPita are diversified and under positive selection at their corresponding loci, while their counterparts, AvrPiz-t, AvrPi54 and Pita are conserved and under balancing selection, in nature. These results imply that rice-M. oryzae populations are engaged in a trench warfare at least at the three R/Avr loci studied. It is a maiden attempt to study the co-evolution of three R-Avr gene pairs in this pathosystem. Knowledge gained from this study will help in understanding the evolutionary dynamics of host-pathogen interaction in a better way and will also aid in developing new durable blast resistant rice varieties in future. Copyright © 2018 Elsevier Inc. All rights reserved.

Diversifying the STEM Pipeline

ERIC Educational Resources Information Center

Boelter, Christina; Link, Tanja C.; Perry, Brea L.; Leukefeld, Carl

2015-01-01

Middle school students from low-income and minority backgrounds (n = 166) were targeted to participate in a 2-year, intensive, hands-on science and technology intervention to increase their interest in biomedical and health sciences. Qualitative student responses collected during the 2nd year of participation revealed positive attitudes toward the…

AQUATIC PLANT SPECIATION AFFECTED BY DIVERSIFYING SELECTION OF ORGANELLE DNA REGIONS(1).

PubMed

Kato, Syou; Misawa, Kazuharu; Takahashi, Fumio; Sakayama, Hidetoshi; Sano, Satomi; Kosuge, Keiko; Kasai, Fumie; Watanabe, Makoto M; Tanaka, Jiro; Nozaki, Hisayoshi

2011-10-01

Many of the genes that control photosynthesis are carried in the chloroplast. These genes differ among species. However, evidence has yet to be reported revealing the involvement of organelle genes in the initial stages of plant speciation. To elucidate the molecular basis of aquatic plant speciation, we focused on the unique plant species Chara braunii C. C. Gmel. that inhabits both shallow and deep freshwater habitats and exhibits habitat-based dimorphism of chloroplast DNA (cpDNA). Here, we examined the "shallow" and "deep" subpopulations of C. braunii using two nuclear DNA (nDNA) markers and cpDNA. Genetic differentiation between the two subpopulations was measured in both nDNA and cpDNA regions, although phylogenetic analyses suggested nuclear gene flow between subpopulations. Neutrality tests based on Tajima's D demonstrated diversifying selection acting on organelle DNA regions. Furthermore, both "shallow" and "deep" haplotypes of cpDNA detected in cultures originating from bottom soils of three deep environments suggested that migration of oospores (dormant zygotes) between the two habitats occurs irrespective of the complete habitat-based dimorphism of cpDNA from field-collected vegetative thalli. Therefore, the two subpopulations are highly selected by their different aquatic habitats and show prezygotic isolation, which represents an initial process of speciation affected by ecologically based divergent selection of organelle genes. © 2011 Phycological Society of America.

78 FR 70610 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Filing of Proposed Rule Change Relating...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-26

...-traded futures contracts, options on futures contracts and swap agreements. Generally, derivatives are... to invest in derivative instruments, such as options contracts, futures contracts and swap agreements... derivatives will allow the Fund to selectively add diversifying sources of return from selling options. Option...

White Clinical Psychology Trainees' Views on Racial Equity within Programme Selection in South Africa

ERIC Educational Resources Information Center

Traub, Craig M.; Swartz, Leslie

2013-01-01

The issue of diversity in both physical and epistemological access to programmes in higher education is an important concern worldwide. In South Africa, as elsewhere, access to professional clinical psychology training programmes is extremely competitive, and there is an important imperative to diversify the student profile. Perspectives of black…

Grouped fuzzy SVM with EM-based partition of sample space for clustered microcalcification detection.

PubMed

Wang, Huiya; Feng, Jun; Wang, Hongyu

2017-07-20

Detection of clustered microcalcification (MC) from mammograms plays essential roles in computer-aided diagnosis for early stage breast cancer. To tackle problems associated with the diversity of data structures of MC lesions and the variability of normal breast tissues, multi-pattern sample space learning is required. In this paper, a novel grouped fuzzy Support Vector Machine (SVM) algorithm with sample space partition based on Expectation-Maximization (EM) (called G-FSVM) is proposed for clustered MC detection. The diversified pattern of training data is partitioned into several groups based on EM algorithm. Then a series of fuzzy SVM are integrated for classification with each group of samples from the MC lesions and normal breast tissues. From DDSM database, a total of 1,064 suspicious regions are selected from 239 mammography, and the measurement of Accuracy, True Positive Rate (TPR), False Positive Rate (FPR) and EVL = TPR* 1-FPR are 0.82, 0.78, 0.14 and 0.72, respectively. The proposed method incorporates the merits of fuzzy SVM and multi-pattern sample space learning, decomposing the MC detection problem into serial simple two-class classification. Experimental results from synthetic data and DDSM database demonstrate that our integrated classification framework reduces the false positive rate significantly while maintaining the true positive rate.

Ancient Diversification of Three-Finger Toxins in Micrurus Coral Snakes.

PubMed

Dashevsky, Daniel; Fry, Bryan G

2018-01-01

Coral snakes, most notably the genus Micrurus, are the only terrestrial elapid snakes in the Americas. Elapid venoms are generally known for their potent neurotoxicity which is usually caused by Three-Finger Toxin (3FTx) proteins. These toxins can have a wide array of functions that have been characterized from the venom of other elapids. We examined publicly available sequences from Micrurus 3FTx to show that they belong to 8 monophyletic clades that diverged as deep in the 3FTx phylogenetic tree as the other clades with characterized functions. Functional residues from previously characterized clades of 3FTx are not well conserved in most of the Micrurus toxin clades. We also analyzed the patterns of selection on these toxins and find that they have been diversifying at different rates, with some having undergone extreme diversifying selection. This suggests that Micrurus 3FTx may contain a previously underappreciated functional diversity that has implications for the clinical outcomes of bite victims, the evolution and ecology of the genus, as well as the potential for biodiscovery efforts focusing on these toxins.

Characterization of the hrpZ gene from Pseudomonas syringae pv. maculicola M2.

PubMed

Álvarez-Mejía, César; Rodríguez-Ríos, Dalia; Hernández-Guzmán, Gustavo; López-Ramírez, Varinia; Valenzuela-Soto, Humberto; Marsch, Rodolfo

2015-01-01

Pseudomonas syringae pv. maculicola is a natural pathogen of members of the Brassicaceae plant family. Using a transposon-based mutagenesis strategy in Pseudomonas syringaepv. maculicola M2 (PsmM2), we conducted a genetic screen to identify mutants that were capable of growing in M9 medium supplemented with a crude extract from the leaves of Arabidopsis thaliana. A mutant containing a transposon insertion in the hrpZ gene (PsmMut8) was unable to infect adult plants from Arabidopsis thaliana or Brassica oleracea, suggesting a loss of pathogenicity. The promotorless cat reporter present in the gene trap was expressed if PsmMut8 was grown in minimal medium (M9) supplemented with the leaf extract but not if grown in normal rich medium (KB). We conducted phylogenetic analysis using hrpAZB genes, showing the classical 5-clade distribution, and nucleotide diversity analysis, showing the putative position for selective pressure in this operon. Our results indicate that the hrpAZB operon from Pseudomonas syringaepv. maculicola M2 is necessary for its pathogenicity and that its diversity would be under host-mediated diversifying selection.

Characterization of the hrpZ gene from Pseudomonas syringae pv. maculicolaM2

PubMed Central

Álvarez-Mejía, César; Rodríguez-Ríos, Dalia; Hernández-Guzmán, Gustavo; López-Ramírez, Varinia; Valenzuela-Soto, Humberto; Marsch, Rodolfo

2015-01-01

Pseudomonas syringae pv. maculicola is a natural pathogen of members of the Brassicaceae plant family. Using a transposon-based mutagenesis strategy in Pseudomonas syringaepv. maculicola M2 (PsmM2), we conducted a genetic screen to identify mutants that were capable of growing in M9 medium supplemented with a crude extract from the leaves of Arabidopsis thaliana. A mutant containing a transposon insertion in the hrpZ gene (PsmMut8) was unable to infect adult plants from Arabidopsis thaliana or Brassica oleracea, suggesting a loss of pathogenicity. The promotorless cat reporter present in the gene trap was expressed if PsmMut8 was grown in minimal medium (M9) supplemented with the leaf extract but not if grown in normal rich medium (KB). We conducted phylogenetic analysis using hrpAZB genes, showing the classical 5-clade distribution, and nucleotide diversity analysis, showing the putative position for selective pressure in this operon. Our results indicate that the hrpAZB operon from Pseudomonas syringaepv. maculicola M2 is necessary for its pathogenicity and that its diversity would be under host-mediated diversifying selection. PMID:26413080

12 CFR 583.11 - Diversified savings and loan holding company.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Diversified savings and loan holding company... DEFINITIONS FOR REGULATIONS AFFECTING SAVINGS AND LOAN HOLDING COMPANIES § 583.11 Diversified savings and loan holding company. The term diversified savings and loan holding company means any savings and loan holding...

Probing a 2-Aminobenzimidazole Library for Binding to RNA Internal Loops via Two-Dimensional Combinatorial Screening

PubMed Central

Velegapudi, Sai Pradeep; Pushechnikov, Alexei; Labuda, Lucas P.; French, Jonathan M.; Disney, Matthew D.

2012-01-01

There are many potential RNA drug targets in bacterial, viral, and the human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA-ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. In an effort to better understand RNA-ligand interactions, we diversified the 2-aminobenzimidazole core (2AB) and probed the resulting library for binding to a library of RNA internal loops. We chose the 2AB core for these studies because it is a privileged scaffold for binding RNA based on previous reports. These studies identified that N-methyl pyrrolidine, imidazole, and propylamine diversity elements at the R1 position increase binding to internal loops; variability at the R2 position is well tolerated. The preferred RNA loop space was also determined for five ligands using a statistical approach and identified trends that lead to selective recognition. PMID:22958065

Assortative sociality, limited dispersal, infectious disease and the genesis of the global pattern of religion diversity

PubMed Central

Fincher, Corey L; Thornhill, Randy

2008-01-01

Why are religions far more numerous in the tropics compared with the temperate areas? We propose, as an answer, that more religions have emerged and are maintained in the tropics because, through localized coevolutionary races with hosts, infectious diseases select for three anticontagion behaviours: in-group assortative sociality; out-group avoidance; and limited dispersal. These behaviours, in turn, create intergroup boundaries that effectively fractionate, isolate and diversify an original culture leading to the genesis of two or more groups from one. Religion is one aspect of a group's culture that undergoes this process. If this argument is correct then, across the globe, religion diversity should correlate positively with infectious disease diversity, reflecting an evolutionary history of antagonistic coevolution between parasites and hosts and subsequent religion genesis. We present evidence that supports this model: for a global sample of traditional societies, societal range size is reduced in areas with more pathogens compared with areas with few pathogens, and in contemporary countries religion diversity is positively related to two measures of parasite stress. PMID:18664438

Deep sequencing of the Trypanosoma cruzi GP63 surface proteases reveals diversity and diversifying selection among chronic and congenital Chagas disease patients.

PubMed

Llewellyn, Martin S; Messenger, Louisa A; Luquetti, Alejandro O; Garcia, Lineth; Torrico, Faustino; Tavares, Suelene B N; Cheaib, Bachar; Derome, Nicolas; Delepine, Marc; Baulard, Céline; Deleuze, Jean-Francois; Sauer, Sascha; Miles, Michael A

2015-04-01

Chagas disease results from infection with the diploid protozoan parasite Trypanosoma cruzi. T. cruzi is highly genetically diverse, and multiclonal infections in individual hosts are common, but little studied. In this study, we explore T. cruzi infection multiclonality in the context of age, sex and clinical profile among a cohort of chronic patients, as well as paired congenital cases from Cochabamba, Bolivia and Goias, Brazil using amplicon deep sequencing technology. A 450bp fragment of the trypomastigote TcGP63I surface protease gene was amplified and sequenced across 70 chronic and 22 congenital cases on the Illumina MiSeq platform. In addition, a second, mitochondrial target--ND5--was sequenced across the same cohort of cases. Several million reads were generated, and sequencing read depths were normalized within patient cohorts (Goias chronic, n = 43, Goias congenital n = 2, Bolivia chronic, n = 27; Bolivia congenital, n = 20), Among chronic cases, analyses of variance indicated no clear correlation between intra-host sequence diversity and age, sex or symptoms, while principal coordinate analyses showed no clustering by symptoms between patients. Between congenital pairs, we found evidence for the transmission of multiple sequence types from mother to infant, as well as widespread instances of novel genotypes in infants. Finally, non-synonymous to synonymous (dn:ds) nucleotide substitution ratios among sequences of TcGP63Ia and TcGP63Ib subfamilies within each cohort provided powerful evidence of strong diversifying selection at this locus. Our results shed light on the diversity of parasite DTUs within each patient, as well as the extent to which parasite strains pass between mother and foetus in congenital cases. Although we were unable to find any evidence that parasite diversity accumulates with age in our study cohorts, putative diversifying selection within members of the TcGP63I gene family suggests a link between genetic diversity within this gene family and survival in the mammalian host.

IgA Function in Relation to the Intestinal Microbiota.

PubMed

Macpherson, Andrew J; Yilmaz, Bahtiyar; Limenitakis, Julien P; Ganal-Vonarburg, Stephanie C

2018-04-26

IgA is the dominant immunoglobulin isotype produced in mammals, largely secreted across the intestinal mucosal surface. Although induction of IgA has been a hallmark feature of microbiota colonization following colonization in germ-free animals, until recently appreciation of the function of IgA in host-microbial mutualism has depended mainly on indirect evidence of alterations in microbiota composition or penetration of microbes in the absence of somatic mutations in IgA (or compensatory IgM). Highly parallel sequencing techniques that enable high-resolution analysis of either microbial consortia or IgA sequence diversity are now giving us new perspectives on selective targeting of microbial taxa and the trajectory of IgA diversification according to induction mechanisms, between different individuals and over time. The prospects are to link the range of diversified IgA clonotypes to specific antigenic functions in modulating the microbiota composition, position and metabolism to ensure host mutualism.

Tropical Tree Trait Diversity Enhances Forest Biomass Resilience in a Dynamic Global Vegetation Model

NASA Astrophysics Data System (ADS)

Sakschewski, B.; Kirsten, T.; von Bloh, W.; Poorter, L.; Pena-Claros, M.; Boit, A.

2016-12-01

Functional diversity of ecosystems has been found to increase ecosystem functions and therefore enhance ecosystem resilience against environmental stressors. However, global carbon-cycle and biosphere models still classify the global vegetation into a relatively small number of distinct plant functional types (PFT) with constant features over space and time. Therefore, those models might underestimate the resilience and adaptive capacity of natural vegetation under climate change by ignoring positive effects that functional diversity might bring about. We diversified a set a of selected tree traits in a dynamic global vegetation model (LPJmL). In the new subversion, called LPJmL-FIT, Amazon region biomass stocks and forest structure appear significantly more resilient against climate change. Enhanced tree trait diversity enables the simulated rainforests to adjust to new environmental conditions via ecological sorting. These results may stimulate a new debate on the value of biodiversity for climate change mitigation.

Adaptive molecular evolution of the two-pore channel 1 gene TPC1 in the karst-adapted genus Primulina (Gesneriaceae)

PubMed Central

Tao, Junjie; Feng, Chao; Ai, Bin; Kang, Ming

2016-01-01

Background and Aims Limestone karst areas possess high floral diversity and endemism. The genus Primulina, which contributes to the unique calcicole flora, has high species richness and exhibit specific soil-based habitat associations that are mainly distributed on calcareous karst soils. The adaptive molecular evolutionary mechanism of the genus to karst calcium-rich environments is still not well understood. The Ca2+-permeable channel TPC1 was used in this study to test whether its gene is involved in the local adaptation of Primulina to karst high-calcium soil environments. Methods Specific amplification and sequencing primers were designed and used to amplify the full-length coding sequences of TPC1 from cDNA of 76 Primulina species. The sequence alignment without recombination and the corresponding reconstructed phylogeny tree were used in molecular evolutionary analyses at the nucleic acid level and amino acid level, respectively. Finally, the identified sites under positive selection were labelled on the predicted secondary structure of TPC1. Key Results Seventy-six full-length coding sequences of Primulina TPC1 were obtained. The length of the sequences varied between 2220 and 2286 bp and the insertion/deletion was located at the 5′ end of the sequences. No signal of substitution saturation was detected in the sequences, while significant recombination breakpoints were detected. The molecular evolutionary analyses showed that TPC1 was dominated by purifying selection and the selective pressures were not significantly different among species lineages. However, significant signals of positive selection were detected at both TPC1 codon level and amino acid level, and five sites under positive selective pressure were identified by at least three different methods. Conclusions The Ca2+-permeable channel TPC1 may be involved in the local adaptation of Primulina to karst Ca2+-rich environments. Different species lineages suffered similar selective pressure associated with calcium in karst environments, and episodic diversifying selection at a few sites may play a major role in the molecular evolution of Primulina TPC1. PMID:27582362

The Old Normal: Casualization and Contingency in Historical Perspective

ERIC Educational Resources Information Center

Cain, Timothy Reese

2015-01-01

American higher education is in the midst of a staffing crisis. More than three quarters of faculty members work off the tenure track, often with no job security, low wages, and few prospects for advancement. While the contingent labor force is diversified--including highly qualified but part-time laborers piecing together positions at multiple…

Assessing the Impact of Socio-Economic Inequities on College Enrolment: Emerging Differences in the United Arab Emirates

ERIC Educational Resources Information Center

Ghazal Aswad, Noor; Vidican, Georgeta; Samulewicz, Diana

2011-01-01

As the United Arab Emirates diversifies its economy towards knowledge-based industries, maximising the participation of the national workforce, particularly women, in the science, engineering and technology fields is of utmost importance. To accomplish this, identifying the factors that lead students to select their degree programme, as well as…

Insights from a cross-disciplinary seminar: 10 pivotal papers for ecological restoration

Treesearch

Melissa V. Eitzel; Sibyl Diver; Hillary Sardiñas; Lauren M. Hallett; Jessica J. Olson; Adam Romero; Gustavo de L. T. Oliveira; Alex T. Schuknecht; Rob Tidmore; Katharine N. Suding

2011-01-01

Restoration ecology is a deepening and diversifying field with current research incorporating multiple disciplines and infusing long-standing ideas with fresh perspectives. We present a list of 10 recent pivotal papers exemplifying new directions in ecological restoration that were selected by students in a cross-disciplinary graduate seminar at the University of...

Play and Practice in the Development of Sport-Specific Creativity in Team Ball Sports

ERIC Educational Resources Information Center

Memmert, Daniel; Baker, Joseph; Bertsch, Claudia

2010-01-01

Current theoretical approaches regarding the development of creativity support the view that gathering diversified experience over years is an ideal medium for creative thinking. This study examined the role of practice conditions in the development of creative behavior in team ball sports. Twelve trainers selected the most creative and the least…

An Inquiry into the Impact of Admissions Policy that Diversifies the Selection of Pre-Service Teacher Education Candidates

ERIC Educational Resources Information Center

Stead, Virginia

2006-01-01

The world of educational quality in 2006 is infused with conflicting ecopolitical agendas that constitute evidence of social strain and what Cherry Banks (2006) calls the tension between unity and diversity. That tension is increasingly prevalent among growing multicultural communities where centuries of inadequate educational funding have created…

Diversifying California's Community College Leadership: What's Race Got to Do with It? A Qualitative Multiple Case Study

ERIC Educational Resources Information Center

Chochezi, Victoire S.

2013-01-01

This qualitative multiple case study examined diversity perceptions of California community college senior leaders and sought to provide insights into how a senior leader's view of diversity concepts influences their actions in succession planning and selection of leaders and faculty. An in-depth qualitative analysis of participant interviews and…

76 FR 76457 - Self-Regulatory Organizations; NYSE Arca Inc.; Notice of Filing of Proposed Rule Change To List...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-07

... provide diversified exposure to select economies around the world. The Sub-Adviser will rank countries on... its proprietary country ranking model, the Sub-Adviser ranks countries on a monthly basis in order to... growth) factor groups. 3. Rank Countries: Each month the Sub-Adviser will use the weighted individual...

77 FR 4079 - Self-Regulatory Organizations; NYSE Arca, Inc.; Order Granting Approval of Proposed Rule Change...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-26

... diversified exposure to select economies around the world. The Sub-Adviser will rank countries on a monthly... of global equity returns. Through its country ranking model, the Sub-Adviser ranks countries on a... (e.g., earnings growth) factor groups. 3. Rank Countries: Each month the Sub-Adviser will use the...

Entrofy: Participant Selection Made Easy

NASA Astrophysics Data System (ADS)

Huppenkothen, Daniela

2016-03-01

Selection participants for a workshop out of a much larger applicant pool can be a difficult task, especially when the goal is diversifying over a range of criteria (e.g. academic seniority, research field, skill levels, gender etc). In this talk I am presenting our tool, Entrofy, aimed at aiding organizers in this task. Entrofy is an open-source tool using a maximum entropy-based algorithm that aims to select a set of participants out of the applicant pool such that a pre-defined range of criteria are globally maximized. This approach allows for a potentially more transparent and less biased selection process while encouraging organizers to think deeply about the goals and the process of their participant selection.

The NLP toxin family in Phytophthora sojae includes rapidly evolving groups that lack necrosis-inducing activity.

PubMed

Dong, Suomeng; Kong, Guanghui; Qutob, Dinah; Yu, Xiaoli; Tang, Junli; Kang, Jixiong; Dai, Tingting; Wang, Hai; Gijzen, Mark; Wang, Yuanchao

2012-07-01

Necrosis- and ethylene-inducing-like proteins (NLP) are widely distributed in eukaryotic and prokaryotic plant pathogens and are considered to be important virulence factors. We identified, in total, 70 potential Phytophthora sojae NLP genes but 37 were designated as pseudogenes. Sequence alignment of the remaining 33 NLP delineated six groups. Three of these groups include proteins with an intact heptapeptide (Gly-His-Arg-His-Asp-Trp-Glu) motif, which is important for necrosis-inducing activity, whereas the motif is not conserved in the other groups. In total, 19 representative NLP genes were assessed for necrosis-inducing activity by heterologous expression in Nicotiana benthamiana. Surprisingly, only eight genes triggered cell death. The expression of the NLP genes in P. sojae was examined, distinguishing 20 expressed and 13 nonexpressed NLP genes. Real-time reverse-transcriptase polymerase chain reaction results indicate that most NLP are highly expressed during cyst germination and infection stages. Amino acid substitution ratios (Ka/Ks) of 33 NLP sequences from four different P. sojae strains resulted in identification of positive selection sites in a distinct NLP group. Overall, our study indicates that expansion and pseudogenization of the P. sojae NLP family results from an ongoing birth-and-death process, and that varying patterns of expression, necrosis-inducing activity, and positive selection suggest that NLP have diversified in function.

Sex-specific patterns of morphological diversification: evolution of reaction norms and static allometries in neriid flies.

PubMed

Cassidy, Elizabeth J; Bath, Eleanor; Chenoweth, Stephen F; Bonduriansky, Russell

2014-02-01

The consequences of sex-specific selection for patterns of diversification remain poorly known. Because male secondary sexual traits are typically costly to express, and both costs and benefits are likely to depend on ambient environment and individual condition, such traits may be expected to diversify via changes in reaction norms as well as the scaling of trait size with body size (static allometry). We investigated morphological diversification within two species of Australian neriid flies (Telostylinus angusticollis, Telostylinus lineolatus) by rearing larvae from several populations on larval diets varying sixfold in nutrient concentration. Mean body size varied among populations of T. angusticollis, but body size reaction norms did not vary within either species. However, we detected diversification of reaction norms for body shape in males and females within both species. Moreover, unlike females, males also diversified in static allometry slope and reaction norms for static allometry slope of sexual and nonsexual traits. Our findings reveal qualitative sex differences in patterns of morphological diversification, whereby shape-size relationships diversify extensively in males, but remain conserved in females despite extensive evolution of trait means. Our results highlight the importance of incorporating plasticity and allometry in studies of adaptation and diversification. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Genomic Porosity between Invasive Chondrostoma nasus and Endangered Endemic Parachondrostoma toxostoma (Cyprinidae): The Evolution of MHC IIB Genes

PubMed Central

Šimková, Andrea; Civáňová, Kristína; Gettová, Lenka; Gilles, André

2013-01-01

Two cyprinid species, Parachondrostoma toxostoma, an endemic threatened species, and Chondrostoma nasus, an invasive species, live in sympatry in southern France and form two sympatric zones where the presence of intergeneric hybrids is reported. To estimate the potential threat to endemic species linked to the introduction of invasive species, we focused on the DAB genes (functional MHC IIB genes) because of their adaptive significance and role in parasite resistance. More specifically, we investigated (1) the variability of MHC IIB genes, (2) the selection pattern shaping MHC polymorphism, and (3) the extent to which trans-species evolution and intergeneric hybridization affect MHC polymorphism. In sympatric areas, the native species has more diversified MHC IIB genes when compared to the invasive species, probably resulting from the different origins and dispersal of both species. A similar level of MHC polymorphism was found at population level in both species, suggesting similar mechanisms generating MHC diversity. In contrast, a higher number of DAB-like alleles per specimen were found in invasive species. Invasive species tended to express the alleles of two DAB lineages, whilst native species tended to express the alleles of only the DAB3 lineage. Hybrids have a pattern of MHC expression intermediate between both species. Whilst positive selection acting on peptide binding sites (PBS) was demonstrated in both species, a slightly higher number of positively selected sites were identified in C. nasus, which could result from parasite-mediated selection. Bayesian clustering analysis revealed a similar pattern of structuring for the genetic variation when using microsatellites or the MHC approach. We confirmed the importance of trans-species evolution for MHC polymorphism. In addition, we demonstrated bidirectional gene flow for MHC IIB genes in sympatric areas. The positive significant correlation between MHC and microsatellites suggests that demographic factors may contribute to MHC variation on a short time scale. PMID:23824831

Diversifying Selection Underlies the Origin of Allozyme Polymorphism at the Phosphoglucose Isomerase Locus in Tigriopus californicus

PubMed Central

Schoville, Sean D.; Flowers, Jonathan M.; Burton, Ronald S.

2012-01-01

The marine copepod Tigriopus californicus lives in intertidal rock pools along the Pacific coast, where it exhibits strong, temporally stable population genetic structure. Previous allozyme surveys have found high frequency private alleles among neighboring subpopulations, indicating that there is limited genetic exchange between populations. Here we evaluate the factors responsible for the diversification and maintenance of alleles at the phosphoglucose isomerase (Pgi) locus by evaluating patterns of nucleotide variation underlying previously identified allozyme polymorphism. Copepods were sampled from eleven sites throughout California and Baja California, revealing deep genetic structure among populations as well as genetic variability within populations. Evidence of recombination is limited to the sample from Pescadero and there is no support for linkage disequilibrium across the Pgi locus. Neutrality tests and codon-based models of substitution suggest the action of natural selection due to elevated non-synonymous substitutions at a small number of sites in Pgi. Two sites are identified as the charge-changing residues underlying allozyme polymorphisms in T. californicus. A reanalysis of allozyme variation at several focal populations, spanning a period of 26 years and over 200 generations, shows that Pgi alleles are maintained without notable frequency changes. Our data suggest that diversifying selection accounted for the origin of Pgi allozymes, while McDonald-Kreitman tests and the temporal stability of private allozyme alleles suggests that balancing selection may be involved in the maintenance of amino acid polymorphisms within populations. PMID:22768211

Positive selection of the peripheral B cell repertoire in gut-associated lymphoid tissues

PubMed Central

Rhee, Ki-Jong; Jasper, Paul J.; Sethupathi, Periannan; Shanmugam, Malathy; Lanning, Dennis; Knight, Katherine L.

2005-01-01

Gut-associated lymphoid tissues (GALTs) interact with intestinal microflora to drive GALT development and diversify the primary antibody repertoire; however, the molecular mechanisms that link these events remain elusive. Alicia rabbits provide an excellent model to investigate the relationship between GALT, intestinal microflora, and modulation of the antibody repertoire. Most B cells in neonatal Alicia rabbits express VHn allotype immunoglobulin (Ig)M. Within weeks, the number of VHn B cells decreases, whereas VHa allotype B cells increase in number and become predominant. We hypothesized that the repertoire shift from VHn to VHa B cells results from interactions between GALT and intestinal microflora. To test this hypothesis, we surgically removed organized GALT from newborn Alicia pups and ligated the appendix to sequester it from intestinal microflora. Flow cytometry and nucleotide sequence analyses revealed that the VHn to VHa repertoire shift did not occur, demonstrating the requirement for interactions between GALT and intestinal microflora in the selective expansion of VHa B cells. By comparing amino acid sequences of VHn and VHa Ig, we identified a putative VH ligand binding site for a bacterial or endogenous B cell superantigen. We propose that interaction of such a superantigen with VHa B cells results in their selective expansion. PMID:15623575

Molecular analysis of hemagglutinin-1 fragment of avian influenza H5N1 viruses isolated from chicken farms in Indonesia from 2008 to 2010.

PubMed

Mahardika, Gusti N; Jonas, Melina; Murwijati, Theresia; Fitria, Nur; Suartha, I Nyoman; Suartini, I Gusti A A; Wibawan, I Wayan Teguh

2016-04-15

Highly pathogenic avian influenza virus of subtype H5N1 (AIV-H5N1) has been circulating in Indonesia since 2003. To understand the genetic diversity of these viruses, and to predict vaccine efficacy, the hemaglutinin-1 (HA-1) fragment of viruses isolated from chicken farms in Indonesia from 2008 to 2010 was sequenced and analyzed. The effects of these molecular changes were investigated in challenge experiments and HI assays of homologous and heterologous strains. Molecular analysis showed that these AIV-H5N1 isolates had evolved into three distinct sub-lineages from an ancestor circulating since 2003. Although no significant positive selection of residues was detected, 12 negatively selected sites were identified (p<0.05). Moreover, four sites showed evidence of significant episodic diversifying selection. The findings indicated complete protectivity and high HI titers with homologous strains, compared with protectivity ranging from 40 to 100% and lower HI titers with heterologous strains resulting from polymorphisms at antigenic sites. Our findings provide valuable insight into the molecular evolution of AIV and have important implications for vaccine efficacy and future vaccination strategies. Copyright © 2016 Elsevier B.V. All rights reserved.

Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species

PubMed Central

Árnason, Einar

2015-01-01

Natural selection, the most important force in evolution, comes in three forms. Negative purifying selection removes deleterious variation and maintains adaptations. Positive directional selection fixes beneficial variants, producing new adaptations. Balancing selection maintains variation in a population. Important mechanisms of balancing selection include heterozygote advantage, frequency-dependent advantage of rarity, and local and fluctuating episodic selection. A rare pathogen gains an advantage because host defenses are predominantly effective against prevalent types. Similarly, a rare immune variant gives its host an advantage because the prevalent pathogens cannot escape the host’s apostatic defense. Due to the stochastic nature of evolution, neutral variation may accumulate on genealogical branches, but trans-species polymorphisms are rare under neutrality and are strong evidence for balancing selection. Balanced polymorphism maintains diversity at the major histocompatibility complex (MHC) in vertebrates. The Atlantic cod is missing genes for both MHC-II and CD4, vital parts of the adaptive immune system. Nevertheless, cod are healthy in their ecological niche, maintaining large populations that support major commercial fisheries. Innate immunity is of interest from an evolutionary perspective, particularly in taxa lacking adaptive immunity. Here, we analyze extensive amino acid and nucleotide polymorphisms of the cathelicidin gene family in Atlantic cod and closely related taxa. There are three major clusters, Cath1, Cath2, and Cath3, that we consider to be paralogous genes. There is extensive nucleotide and amino acid allelic variation between and within clusters. The major feature of the results is that the variation clusters by alleles and not by species in phylogenetic trees and discriminant analysis of principal components. Variation within the three groups shows trans-species polymorphism that is older than speciation and that is suggestive of balancing selection maintaining the variation. Using Bayesian and likelihood methods positive and negative selection is evident at sites in the conserved part of the genes and, to a larger extent, in the active part which also shows episodic diversifying selection, further supporting the argument for balancing selection. PMID:26038731

Unraveling Selection in the Mitochondrial Genome of Drosophila

PubMed Central

Ballard, JWO.; Kreitman, M.

1994-01-01

We examine mitochondrial DNA variation at the cytochrome b locus within and between three species of Drosophila to determine whether patterns of variation conform to the predictions of neutral molecular evolution. The entire 1137-bp cytochrome b locus was sequenced in 16 lines of Drosophila melanogaster, 18 lines of Drosophila simulans and 13 lines of Drosophila yakuba. Patterns of variation depart from neutrality by several test criteria. Analysis of the evolutionary clock hypothesis shows unequal rates of change along D. simulans lineages. A comparison within and between species of the ratio of amino acid replacement change to synonymous change reveals a relative excess of amino acid replacement polymorphism compared to the neutral prediction, suggestive of slightly deleterious or diversifying selection. There is evidence for excess homozygosity in our world wide sample of D. melanogaster and D. simulans alleles, as well as a reduction in the number of segregating sites in D. simulans, indicative of selective sweeps. Furthermore, a test of neutrality for codon usage shows the direction of mutations at third positions differs among different topological regions of the gene tree. The analyses indicate that molecular variation and evolution of mtDNA are governed by many of the same selective forces that have been shown to govern nuclear genome evolution and suggest caution be taken in the use of mtDNA as a ``neutral'' molecular marker. PMID:7851772

Vocational Education in Developing Countries. A Review of Studies and Project Experience. Education Division Documents No. 34.

ERIC Educational Resources Information Center

Hultin, Mats

This paper looks at the position taken in available literature and evaluation reports of multinational and bilateral agencies in regard to vocational education in developing countries. Section 1 provides background on such topics as links between education and development, support of vocational education, diversified secondary education, foreign…

78 FR 76867 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Filing of Proposed Rule Change Relating...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-19

... codes of ethics. This Rule requires investment advisers to adopt a code of ethics that reflects the... position in gold but diversifies the currencies in which the purchase is financed. The International Gold.../Yen ETF's investments in gold purchased in Japanese Yen will appreciate. Accordingly, in managing the...

Diversifying Our Views of Argument: Dialogue, Respect, and Feminist Rhetoric

ERIC Educational Resources Information Center

Hunzer, Kathleen M.

2005-01-01

The author presents her views on creating respect and dialogue in the Feminist Argument Class. She asserts that the instructor must "create the kind of atmosphere in which students can think honestly and openly about their position on an issue about which they care" (Lamb, "Beyond Argument" 18). When this atmosphere is created, students can be…

Learning to Label: An Investigation into Ways of Conceptualizing Curriculum Diversity in a Korean Unregulated School Choice Area

ERIC Educational Resources Information Center

Sung, Youl-Kwan

2009-01-01

This study seeks to explore whether unregulated school choice has the potential to diversify the high school curriculum, as elitist conservatives and neoliberals in Korean argue. Making use of qualitative research methods, this paper examines how national curriculum policies are implemented at two selected high schools (high-achievement 1,…

Filipino Preservice Teachers' Tendencies and Beliefs about the Teacher's Role in Education: Homogenized or Heterogenized?

ERIC Educational Resources Information Center

de Guzman, Allan B.; de Castro, Belinda V.; Mapa, Amelia, II; Peries, Sr. Maria Goretti; Jung, Yoori

2009-01-01

This study aims to identify the tendencies and beliefs of a select group of Filipino preservice teachers in regard to static institutional roles in democratic and global society and with respect to innovation and their diversified roles. A total of 800 respondents were purposively recruited from six colleges of education in the capital of the…

aCGH Analysis to Estimate Genetic Variations among Domesticated Chickens

PubMed Central

Lin, Mengjie

2016-01-01

Chickens have been familiar to humans since ancient times and have been used not only for culinary purposes but also for cultural purposes including ritual ceremonies and traditional entertainment. The various chicken breeds developed for these purposes often display distinct morphological and/or behavioural traits. For example, the Japanese Shamo is larger and more aggressive than other domesticated chickens, reflecting its role as a fighting cock breed, whereas Japanese Naganakidori breeds, which have long-crowing behaviour, were bred instead for their entertaining and aesthetic qualities. However, the genetic backgrounds of these distinct morphological and behavioural traits remain unclear. Therefore, the question arises as to which genomic regions in these chickens were acted upon by selective pressures through breeding. We compared the entire genomes of six chicken breeds domesticated for various cultural purposes by utilizing array comparative genomic hybridization. From these analyses, we identified 782 regions that underwent insertions, deletions, or mutations, representing man-made selection pressure in these chickens. Furthermore, we found that a number of genes diversified in domesticated chickens bred for cultural or entertainment purposes were different from those diversified in chickens bred for food, such as broilers and layers. PMID:27525263

Sexual selection predicts species richness across the animal kingdom.

PubMed

Janicke, Tim; Ritchie, Michael G; Morrow, Edward H; Marie-Orleach, Lucas

2018-05-16

Our improving knowledge of the animal tree of life consistently demonstrates that some taxa diversify more rapidly than others, but what contributes to this variation remains poorly understood. An influential hypothesis proposes that selection arising from competition for mating partners plays a key role in promoting speciation. However, empirical evidence showing a link between proxies of this sexual selection and species richness is equivocal. Here, we collected standardized metrics of sexual selection for a broad range of animal taxa, and found that taxonomic families characterized by stronger sexual selection on males show relatively higher species richness. Thus, our data support the hypothesis that sexual selection elevates species richness. This could occur either by promoting speciation and/or by protecting species against extinction. © 2018 The Author(s).

Ecology, sexual selection and speciation.

PubMed

Maan, Martine E; Seehausen, Ole

2011-06-01

The spectacular diversity in sexually selected traits among animal taxa has inspired the hypothesis that divergent sexual selection can drive speciation. Unfortunately, speciation biologists often consider sexual selection in isolation from natural selection, even though sexually selected traits evolve in an ecological context: both preferences and traits are often subject to natural selection. Conversely, while behavioural ecologists may address ecological effects on sexual communication, they rarely measure the consequences for population divergence. Herein, we review the empirical literature addressing the mechanisms by which natural selection and sexual selection can interact during speciation. We find that convincing evidence for any of these scenarios is thin. However, the available data strongly support various diversifying effects that emerge from interactions between sexual selection and environmental heterogeneity. We suggest that evaluating the evolutionary consequences of these effects requires a better integration of behavioural, ecological and evolutionary research. © 2011 Blackwell Publishing Ltd/CNRS.

Genetic Variation of Goat Interferon Regulatory Factor 3 Gene and Its Implication in Goat Evolution

PubMed Central

Shu, Liping; Zhang, Yesheng; Wang, Yangzi; Sanni, Timothy M.; Imumorin, Ikhide G.; Peters, Sunday O.; Zhang, Jiajin; Dong, Yang; Wang, Wen

2016-01-01

The immune systems are fundamentally vital for evolution and survival of species; as such, selection patterns in innate immune loci are of special interest in molecular evolutionary research. The interferon regulatory factor (IRF) gene family control many different aspects of the innate and adaptive immune responses in vertebrates. Among these, IRF3 is known to take active part in very many biological processes. We assembled and evaluated 1356 base pairs of the IRF3 gene coding region in domesticated goats from Africa (Nigeria, Ethiopia and South Africa) and Asia (Iran and China) and the wild goat (Capra aegagrus). Five segregating sites with θ value of 0.0009 for this gene demonstrated a low diversity across the goats’ populations. Fu and Li tests were significantly positive but Tajima’s D test was significantly negative, suggesting its deviation from neutrality. Neighbor joining tree of IRF3 gene in domesticated goats, wild goat and sheep showed that all domesticated goats have a closer relationship than with the wild goat and sheep. Maximum likelihood tree of the gene showed that different domesticated goats share a common ancestor and suggest single origin. Four unique haplotypes were observed across all the sequences, of which, one was particularly common to African goats (MOCH-K14-0425, Poitou and WAD). In assessing the evolution mode of the gene, we found that the codon model dN/dS ratio for all goats was greater than one. Phylogenetic Analysis by Maximum Likelihood (PAML) gave a ω0 (dN/dS) value of 0.067 with LnL value of -6900.3 for the first Model (M1) while ω2 = 1.667 in model M2 with LnL value of -6900.3 with positive selection inferred in 3 codon sites. Mechanistic empirical combination (MEC) model for evaluating adaptive selection pressure on particular codons also confirmed adaptive selection pressure in three codons (207, 358 and 408) in IRF3 gene. Positive diversifying selection inferred with recent evolutionary changes in domesticated goat IRF3 led us to conclude that the gene evolution may have been influenced by domestication processes in goats. PMID:27598391

Genetic Variation of Goat Interferon Regulatory Factor 3 Gene and Its Implication in Goat Evolution.

PubMed

Okpeku, Moses; Esmailizadeh, Ali; Adeola, Adeniyi C; Shu, Liping; Zhang, Yesheng; Wang, Yangzi; Sanni, Timothy M; Imumorin, Ikhide G; Peters, Sunday O; Zhang, Jiajin; Dong, Yang; Wang, Wen

2016-01-01

The immune systems are fundamentally vital for evolution and survival of species; as such, selection patterns in innate immune loci are of special interest in molecular evolutionary research. The interferon regulatory factor (IRF) gene family control many different aspects of the innate and adaptive immune responses in vertebrates. Among these, IRF3 is known to take active part in very many biological processes. We assembled and evaluated 1356 base pairs of the IRF3 gene coding region in domesticated goats from Africa (Nigeria, Ethiopia and South Africa) and Asia (Iran and China) and the wild goat (Capra aegagrus). Five segregating sites with θ value of 0.0009 for this gene demonstrated a low diversity across the goats' populations. Fu and Li tests were significantly positive but Tajima's D test was significantly negative, suggesting its deviation from neutrality. Neighbor joining tree of IRF3 gene in domesticated goats, wild goat and sheep showed that all domesticated goats have a closer relationship than with the wild goat and sheep. Maximum likelihood tree of the gene showed that different domesticated goats share a common ancestor and suggest single origin. Four unique haplotypes were observed across all the sequences, of which, one was particularly common to African goats (MOCH-K14-0425, Poitou and WAD). In assessing the evolution mode of the gene, we found that the codon model dN/dS ratio for all goats was greater than one. Phylogenetic Analysis by Maximum Likelihood (PAML) gave a ω0 (dN/dS) value of 0.067 with LnL value of -6900.3 for the first Model (M1) while ω2 = 1.667 in model M2 with LnL value of -6900.3 with positive selection inferred in 3 codon sites. Mechanistic empirical combination (MEC) model for evaluating adaptive selection pressure on particular codons also confirmed adaptive selection pressure in three codons (207, 358 and 408) in IRF3 gene. Positive diversifying selection inferred with recent evolutionary changes in domesticated goat IRF3 led us to conclude that the gene evolution may have been influenced by domestication processes in goats.

The Hidden Leaves of the Baobab Tree: Lived Experiences of African American Female Chief Academic Officers

ERIC Educational Resources Information Center

Bailey, Kyeanna Mozzel

2010-01-01

The chief academic officer (CAO) role is critical to the academic and often administrative mission of an institution of higher education. Key constituents served by CAOs are become more diverse; however the individuals serving in the position are not diversifying at the same rate. The purpose of this study was to collect and portray the…

Deep Sequencing of the Trypanosoma cruzi GP63 Surface Proteases Reveals Diversity and Diversifying Selection among Chronic and Congenital Chagas Disease Patients

PubMed Central

Llewellyn, Martin S.; Messenger, Louisa A.; Luquetti, Alejandro O.; Garcia, Lineth; Torrico, Faustino; Tavares, Suelene B. N.; Cheaib, Bachar; Derome, Nicolas; Delepine, Marc; Baulard, Céline; Deleuze, Jean-Francois; Sauer, Sascha; Miles, Michael A.

2015-01-01

Background Chagas disease results from infection with the diploid protozoan parasite Trypanosoma cruzi. T. cruzi is highly genetically diverse, and multiclonal infections in individual hosts are common, but little studied. In this study, we explore T. cruzi infection multiclonality in the context of age, sex and clinical profile among a cohort of chronic patients, as well as paired congenital cases from Cochabamba, Bolivia and Goias, Brazil using amplicon deep sequencing technology. Methodology/ Principal Findings A 450bp fragment of the trypomastigote TcGP63I surface protease gene was amplified and sequenced across 70 chronic and 22 congenital cases on the Illumina MiSeq platform. In addition, a second, mitochondrial target—ND5—was sequenced across the same cohort of cases. Several million reads were generated, and sequencing read depths were normalized within patient cohorts (Goias chronic, n = 43, Goias congenital n = 2, Bolivia chronic, n = 27; Bolivia congenital, n = 20), Among chronic cases, analyses of variance indicated no clear correlation between intra-host sequence diversity and age, sex or symptoms, while principal coordinate analyses showed no clustering by symptoms between patients. Between congenital pairs, we found evidence for the transmission of multiple sequence types from mother to infant, as well as widespread instances of novel genotypes in infants. Finally, non-synonymous to synonymous (dn:ds) nucleotide substitution ratios among sequences of TcGP63Ia and TcGP63Ib subfamilies within each cohort provided powerful evidence of strong diversifying selection at this locus. Conclusions/Significance Our results shed light on the diversity of parasite DTUs within each patient, as well as the extent to which parasite strains pass between mother and foetus in congenital cases. Although we were unable to find any evidence that parasite diversity accumulates with age in our study cohorts, putative diversifying selection within members of the TcGP63I gene family suggests a link between genetic diversity within this gene family and survival in the mammalian host. PMID:25849488

Complex dissemination of the diversified mcr-1-harbouring plasmids in Escherichia coli of different sequence types

PubMed Central

Lin, Jingxia; Wang, Xiuna; Deng, Xianbo; Feng, Youjun

2016-01-01

The emergence of the mobilized colistin resistance gene, representing a novel mechanism for bacterial drug resistance, challenges the last resort against the severe infections by Gram-negative bacteria with multi-drug resistances. Very recently, we showed the diversity in the mcr-1-carrying plasmid reservoirs from the gut microbiota. Here, we reported that a similar but more complex scenario is present in the healthy swine populations, Southern China, 2016. Amongst the 1026 pieces of Escherichia coli isolates from 3 different pig farms, 302 E. coli isolates were determined to be positive for the mcr-1 gene (30%, 302/1026). Multi-locus sequence typing assigned no less than 11 kinds of sequence types including one novel Sequence Type to these mcr-1-positive strains. PCR analyses combined with the direct DNA sequencing revealed unexpected complexity of the mcr-1-harbouring plasmids whose backbones are at least grouped into 6 types four of which are new. Transcriptional analyses showed that the mcr-1 promoter of different origins exhibits similar activity. It seems likely that complex dissemination of the diversified mcr-1-bearing plasmids occurs amongst the various ST E. coli inhabiting the healthy swine populations, in Southern China. PMID:27741523

Does Size Matter? Atmospheric CO2 May Be a Stronger Driver of Stomatal Closing Rate Than Stomatal Size in Taxa That Diversified under Low CO2.

PubMed

Elliott-Kingston, Caroline; Haworth, Matthew; Yearsley, Jon M; Batke, Sven P; Lawson, Tracy; McElwain, Jennifer C

2016-01-01

One strategy for plants to optimize stomatal function is to open and close their stomata quickly in response to environmental signals. It is generally assumed that small stomata can alter aperture faster than large stomata. We tested the hypothesis that species with small stomata close faster than species with larger stomata in response to darkness by comparing rate of stomatal closure across an evolutionary range of species including ferns, cycads, conifers, and angiosperms under controlled ambient conditions (380 ppm CO2; 20.9% O2). The two species with fastest half-closure time and the two species with slowest half-closure time had large stomata while the remaining three species had small stomata, implying that closing rate was not correlated with stomatal size in these species. Neither was response time correlated with stomatal density, phylogeny, functional group, or life strategy. Our results suggest that past atmospheric CO2 concentration during time of taxa diversification may influence stomatal response time. We show that species which last diversified under low or declining atmospheric CO2 concentration close stomata faster than species that last diversified in a high CO2 world. Low atmospheric [CO2] during taxa diversification may have placed a selection pressure on plants to accelerate stomatal closing to maintain adequate internal CO2 and optimize water use efficiency.

Does Size Matter? Atmospheric CO2 May Be a Stronger Driver of Stomatal Closing Rate Than Stomatal Size in Taxa That Diversified under Low CO2

PubMed Central

Elliott-Kingston, Caroline; Haworth, Matthew; Yearsley, Jon M.; Batke, Sven P.; Lawson, Tracy; McElwain, Jennifer C.

2016-01-01

One strategy for plants to optimize stomatal function is to open and close their stomata quickly in response to environmental signals. It is generally assumed that small stomata can alter aperture faster than large stomata. We tested the hypothesis that species with small stomata close faster than species with larger stomata in response to darkness by comparing rate of stomatal closure across an evolutionary range of species including ferns, cycads, conifers, and angiosperms under controlled ambient conditions (380 ppm CO2; 20.9% O2). The two species with fastest half-closure time and the two species with slowest half-closure time had large stomata while the remaining three species had small stomata, implying that closing rate was not correlated with stomatal size in these species. Neither was response time correlated with stomatal density, phylogeny, functional group, or life strategy. Our results suggest that past atmospheric CO2 concentration during time of taxa diversification may influence stomatal response time. We show that species which last diversified under low or declining atmospheric CO2 concentration close stomata faster than species that last diversified in a high CO2 world. Low atmospheric [CO2] during taxa diversification may have placed a selection pressure on plants to accelerate stomatal closing to maintain adequate internal CO2 and optimize water use efficiency. PMID:27605929

Autoimmunity and asthma: The dirt on the hygiene hypothesis.

PubMed

Mannie, Mark D

2010-04-01

Self peptides shape T-cell development through selectional processes in the thymus and secondary lymphoid organs to promote a diverse and balanced repertoire of conventional and regulatory T cells. Foreign proteins and their derivative peptides permeate our mucosal tissues to constitute another diverse array of peptides that may specify and diversify the mucosal T-cell repertoire. Indeed, the distinction between self peptides and environmental foreign peptides may be academic if both are present constantly within the body. The premise here is that the plethora of foreign peptides, present ubiquitously in our environment and body, form homeostatic niches to foster highly diversified repertoires of conventional and regulatory T cells that recognize persistent environmental peptides as self. Highly diversified repertoires that recognize myriads of self and environmental foreign peptides as homeostatic ligands may be critical for adaptive distinctions of friend or foe in mucosal tissues. The change from our agrarian past to the highly sterile environments of today may adversely impact the diversity and concentrations of foreign peptides that shape the mucosal T-cell repertoire. Various hygiene hypotheses postulate that the lack of factors such as infectious pathogens, innate receptor engagement or Th1 bias is key to the marked increase in immunological disease in modern society. In this version of the hygiene hypothesis, highly diverse constellations of innocuous environmental peptides are postulated to be the critical factor for immune balance and homeostasis.

Genetic variability and natural selection at the ligand domain of the Duffy binding protein in brazilian Plasmodium vivax populations

PubMed Central

2010-01-01

Background Plasmodium vivax malaria is a major public health challenge in Latin America, Asia and Oceania, with 130-435 million clinical cases per year worldwide. Invasion of host blood cells by P. vivax mainly depends on a type I membrane protein called Duffy binding protein (PvDBP). The erythrocyte-binding motif of PvDBP is a 170 amino-acid stretch located in its cysteine-rich region II (PvDBPII), which is the most variable segment of the protein. Methods To test whether diversifying natural selection has shaped the nucleotide diversity of PvDBPII in Brazilian populations, this region was sequenced in 122 isolates from six different geographic areas. A Bayesian method was applied to test for the action of natural selection under a population genetic model that incorporates recombination. The analysis was integrated with a structural model of PvDBPII, and T- and B-cell epitopes were localized on the 3-D structure. Results The results suggest that: (i) recombination plays an important role in determining the haplotype structure of PvDBPII, and (ii) PvDBPII appears to contain neutrally evolving codons as well as codons evolving under natural selection. Diversifying selection preferentially acts on sites identified as epitopes, particularly on amino acid residues 417, 419, and 424, which show strong linkage disequilibrium. Conclusions This study shows that some polymorphisms of PvDBPII are present near the erythrocyte-binding domain and might serve to elude antibodies that inhibit cell invasion. Therefore, these polymorphisms should be taken into account when designing vaccines aimed at eliciting antibodies to inhibit erythrocyte invasion. PMID:21092207

Population structure, migration, and diversifying selection in the Netherlands

PubMed Central

Abdellaoui, Abdel; Hottenga, Jouke-Jan; Knijff, Peter de; Nivard, Michel G; Xiao, Xiangjun; Scheet, Paul; Brooks, Andrew; Ehli, Erik A; Hu, Yueshan; Davies, Gareth E; Hudziak, James J; Sullivan, Patrick F; van Beijsterveldt, Toos; Willemsen, Gonneke; de Geus, Eco J; Penninx, Brenda W J H; Boomsma, Dorret I

2013-01-01

Genetic variation in a population can be summarized through principal component analysis (PCA) on genome-wide data. PCs derived from such analyses are valuable for genetic association studies, where they can correct for population stratification. We investigated how to capture the genetic population structure in a well-characterized sample from the Netherlands and in a worldwide data set and examined whether (1) removing long-range linkage disequilibrium (LD) regions and LD-based SNP pruning significantly improves correlations between PCs and geography and (2) whether genetic differentiation may have been influenced by migration and/or selection. In the Netherlands, three PCs showed significant correlations with geography, distinguishing between: (1) North and South; (2) East and West; and (3) the middle-band and the rest of the country. The third PC only emerged with minimized LD, which also significantly increased correlations with geography for the other two PCs. In addition to geography, the Dutch North–South PC showed correlations with genome-wide homozygosity (r=0.245), which may reflect a serial-founder effect due to northwards migration, and also with height (♂: r=0.142, ♀: r=0.153). The divergence between subpopulations identified by PCs is partly driven by selection pressures. The first three PCs showed significant signals for diversifying selection (545 SNPs - the majority within 184 genes). The strongest signal was observed between North and South for the functional SNP in HERC2 that determines human blue/brown eye color. Thus, this study demonstrates how to increase ancestry signals in a relatively homogeneous population and how those signals can reveal evolutionary history. PMID:23531865

Spatial variation of the Universal Thermal Climate Index in Lublin in specified weather scenarios / Zróżnicowanie przestrzenne wskaźnika UTCI w Lublinie w określonych scenariuszach pogodowych

NASA Astrophysics Data System (ADS)

Dobek, Mateusz; Demczuk, Piotr; Nowosad, Marek

2013-06-01

Due to the diversified land relief and presence of numerous gorge dissections intensively used by man largely for recreational purposes, Lublin is a valuable study area in terms of bioclimatology. The results of modelling of the variation of the bioclimatic conditions of Lublin provide information useful e.g. in the economy and spatial planning. The determined features of the city's bioclimate can be a significant element in the selection of locations for new residential and recreational investments. Knowledge on the spatial variation of biometeorological situations positively and negatively influencing the human organism can also find application in activities concerning the improvement of life quality and health protection, as well as in tourism and recreation. The objective of the paper is to present the spatial variation of biometeorological conditions in Lublin based on the example of specified weather scenarios.

Pollination decays in biodiversity hotspots.

PubMed

Vamosi, Jana C; Knight, Tiffany M; Steets, Janette A; Mazer, Susan J; Burd, Martin; Ashman, Tia-Lynn

2006-01-24

As pollinators decline globally, competition for their services is expected to intensify, and this antagonism may be most severe where the number of plant species is the greatest. Using meta-analysis and comparative phylogenetic analysis, we provide a global-scale test of whether reproduction becomes more limited by pollen receipt (pollen limitation) as the number of coexisting plant species increases. As predicted, we find a significant positive relationship between pollen limitation and species richness. In addition, this pattern is particularly strong for species that are obligately outcrossing and for trees relative to herbs or shrubs. We suggest that plants occurring in species-rich communities may be more prone to pollen limitation because of interspecific competition for pollinators. As a consequence, plants in biodiversity hotspots may have a higher risk of extinction and/or experience increased selection pressure to specialize on certain pollinators or diversify into different phenological niches. The combination of higher pollen limitation and habitat destruction represents a dual risk to tropical plant species that has not been previously identified.

Diversified Research Methods Education in LIS: Thinking outside the Box

ERIC Educational Resources Information Center

Luo, Lili

2017-01-01

A small number of LIS degree programs have adopted a diversified approach to research methods education, including offering an array of specialized research methods courses in addition to a general introductory course. The current study conducted an in-depth investigation of the diversified research methods curriculum of the LIS program at San…

Comparative tests of the role of dewlap size in Anolis lizard speciation

PubMed Central

Harrison, Alexis; Mahler, D. Luke; Castañeda, María del Rosario; Glor, Richard E.; Herrel, Anthony; Stuart, Yoel E.; Losos, Jonathan B.

2016-01-01

Phenotypic traits may be linked to speciation in two distinct ways: character values may influence the rate of speciation or diversification in the trait may be associated with speciation events. Traits involved in signal transmission, such as the dewlap of Anolis lizards, are often involved in the speciation process. The dewlap is an important visual signal with roles in species recognition and sexual selection, and dewlaps vary among species in relative size as well as colour and pattern. We compile a dataset of relative dewlap size digitized from photographs of 184 anole species from across the genus' geographical range. We use phylogenetic comparative methods to test two hypotheses: that larger dewlaps are associated with higher speciation rates, and that relative dewlap area diversifies according to a speciational model of evolution. We find no evidence of trait-dependent speciation, indicating that larger signals do not enhance any role the dewlap has in promoting speciation. Instead, we find a signal of mixed speciational and gradual trait evolution, with a particularly strong signal of speciational change in the dewlaps of mainland lineages. This indicates that dewlap size diversifies in association with the speciation process, suggesting that divergent selection may play a role in the macroevolution of this signalling trait. PMID:28003450

Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China.

PubMed

Xiao, Yang; Cheng, Xuanjin; Liu, Jun; Li, Chuang; Nong, Wenyan; Bian, Yinbing; Cheung, Man Kit; Kwan, Hoi Shan

2016-11-10

The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the Chinese L. edodes population with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains of L. edodes in China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence of L. edodes in China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits of L. edodes cultivars in China.

Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China

PubMed Central

Xiao, Yang; Cheng, Xuanjin; Liu, Jun; Li, Chuang; Nong, Wenyan; Bian, Yinbing; Cheung, Man Kit; Kwan, Hoi Shan

2016-01-01

The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the Chinese L. edodes population with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains of L. edodes in China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence of L. edodes in China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits of L. edodes cultivars in China. PMID:27830835

Genetic variation and selection of MHC class I loci differ in two congeneric frogs.

PubMed

Kiemnec-Tyburczy, Karen M; Tracy, Karen E; Lips, Karen R; Zamudio, Kelly R

2018-04-01

Major histocompatibility complex (MHC) genes encode proteins in the acquired immune response pathway that often show distinctive selection-driven patterns in wild vertebrate populations. We examined genetic variation and signatures of selection in the MHC class I alpha 1 (A1)- and alpha 2 (A2)-domain encoding exons of two frog congeners [Agalychnis callidryas (n = 20) and A. lemur (n = 20)] from a single locality in Panama. We also investigated how historical demographic processes may have impacted MHC genetic diversity by analyzing a neutral mitochondrial marker. We found that both MHC domains were highly variable in both species, with both species likely expressing three loci. Our analyses revealed different signatures of selection between the two species, most notably that the A. callidryas A2 domain had experienced positive selection while the A2 domain of A. lemur had not. Diversifying selection acted on the same number of A1 and A2 allelic lineages, but on a higher percentage of A1 sites compared to A2 sites. Neutrality tests of mitochondrial haplotypes predominately indicated that the two species were at genetic equilibrium when the samples were collected. In addition, two historical tests of demography indicated both species have had relatively stable population sizes over the past 100,000 years; thus large population size changes are unlikely to have greatly influenced MHC diversity in either species during this time period. In conclusion, our results suggest that the impact of selection on MHC diversity varied between these two closely related species, likely due to a combination of distinct ecological conditions and past pathogenic pressures.

Positive selection of the peripheral B cell repertoire in gut-associated lymphoid tissues.

PubMed

Rhee, Ki-Jong; Jasper, Paul J; Sethupathi, Periannan; Shanmugam, Malathy; Lanning, Dennis; Knight, Katherine L

2005-01-03

Gut-associated lymphoid tissues (GALTs) interact with intestinal microflora to drive GALT development and diversify the primary antibody repertoire; however, the molecular mechanisms that link these events remain elusive. Alicia rabbits provide an excellent model to investigate the relationship between GALT, intestinal microflora, and modulation of the antibody repertoire. Most B cells in neonatal Alicia rabbits express V(H)n allotype immunoglobulin (Ig)M. Within weeks, the number of V(H)n B cells decreases, whereas V(H)a allotype B cells increase in number and become predominant. We hypothesized that the repertoire shift from V(H)n to V(H)a B cells results from interactions between GALT and intestinal microflora. To test this hypothesis, we surgically removed organized GALT from newborn Alicia pups and ligated the appendix to sequester it from intestinal microflora. Flow cytometry and nucleotide sequence analyses revealed that the V(H)n to V(H)a repertoire shift did not occur, demonstrating the requirement for interactions between GALT and intestinal microflora in the selective expansion of V(H)a B cells. By comparing amino acid sequences of V(H)n and V(H)a Ig, we identified a putative V(H) ligand binding site for a bacterial or endogenous B cell superantigen. We propose that interaction of such a superantigen with V(H)a B cells results in their selective expansion.

Macroevolutionary diversification with limited niche disparity in a species-rich lineage of cold-climate lizards.

PubMed

Reaney, Ashley M; Saldarriaga-Córdoba, Mónica; Pincheira-Donoso, Daniel

2018-02-06

Life diversifies via adaptive radiation when natural selection drives the evolution of ecologically distinct species mediated by their access to novel niche space, or via non-adaptive radiation when new species diversify while retaining ancestral niches. However, while cases of adaptive radiation are widely documented, examples of non-adaptively radiating lineages remain rarely observed. A prolific cold-climate lizard radiation from South America (Phymaturus), sister to a hyper-diverse adaptive radiation (Liolaemus), has extensively diversified phylogenetically and geographically, but with exceptionally minimal ecological and life-history diversification. This lineage, therefore, may offer unique opportunities to investigate the non-adaptive basis of diversification, and in combination with Liolaemus, to cover the whole spectrum of modes of diversification predicted by theory, from adaptive to non-adaptive. Using phylogenetic macroevolutionary modelling performed on a newly created 58-species molecular tree, we establish the tempo and mode of diversification in the Phymaturus radiation. Lineage accumulation in Phymaturus opposes a density-dependent (or 'niche-filling') process of diversification. Concurrently, we found that body size diversification is better described by an Ornstein-Uhlenbeck evolutionary model, suggesting stabilizing selection as the mechanism underlying niche conservatism (i.e., maintaining two fundamental size peaks), and which has predominantly evolved around two major adaptive peaks on a 'Simpsonian' adaptive landscape. Lineage diversification of the Phymaturus genus does not conform to an adaptive radiation, as it is characterised by a constant rate of species accumulation during the clade's history. Their strict habitat requirements (rocky outcrops), predominantly invariant herbivory, and especially the constant viviparous reproduction across species have likely limited their opportunities for adaptive diversifications throughout novel environments. This mode of diversification contrasts dramatically with its sister lineage Liolaemus, which geographically overlaps with Phymaturus, but exploits all possible microhabitats in these and other bioclimatic areas. Our study contributes importantly to consolidate these lizards (liolaemids) as promising model systems to investigate the entire spectrum of modes of species formations, from the adaptive to the non-adaptive extremes of the continuum.

Likelihood inference of non-constant diversification rates with incomplete taxon sampling.

PubMed

Höhna, Sebastian

2014-01-01

Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e.g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e.g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models--ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models--on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be violated.

Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint

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

Ramamurthy, Vidhyashankar; Krystek, Jr., Stanley R.; Bush, Alexander

2014-10-02

Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibodymore » combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.« less

76 FR 27738 - Order of Suspension of Trading; In the Matter of Diversified Investors Corp. (n/k/a Diverse...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-12

... of Diversified Investors Corp. (n/k/a Diverse Holdings Corp.), Drew Resources (n/k/a Galloway Energy, Inc.), DTI Medical Corp., DTLL, Inc. (n/k/a Solstice Resorts, Inc.), and Dunn's Supply Store, Inc. May... accurate information concerning the securities of Diversified Investors Corp. (n/k/a Diverse Holdings Corp...

Molecular evolution of respiratory syncytial virus subgroup A genotype NA1 and ON1 attachment glycoprotein (G) gene in central Vietnam.

PubMed

Yoshihara, Keisuke; Le, Minh Nhat; Nagasawa, Koo; Tsukagoshi, Hiroyuki; Nguyen, Hien Anh; Toizumi, Michiko; Moriuchi, Hiroyuki; Hashizume, Masahiro; Ariyoshi, Koya; Dang, Duc Anh; Kimura, Hirokazu; Yoshida, Lay-Myint

2016-11-01

We performed molecular evolutionary analyses of the G gene C-terminal 3rd hypervariable region of RSV-A genotypes NA1 and ON1 strains from the paediatric acute respiratory infection patients in central Vietnam during the 2010-2012 study period. Time-scaled phylogenetic analyses were performed using Bayesian Markov Chain Monte Carlo (MCMC) method, and pairwise distances (p-distances) were calculated. Bayesian Skyline Plot (BSP) was constructed to analyze the time-trend relative genetic diversity of central Vietnam RSV-A strains. We also estimated the N-glycosylation sites within G gene hypervariable region. Amino acid substitutions under positive and negative selection pressure were examined using Conservative Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), Internal Fixed Effects Likelihood (IFEL) and Mixed Effects Model for Episodic Diversifying Selection (MEME) models. The majority of central Vietnam ON1 strains detected in 2012 were classified into lineage 1 with few positively selected substitutions. As for the Vietnamese NA1 strains, four lineages were circulating during the study period with a few positive selection sites. Shifting patterns of the predominantly circulating NA1 lineage were observed in each year during the investigation period. Median p-distance of central Vietnam NA1 strains was wider (p-distance=0.028) than that of ON1 (p-distance=0.012). The molecular evolutionary rate of central Vietnam ON1 strains was estimated to be 2.55×10 -2 (substitutions/site/year) and was faster than NA1 (7.12×10 -3 (substitutions/site/year)). Interestingly, the evolutionary rates of both genotypes ON1 and NA1 strains from central Vietnam were faster than the global strains respectively. Furthermore, the shifts of N-glycosylation pattern within the G gene 3rd hypervariable region of Vietnamese NA1 strains were observed in each year. BSP analysis indicated the rapid growth of RSV-A effective population size in early 2012. These results suggested that the molecular evolution of RSV-A G gene detected in central Vietnam was fast with unique evolutionary dynamics. Copyright © 2016 Elsevier B.V. All rights reserved.

DRIFTSEL: an R package for detecting signals of natural selection in quantitative traits.

PubMed

Karhunen, M; Merilä, J; Leinonen, T; Cano, J M; Ovaskainen, O

2013-07-01

Approaches and tools to differentiate between natural selection and genetic drift as causes of population differentiation are of frequent demand in evolutionary biology. Based on the approach of Ovaskainen et al. (2011), we have developed an R package (DRIFTSEL) that can be used to differentiate between stabilizing selection, diversifying selection and random genetic drift as causes of population differentiation in quantitative traits when neutral marker and quantitative genetic data are available. Apart from illustrating the use of this method and the interpretation of results using simulated data, we apply the package on data from three-spined sticklebacks (Gasterosteus aculeatus) to highlight its virtues. DRIFTSEL can also be used to perform usual quantitative genetic analyses in common-garden study designs. © 2013 John Wiley & Sons Ltd.

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

Rapid diversification of five Oryza AA genomes associated with rice adaptation.

PubMed

Zhang, Qun-Jie; Zhu, Ting; Xia, En-Hua; Shi, Chao; Liu, Yun-Long; Zhang, Yun; Liu, Yuan; Jiang, Wen-Kai; Zhao, You-Jie; Mao, Shu-Yan; Zhang, Li-Ping; Huang, Hui; Jiao, Jun-Ying; Xu, Ping-Zhen; Yao, Qiu-Yang; Zeng, Fan-Chun; Yang, Li-Li; Gao, Ju; Tao, Da-Yun; Wang, Yue-Ju; Bennetzen, Jeffrey L; Gao, Li-Zhi

2014-11-18

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.

Rapid diversification of five Oryza AA genomes associated with rice adaptation

PubMed Central

Zhang, Qun-Jie; Zhu, Ting; Xia, En-Hua; Shi, Chao; Liu, Yun-Long; Zhang, Yun; Liu, Yuan; Jiang, Wen-Kai; Zhao, You-Jie; Mao, Shu-Yan; Zhang, Li-Ping; Huang, Hui; Jiao, Jun-Ying; Xu, Ping-Zhen; Yao, Qiu-Yang; Zeng, Fan-Chun; Yang, Li-Li; Gao, Ju; Tao, Da-Yun; Wang, Yue-Ju; Bennetzen, Jeffrey L.; Gao, Li-Zhi

2014-01-01

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm. PMID:25368197

PLA composites: From production to properties.

PubMed

Murariu, Marius; Dubois, Philippe

2016-12-15

Poly(lactic acid) or polylactide (PLA), a biodegradable polyester produced from renewable resources, is used for various applications (biomedical, packaging, textile fibers and technical items). Due to its inherent properties, PLA has a key-position in the market of biopolymers, being one of the most promising candidates for further developments. Unfortunately, PLA suffers from some shortcomings, whereas for the different applications specific end-use properties are required. Therefore, the addition of reinforcing fibers, micro- and/or nanofillers, and selected additives within PLA matrix is considered as a powerful method for obtaining specific end-use characteristics and major improvements of properties. This review highlights recent developments, current results and trends in the field of composites based on PLA. It presents the main advances in PLA properties and reports selected results in relation to the preparation and characterization of the most representative PLA composites. To illustrate the possibility to design the properties of composites, a section is devoted to the production and characterization of innovative PLA-based products filled with thermally-treated calcium sulfate, a by-product from the lactic acid production process. Moreover, are emphasized the last tendencies strongly evidenced in the case of PLA, i.e., the high interest to diversify its uses by moving from biomedical and packaging (biodegradation properties, "disposables") to technical applications ("durables"). Copyright © 2016 Elsevier B.V. All rights reserved.

Is sexual selection driving diversification of the bioluminescent ponyfishes (Teleostei: Leiognathidae)?

PubMed

Chakrabarty, Prosanta; Davis, Matthew P; Smith, W Leo; Baldwin, Zachary H; Sparks, John S

2011-07-01

Sexual selection may facilitate genetic isolation among populations and result in increased rates of diversification. As a mechanism driving diversification, sexual selection has been invoked and upheld in numerous empirical studies across disparate taxa, including birds, plants and spiders. In this study, we investigate the potential impact of sexual selection on the tempo and mode of ponyfish evolution. Ponyfishes (Leiognathidae) are bioluminescent marine fishes that exhibit sexually dimorphic features of their unique light-organ system (LOS). Although sexual selection is widely considered to be the driving force behind ponyfish speciation, this hypothesis has never been formally tested. Given that some leiognathid species have a sexually dimorphic LOS, whereas others do not, this family provides an excellent system within which to study the potential role of sexual selection in diversification and morphological differentiation. In this study, we estimate the phylogenetic relationships and divergence times for Leiognathidae, investigate the tempo and mode of ponyfish diversification, and explore morphological shape disparity among leiognathid clades. We recover strong support for a monophyletic Leiognathidae and estimate that all major ponyfish lineages evolved during the Paleogene. Our studies of ponyfish diversification demonstrate that there is no conclusive evidence that sexually dimorphic clades are significantly more species rich than nonsexually dimorphic lineages and that evidence is lacking to support any significant diversification rate increases within ponyfishes. Further, we detected a lineage-through-time signal indicating that ponyfishes have continuously diversified through time, which is in contrast to many recent diversification studies that identify lineage-through-time patterns that support mechanisms of density-dependent speciation. Additionally, there is no evidence of sexual selection hindering morphological diversity, as sexually dimorphic taxa are shown to be more disparate in overall shape morphology than nonsexually dimorphic taxa. Our results suggest that if sexual selection is occurring in ponyfish evolution, it is likely acting only as a genetic isolating mechanism that has allowed ponyfishes to continuously diversify over time, with no overall impact on increases in diversification rate or morphological disparity. © 2011 Blackwell Publishing Ltd.

HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC.

PubMed

Wood, Natasha; Bhattacharya, Tanmoy; Keele, Brandon F; Giorgi, Elena; Liu, Michael; Gaschen, Brian; Daniels, Marcus; Ferrari, Guido; Haynes, Barton F; McMichael, Andrew; Shaw, George M; Hahn, Beatrice H; Korber, Bette; Seoighe, Cathal

2009-05-01

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not of mutational hotspots. Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections.

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC

PubMed Central

Wood, Natasha; Bhattacharya, Tanmoy; Keele, Brandon F.; Giorgi, Elena; Liu, Michael; Gaschen, Brian; Daniels, Marcus; Ferrari, Guido; Haynes, Barton F.; McMichael, Andrew; Shaw, George M.; Hahn, Beatrice H.; Korber, Bette; Seoighe, Cathal

2009-01-01

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not of mutational hotspots. Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections. PMID:19424423

Information specialist for a coming age (9)

NASA Astrophysics Data System (ADS)

Shibata, Ryosuke

As competition among enterprises has become severe, the role of information center has increased. The larger the organization becomes because of a diversified business operation, the harder the personnels in charge of business, planning encounter their necessary information. Here is role of information center that it gets users to find appropriate information they need. Also enterprises must select information among vast amount of back-up information, which produces some indication when constructing the strategy. If the information center serves to select such information, analyze and process it, that is exactly categorized as strategic information activities. To promote those activities we have to consider how information centers should be located inside the enterprises.

Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations.

PubMed

Shea, Patrick R; Beres, Stephen B; Flores, Anthony R; Ewbank, Amy L; Gonzalez-Lugo, Javier H; Martagon-Rosado, Alexandro J; Martinez-Gutierrez, Juan C; Rehman, Hina A; Serrano-Gonzalez, Monica; Fittipaldi, Nahuel; Ayers, Stephen D; Webb, Paul; Willey, Barbara M; Low, Donald E; Musser, James M

2011-03-22

Many pathogens colonize different anatomical sites, but the selective pressures contributing to survival in the diverse niches are poorly understood. Group A Streptococcus (GAS) is a human-adapted bacterium that causes a range of infections. Much effort has been expended to dissect the molecular basis of invasive (sterile-site) infections, but little is known about the genomes of strains causing pharyngitis (streptococcal "sore throat"). Additionally, there is essentially nothing known about the genetic relationships between populations of invasive and pharyngitis strains. In particular, it is unclear if invasive strains represent a distinct genetic subpopulation of strains that cause pharyngitis. We compared the genomes of 86 serotype M3 GAS pharyngitis strains with those of 215 invasive M3 strains from the same geographical location. The pharyngitis and invasive groups were highly related to each other and had virtually identical phylogenetic structures, indicating they belong to the same genetic pool. Despite the overall high degree of genetic similarity, we discovered that strains from different host environments (i.e., throat, normally sterile sites) have distinct patterns of diversifying selection at the nucleotide level. In particular, the pattern of polymorphisms in the hyaluronic acid capsule synthesis operon was especially different between the two strain populations. This finding was mirrored by data obtained from full-genome analysis of strains sequentially cultured from nonhuman primates. Our results answer the long-standing question of the genetic relationship between GAS pharyngitis and invasive strains. The data provide previously undescribed information about the evolutionary history of pathogenic microbes that cause disease in different anatomical sites.

Silencing, positive selection and parallel evolution: busy history of primate cytochromes C.

PubMed

Pierron, Denis; Opazo, Juan C; Heiske, Margit; Papper, Zack; Uddin, Monica; Chand, Gopi; Wildman, Derek E; Romero, Roberto; Goodman, Morris; Grossman, Lawrence I

2011-01-01

Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades.

Silencing, Positive Selection and Parallel Evolution: Busy History of Primate Cytochromes c

PubMed Central

Pierron, Denis; Opazo, Juan C.; Heiske, Margit; Papper, Zack; Uddin, Monica; Chand, Gopi; Wildman, Derek E.; Romero, Roberto; Goodman, Morris; Grossman, Lawrence I.

2011-01-01

Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades. PMID:22028846

The evolution of floral nectaries in Disa (Orchidaceae: Disinae): recapitulation or diversifying innovation?

PubMed

Hobbhahn, Nina; Johnson, Steven D; Bytebier, Benny; Yeung, Edward C; Harder, Lawrence D

2013-11-01

The Orchidaceae have a history of recurring convergent evolution in floral function as nectar production has evolved repeatedly from an ancestral nectarless state. However, orchids exhibit considerable diversity in nectary type, position and morphology, indicating that this convergence arose from alternative adaptive solutions. Using the genus Disa, this study asks whether repeated evolution of floral nectaries involved recapitulation of the same nectary type or diversifying innovation. Epidermis morphology of closely related nectar-producing and nectarless species is also compared in order to identify histological changes that accompanied the gain or loss of nectar production. The micromorphology of nectaries and positionally equivalent tissues in nectarless species was examined with light and scanning electron microscopy. This information was subjected to phylogenetic analyses to reconstruct nectary evolution and compare characteristics of nectar-producing and nectarless species. Two nectary types evolved in Disa. Nectar exudation by modified stomata in floral spurs evolved twice, whereas exudation by a secretory epidermis evolved six times in different perianth segments. The spur epidermis of nectarless species exhibited considerable micromorphological variation, including strongly textured surfaces and non-secreting stomata in some species. Epidermis morphology of nectar-producing species did not differ consistently from that of rewardless species at the magnifications used in this study, suggesting that transitions from rewardlessness to nectar production are not necessarily accompanied by visible morphological changes but only require sub-cellular modification. Independent nectary evolution in Disa involved both repeated recapitulation of secretory epidermis, which is present in the sister genus Brownleea, and innovation of stomatal nectaries. These contrasting nectary types and positional diversity within types imply weak genetic, developmental or physiological constraints in ancestral, nectarless Disa. Such functional convergence generated by morphologically diverse solutions probably also underlies the extensive diversity of nectary types and positions in the Orchidaceae.

Maximizing lipocalin prediction through balanced and diversified training set and decision fusion.

PubMed

Nath, Abhigyan; Subbiah, Karthikeyan

2015-12-01

Lipocalins are short in sequence length and perform several important biological functions. These proteins are having less than 20% sequence similarity among paralogs. Experimentally identifying them is an expensive and time consuming process. The computational methods based on the sequence similarity for allocating putative members to this family are also far elusive due to the low sequence similarity existing among the members of this family. Consequently, the machine learning methods become a viable alternative for their prediction by using the underlying sequence/structurally derived features as the input. Ideally, any machine learning based prediction method must be trained with all possible variations in the input feature vector (all the sub-class input patterns) to achieve perfect learning. A near perfect learning can be achieved by training the model with diverse types of input instances belonging to the different regions of the entire input space. Furthermore, the prediction performance can be improved through balancing the training set as the imbalanced data sets will tend to produce the prediction bias towards majority class and its sub-classes. This paper is aimed to achieve (i) the high generalization ability without any classification bias through the diversified and balanced training sets as well as (ii) enhanced the prediction accuracy by combining the results of individual classifiers with an appropriate fusion scheme. Instead of creating the training set randomly, we have first used the unsupervised Kmeans clustering algorithm to create diversified clusters of input patterns and created the diversified and balanced training set by selecting an equal number of patterns from each of these clusters. Finally, probability based classifier fusion scheme was applied on boosted random forest algorithm (which produced greater sensitivity) and K nearest neighbour algorithm (which produced greater specificity) to achieve the enhanced predictive performance than that of individual base classifiers. The performance of the learned models trained on Kmeans preprocessed training set is far better than the randomly generated training sets. The proposed method achieved a sensitivity of 90.6%, specificity of 91.4% and accuracy of 91.0% on the first test set and sensitivity of 92.9%, specificity of 96.2% and accuracy of 94.7% on the second blind test set. These results have established that diversifying training set improves the performance of predictive models through superior generalization ability and balancing the training set improves prediction accuracy. For smaller data sets, unsupervised Kmeans based sampling can be an effective technique to increase generalization than that of the usual random splitting method. Copyright © 2015 Elsevier Ltd. All rights reserved.

Time-Sampled Population Sequencing Reveals the Interplay of Selection and Genetic Drift in Experimental Evolution of Potato Virus Y

PubMed Central

2017-01-01

ABSTRACT RNA viruses are one of the fastest-evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection, and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant-pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly generated variations in the evolving viral lineages. A time-sampled approach allowed us to (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less-susceptible host (efficient in the accumulation of salicylic acid). IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes. PMID:28592544

Aposematism increases acoustic diversification and speciation in poison frogs

PubMed Central

Santos, Juan C.; Baquero, Margarita; Barrio-Amorós, César; Coloma, Luis A.; Erdtmann, Luciana K.; Lima, Albertina P.; Cannatella, David C.

2014-01-01

Multimodal signals facilitate communication with conspecifics during courtship, but they can also alert eavesdropper predators. Hence, signallers face two pressures: enticing partners to mate and avoiding detection by enemies. Undefended organisms with limited escape abilities are expected to minimize predator recognition over mate attraction by limiting or modifying their signalling. Alternatively, organisms with anti-predator mechanisms such as aposematism (i.e. unprofitability signalled by warning cues) might elaborate mating signals as a consequence of reduced predation. We hypothesize that calls diversified in association with aposematism. To test this, we assembled a large acoustic signal database for a diurnal lineage of aposematic and cryptic/non-defended taxa, the poison frogs. First, we showed that aposematic and non-aposematic species share similar extinction rates, and aposematic lineages diversify more and rarely revert to the non-aposematic phenotype. We then characterized mating calls based on morphological (spectral), behavioural/physiological (temporal) and environmental traits. Of these, only spectral and temporal features were associated with aposematism. We propose that with the evolution of anti-predator defences, reduced predation facilitated the diversification of vocal signals, which then became elaborated or showy via sexual selection. PMID:25320164

Crop diversification and livelihoods of smallholder farmers in Zimbabwe: adaptive management for environmental change.

PubMed

Makate, Clifton; Wang, Rongchang; Makate, Marshall; Mango, Nelson

2016-01-01

This paper demonstrates how crop diversification impacts on two outcomes of climate smart agriculture; increased productivity (legume and cereal crop productivity) and enhanced resilience (household income, food security, and nutrition) in rural Zimbabwe. Using data from over 500 smallholder farmers, we jointly estimate crop diversification and each of the outcome variables within a conditional (recursive) mixed process framework that corrects for selectivity bias arising due to the voluntary nature of crop diversification. We find that crop diversification depends on the land size, farming experience, asset wealth, location, access to agricultural extension services, information on output prices, low transportation costs and general information access. Our results also indicate that an increase in the rate of adoption improves crop productivity, income, food security and nutrition at household level. Overall, our results are indicative of the importance of crop diversification as a viable climate smart agriculture practice that significantly enhances crop productivity and consequently resilience in rural smallholder farming systems. We, therefore, recommend wider adoption of diversified cropping systems notably those currently less diversified for greater adaptation to the ever-changing climate.

Facilitating Research in Physician Assistant Programs: Creating a Student-Level Longitudinal Database.

PubMed

Morgan, Perri; Humeniuk, Katherine M; Everett, Christine M

2015-09-01

As physician assistant (PA) roles expand and diversify in the United States and around the world, there is a pressing need for research that illuminates how PAs may best be selected, educated, and used in health systems to maximize their potential contributions to health. Physician assistant education programs are well positioned to advance this research by collecting and organizing data on applicants, students, and graduates. Our PA program is creating a permanent longitudinal education database for research that contains extensive student-level data. This database will allow us to conduct research on all phases of PA education, from admission processes through the professional practice of our graduates. In this article, we describe our approach to constructing a longitudinal student-level research database and discuss the strengths and limitations of longitudinal databases for research on education and the practice of PAs. We hope to encourage other PA programs to initiate similar projects so that, in the future, data can be combined for use in multi-institutional research that can contribute to improved education for PA students across programs.

Multi-Attribute Selection of Coal Center Location: A Case Study in Thailand

NASA Astrophysics Data System (ADS)

Kuakunrittiwong, T.; Ratanakuakangwan, S.

2016-11-01

Under Power Development Plan 2015, Thailand has to diversify its heavily gas-fired electricity generation. The main owner of electricity transmission grids is responsible to implement several coal-fired power plants with clean coal technology. To environmentally handle and economically transport unprecedented quantities of sub-bituminous and bituminous coal, a coal center is required. The location of such facility is an important strategic decision and a paramount to the success of the energy plan. As site selection involves many criteria, Fuzzy Analytical Hierarchy Process or Fuzzy-AHP is applied to select the most suitable location among three candidates. Having analyzed relevant criteria and the potential alternatives, the result reveals that engineering and socioeconomic are important criteria and Map Ta Phut is the most suitable site for the coal center.

Electric utility of the year for 1984: Potomac Electric Power

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

Not Available

1984-11-01

High performance, efficiency improvements, a modest construction program, a clear balance sheet, and an effort to expend power plant life were among the qualities that earned Potomac Electric Power (PEPCO) the title of 1984 Utility of the Year. Other key elements in the utility's selection were its strategy for purchasing power, a load management plan, diversified investments into subsidiary businesses, community concern that considers the aesthetics of transmission facilities, and its interest in personnel development, especially among minorities. 3 figures.

Multi-objective possibilistic model for portfolio selection with transaction cost

NASA Astrophysics Data System (ADS)

Jana, P.; Roy, T. K.; Mazumder, S. K.

2009-06-01

In this paper, we introduce the possibilistic mean value and variance of continuous distribution, rather than probability distributions. We propose a multi-objective Portfolio based model and added another entropy objective function to generate a well diversified asset portfolio within optimal asset allocation. For quantifying any potential return and risk, portfolio liquidity is taken into account and a multi-objective non-linear programming model for portfolio rebalancing with transaction cost is proposed. The models are illustrated with numerical examples.

Rates of ecological divergence and body size evolution are correlated with species diversification in scaly tree ferns

PubMed Central

Ramírez-Barahona, Santiago; Barrera-Redondo, Josué; Eguiarte, Luis E.

2016-01-01

Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this ‘ancient’ fern lineage across the tropics. PMID:27412279

Rates of ecological divergence and body size evolution are correlated with species diversification in scaly tree ferns.

PubMed

Ramírez-Barahona, Santiago; Barrera-Redondo, Josué; Eguiarte, Luis E

2016-07-13

Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this 'ancient' fern lineage across the tropics. © 2016 The Author(s).

Geographical gradients in selection can reveal genetic constraints for evolutionary responses to ocean acidification

PubMed Central

Gaitán-Espitia, Juan Diego; Marshall, Dustin; Dupont, Sam; Bacigalupe, Leonardo D.; Bodrossy, Levente; Hobday, Alistair J.

2017-01-01

Geographical gradients in selection can shape different genetic architectures in natural populations, reflecting potential genetic constraints for adaptive evolution under climate change. Investigation of natural pH/pCO2 variation in upwelling regions reveals different spatio-temporal patterns of natural selection, generating genetic and phenotypic clines in populations, and potentially leading to local adaptation, relevant to understanding effects of ocean acidification (OA). Strong directional selection, associated with intense and continuous upwellings, may have depleted genetic variation in populations within these upwelling regions, favouring increased tolerances to low pH but with an associated cost in other traits. In contrast, diversifying or weak directional selection in populations with seasonal upwellings or outside major upwelling regions may have resulted in higher genetic variances and the lack of genetic correlations among traits. Testing this hypothesis in geographical regions with similar environmental conditions to those predicted under climate change will build insights into how selection may act in the future and how populations may respond to stressors such as OA. PMID:28148831

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

A critical approach to the definition of Darwinian units of selection.

PubMed

Rinkevich, B

2000-12-01

What are the biological units of selection? In fact, the notion of "unit of selection" (UOS) is blurred by ambiguity and controversy. To further evaluate the biological entities that are the objects of natural selection, three novel conceptual criteria (holism, minimalism, functionalism) are critically applied; they reveal, in addition to the self-evident case of the "individual," at least six distinct types of UOSs. These UOSs do not always have a defined structural organization; they can be parts of a living organism, a cohesive group of conspecifics, a multiunit entity, a totipotent cell, a DNA fragment, or a whole organism. UOS types diversify by amalgamation or parcelation processes of apparent entities. Therefore, previous attempts to characterize the UOSs solely on some morphological levels (gene, individual, group) without applying stringent criteria have failed to cope with the structural variations of natural phenomena and have led to the ambiguity of terms used.

Phylogenetic divergence of cell biological features

PubMed Central

2018-01-01

Most cellular features have a range of states, but understanding the mechanisms responsible for interspecific divergence is a challenge for evolutionary cell biology. Models are developed for the distribution of mean phenotypes likely to evolve under the joint forces of mutation and genetic drift in the face of constant selection pressures. Mean phenotypes will deviate from optimal states to a degree depending on the effective population size, potentially leading to substantial divergence in the absence of diversifying selection. The steady-state distribution for the mean can even be bimodal, with one domain being largely driven by selection and the other by mutation pressure, leading to the illusion of phenotypic shifts being induced by movement among alternative adaptive domains. These results raise questions as to whether lineage-specific selective pressures are necessary to account for interspecific divergence, providing a possible platform for the establishment of null models for the evolution of cell-biological traits. PMID:29927740

Ecological opportunity and the adaptive diversification of lineages

PubMed Central

Wellborn, Gary A; Langerhans, R Brian

2015-01-01

The tenet that ecological opportunity drives adaptive diversification has been central to theories of speciation since Darwin, yet no widely accepted definition or mechanistic framework for the concept currently exists. We propose a definition for ecological opportunity that provides an explicit mechanism for its action. In our formulation, ecological opportunity refers to environmental conditions that both permit the persistence of a lineage within a community, as well as generate divergent natural selection within that lineage. Thus, ecological opportunity arises from two fundamental elements: (1) niche availability, the ability of a population with a phenotype previously absent from a community to persist within that community and (2) niche discordance, the diversifying selection generated by the adaptive mismatch between a population's niche-related traits and the newly encountered ecological conditions. Evolutionary response to ecological opportunity is primarily governed by (1) spatiotemporal structure of ecological opportunity, which influences dynamics of selection and development of reproductive isolation and (2) diversification potential, the biological properties of a lineage that determine its capacity to diversify. Diversification under ecological opportunity proceeds as an increase in niche breadth, development of intraspecific ecotypes, speciation, and additional cycles of diversification that may themselves be triggered by speciation. Extensive ecological opportunity may exist in depauperate communities, but it is unclear whether ecological opportunity abates in species-rich communities. Because ecological opportunity should generally increase during times of rapid and multifarious environmental change, human activities may currently be generating elevated ecological opportunity – but so far little work has directly addressed this topic. Our framework highlights the need for greater synthesis of community ecology and evolutionary biology, unifying the four major components of the concept of ecological opportunity. PMID:25628875

Ecological opportunity and the adaptive diversification of lineages.

PubMed

Wellborn, Gary A; Langerhans, R Brian

2015-01-01

The tenet that ecological opportunity drives adaptive diversification has been central to theories of speciation since Darwin, yet no widely accepted definition or mechanistic framework for the concept currently exists. We propose a definition for ecological opportunity that provides an explicit mechanism for its action. In our formulation, ecological opportunity refers to environmental conditions that both permit the persistence of a lineage within a community, as well as generate divergent natural selection within that lineage. Thus, ecological opportunity arises from two fundamental elements: (1) niche availability, the ability of a population with a phenotype previously absent from a community to persist within that community and (2) niche discordance, the diversifying selection generated by the adaptive mismatch between a population's niche-related traits and the newly encountered ecological conditions. Evolutionary response to ecological opportunity is primarily governed by (1) spatiotemporal structure of ecological opportunity, which influences dynamics of selection and development of reproductive isolation and (2) diversification potential, the biological properties of a lineage that determine its capacity to diversify. Diversification under ecological opportunity proceeds as an increase in niche breadth, development of intraspecific ecotypes, speciation, and additional cycles of diversification that may themselves be triggered by speciation. Extensive ecological opportunity may exist in depauperate communities, but it is unclear whether ecological opportunity abates in species-rich communities. Because ecological opportunity should generally increase during times of rapid and multifarious environmental change, human activities may currently be generating elevated ecological opportunity - but so far little work has directly addressed this topic. Our framework highlights the need for greater synthesis of community ecology and evolutionary biology, unifying the four major components of the concept of ecological opportunity.

Superstar of the Sloan Minority Ph.D. Program.

PubMed

Greenwood, Ted

2013-01-01

In AY 1994-95 the Alfred P. Sloan Foundation launched a program, later known as the Minority Ph.D. Program, to increase the number of underrepresented minority students earning Ph.D.s in natural sciences, engineering and mathematics (SEM). This program emerged from a recognition that African Americans, Hispanic Americans and American Indians were very underrepresented at all levels and in all aspects of SEM disciplines and that, although undergraduate education had received and continued to received much attention by universities, private funders and government agencies, there was still relatively little attention being paid to the graduate and especially the Ph.D. level. Because earning the Ph.D. is a necessary milestone along the pathway to a faculty position and the effort to diversify the graduates of SEM disciplines depends, in large part, on diversifying the faculty at American universities, this relative lack of attention to Ph.D. education was, in the opinion of the Sloan Foundation, a significant deficiency of national efforts. As a Program Director at the Sloan Foundation, I initiated this Minority Ph.D. Program and ran it until my retirement in June 2011.

An overview of international issues in astronaut psychological selection.

PubMed

Santy, P A; Jones, D R

1994-10-01

The NASA Johnson Space Center Medical Sciences Division convened an In-House Working Group on Psychiatric and Psychological Selection of Astronauts in 1988. Working with the European Space Agency (ESA) and the National Space Development Agency (NASDA) of Japan, psychiatrists and psychologists experienced in selecting individuals for training as astronauts or analogous duties studied the development of appropriate criteria. Psychiatric criteria generally concern the detection of pathological conditions, and thus "select-out" applicants by disqualification. Psychological criteria may be used to identify specific affirmative criteria that make an individual particularly well-qualified for such duties, and thus concern "select-in" processes for operational crews. As space missions grow longer, and as crews become larger and more demographically diversified, the long-ignored questions, "What sort of healthy individuals should be selected for such missions," and "How do we know this?" will become more critical to the success of space exploration. The papers included in this Panel concern the results of these investigations, and represent long-needed quantification of these two selection processes, select-out and select-in, in several cultures.

Diversified integration of practical teaching resources in ideological and political course in colleges and universities

NASA Astrophysics Data System (ADS)

Xu, Jin; Chu, Biao

2018-03-01

To promote diversified integration and integrated use of practical teaching resources in ideological and political education in colleges and universities is helpful to extend the ideological and political teaching activities in colleges and universities, to update and supplement ideological and political knowledge, to build a harmonious learning environment for students and to comprehensively improve their ideological and political accomplishments. This article will analyze of ideological and political practical teaching resources diversified integration and the integration of programs by examples, and put forward personal opinions.

Selection Gradients, the Opportunity for Selection, and the Coefficient of Determination

PubMed Central

Moorad, Jacob A.; Wade, Michael J.

2013-01-01

We derive the relationship between R2 (the coefficient of determination), selection gradients, and the opportunity for selection for univariate and multivariate cases. Our main result is to show that the portion of the opportunity for selection that is caused by variation for any trait is equal to the product of its selection gradient and its selection differential. This relationship is a corollary of the first and second fundamental theorems of natural selection, and it permits one to investigate the portions of the total opportunity for selection that are involved in directional selection, stabilizing (and diversifying) selection, and correlational selection, which is important to morphological integration. It also allows one to determine the fraction of fitness variation not explained by variation in measured phenotypes and therefore attributable to random (or, at least, unknown) influences. We apply our methods to a human data set to show how sex-specific mating success as a component of fitness variance can be decoupled from that owing to prereproductive mortality. By quantifying linear sources of sexual selection and quadratic sources of sexual selection, we illustrate that the former is stronger in males, while the latter is stronger in females. PMID:23448880

Selection gradients, the opportunity for selection, and the coefficient of determination.

PubMed

Moorad, Jacob A; Wade, Michael J

2013-03-01

Abstract We derive the relationship between R(2) (the coefficient of determination), selection gradients, and the opportunity for selection for univariate and multivariate cases. Our main result is to show that the portion of the opportunity for selection that is caused by variation for any trait is equal to the product of its selection gradient and its selection differential. This relationship is a corollary of the first and second fundamental theorems of natural selection, and it permits one to investigate the portions of the total opportunity for selection that are involved in directional selection, stabilizing (and diversifying) selection, and correlational selection, which is important to morphological integration. It also allows one to determine the fraction of fitness variation not explained by variation in measured phenotypes and therefore attributable to random (or, at least, unknown) influences. We apply our methods to a human data set to show how sex-specific mating success as a component of fitness variance can be decoupled from that owing to prereproductive mortality. By quantifying linear sources of sexual selection and quadratic sources of sexual selection, we illustrate that the former is stronger in males, while the latter is stronger in females.

Biochronostratigraphy and paleoenvironment analysis of Neogene deposits from the Pelotas Basin (well 2-TG-96-RS), Southernmost Brazil.

PubMed

Silva, Wagner G; Zerfass, Geise S A; Souza, Paulo A; Helenes, Javier

2015-09-01

This paper presents the integration of micropaleontological (palynology and foraminifera) and isotopic (87Sr/86Sr) analysis of a selected interval from the well 2-TG-96-RS, drilled on the onshore portion of the Pelotas Basin, Rio Grande do Sul, Brazil. A total of eight samples of the section between 140.20 and 73.50 m in depth was selected for palynological analysis, revealing diversified and abundant palynomorph associations. Species of spores, pollen grains and dinoflagellate cysts are the most common palynomorphs found. Planktic and benthic calcareous foraminifera were recovered from the lowest two levels of the section (140.20 and 134.30 m). Based on the stratigraphic range of the species of dinoflagellate cysts and sporomorphs, a span age from Late Miocene to Early Pliocene is assigned. The relative age obtained from the 87Sr/86Sr ratio in shells of calcareous foraminifers indicates a Late Miocene (Messinian) correspondence, corroborating the biostratigraphic positioning performed with palynomorphs. Paleoenvironmental interpretations based on the quantitative distribution of organic components (palynomorphs, phytoclasts and amorphous organic matter) throughout the section and on foraminiferal associations indicate a shallow marine depositional environment for the section. Two palynologicals intervals were recognized based on palynofacies analysis, related to middle to outer shelf (140.20 to 128.90 m) and inner shelf (115.75 to 73.50 m) conditions.

The role of extinction in evolution

NASA Technical Reports Server (NTRS)

Raup, D. M.

1994-01-01

The extinction of species is not normally considered an important element of neodarwinian theory, in contrast to the opposite phenomenon, speciation. This is surprising in view of the special importance Darwin attached to extinction, and because the number of species extinctions in the history of life is almost the same as the number of originations; present-day biodiversity is the result of a trivial surplus of originations, cumulated over millions of years. For an evolutionary biologist to ignore extinction is probably as foolhardy as for a demographer to ignore mortality. The past decade has seen a resurgence of interest in extinction, yet research on the topic is still at a reconnaissance level, and our present understanding of its role in evolution is weak. Despite uncertainties, extinction probably contains three important elements. (i) For geographically widespread species, extinction is likely only if the killing stress is one so rare as to be beyond the experience of the species, and thus outside the reach of natural selection. (ii) The largest mass extinctions produce major restructuring of the biosphere wherein some successful groups are eliminated, allowing previously minor groups to expand and diversify. (iii) Except for a few cases, there is little evidence that extinction is selective in the positive sense argued by Darwin. It has generally been impossible to predict, before the fact, which species will be victims of an extinction event.

[Idea and practice of ZHU Lian concerning acupuncture education].

PubMed

Zhang, Li-Jian; Liu, Bing; Xu, Qing-Yan; Ran, Sheng-Qi

2014-08-01

ZHU Lian is a deceased famous acupuncture and Moxibustion specialist, the first director and the founder of institute of Acupuncture-Moxibustion of China Academy of Chinese Medical Sciences. This article discusses the thought and idea of education and teaching of acupuncture-moxibustion from the following three aspects: diversified education and training mode, teaching idea of new acupuncture-moxibustion with a lot of characteristics, and the founding of professional acupuncture-moxibustion college. All above have both distinct characteristics of the times and positively enlightening significance of reality.

Will China Be Caught in the Middle-Income Trap? The Economic Path of South Korea and Malaysia May Help Provide the Answer

DTIC Science & Technology

2014-12-01

outcomes. Child mortality, education of children , and income distribution has been show to be positively affected by strong education policy. 31 In a...and science, but are less rigid and more diversified, create a paradigm that fosters innovation and entrepreneurship .35 Research show that innovation...Ratio of children and old people to people of working age. 42 Aiyar et al., Growth Slowdowns and the Middle-Income Trap, 19. 17 B. CASE EXAMPLES The

Asymmetry of price returns—Analysis and perspectives from a non-extensive statistical physics point of view

PubMed Central

Bil, Łukasz; Zienowicz, Magdalena

2017-01-01

We study how the approach grounded on non-extensive statistical physics can be applied to describe and distinguish different stages of the stock and money market development. A particular attention is given to asymmetric behavior of fat tailed distributions of positive and negative returns. A new method to measure this asymmetry is proposed. It is based on the value of the non-extensive Tsallis parameter q. The new quantifier of the relative asymmetry level between tails in terms of the Tsallis parameters q± is provided to analyze the effect of memory in data caused by nonlinear autocorrelations. The presented analysis takes into account data of separate stocks from the main developing stock market in Europe, i.e., the Warsaw Stock Exchange (WSE) in Poland and—for comparison—data from the most mature money market (Forex). It is argued that the proposed new quantifier is able to describe the stage of market development and its robustness to speculation. The main strength is put on a description and interpretation of the asymmetry between statistical properties of positive and negative returns for various stocks and for diversified time-lags Δt of data counting. The particular caution in this context is addressed to the difference between intraday and interday returns. Our search is extended to study memory effects and their dependence on the quotation frequency for similar large companies—owners of food-industrial retail supermarkets acting on both Polish and European markets (Eurocash, Jeronimo-Martins, Carrefour, Tesco)—but traded on various European stock markets of diversified economical maturity (respectively in Warsaw, Lisbon, Paris and London). The latter analysis seems to indicate quantitatively that stocks from the same economic sector traded on different markets within European Union (EU) may be a target of diversified level of speculations involved in trading independently on the true economic situation of the company. Our work thus gives indications that the statement:” where you are is more important than who you are” is true on trading markets. PMID:29190696

Asymmetry of price returns-Analysis and perspectives from a non-extensive statistical physics point of view.

PubMed

Bil, Łukasz; Grech, Dariusz; Zienowicz, Magdalena

2017-01-01

We study how the approach grounded on non-extensive statistical physics can be applied to describe and distinguish different stages of the stock and money market development. A particular attention is given to asymmetric behavior of fat tailed distributions of positive and negative returns. A new method to measure this asymmetry is proposed. It is based on the value of the non-extensive Tsallis parameter q. The new quantifier of the relative asymmetry level between tails in terms of the Tsallis parameters q± is provided to analyze the effect of memory in data caused by nonlinear autocorrelations. The presented analysis takes into account data of separate stocks from the main developing stock market in Europe, i.e., the Warsaw Stock Exchange (WSE) in Poland and-for comparison-data from the most mature money market (Forex). It is argued that the proposed new quantifier is able to describe the stage of market development and its robustness to speculation. The main strength is put on a description and interpretation of the asymmetry between statistical properties of positive and negative returns for various stocks and for diversified time-lags Δt of data counting. The particular caution in this context is addressed to the difference between intraday and interday returns. Our search is extended to study memory effects and their dependence on the quotation frequency for similar large companies-owners of food-industrial retail supermarkets acting on both Polish and European markets (Eurocash, Jeronimo-Martins, Carrefour, Tesco)-but traded on various European stock markets of diversified economical maturity (respectively in Warsaw, Lisbon, Paris and London). The latter analysis seems to indicate quantitatively that stocks from the same economic sector traded on different markets within European Union (EU) may be a target of diversified level of speculations involved in trading independently on the true economic situation of the company. Our work thus gives indications that the statement:" where you are is more important than who you are" is true on trading markets.

5 CFR 2634.1006 - Rollover into permitted property.

Code of Federal Regulations, 2010 CFR

2010-01-01

... proceeds in such securities. However, she may invest the proceeds in a diversified mutual fund. See the... the proceeds of the sale and reinvest them in an S&P Index Fund, a diversified Growth Stock Fund, and...

5 CFR 2634.1006 - Rollover into permitted property.

Code of Federal Regulations, 2011 CFR

2011-01-01

... proceeds in such securities. However, she may invest the proceeds in a diversified mutual fund. See the... the proceeds of the sale and reinvest them in an S&P Index Fund, a diversified Growth Stock Fund, and...

Relative frequencies of DRB1*11 alleles and their DRB3 associations in five major population groups in a United States bone marrow registry.

PubMed

Tang, T F; Huang, A Y; Pappas, A; Slack, R; Ng, J; Hartzman, R J; Hurley, C K

2000-08-01

One hundred sixty-one individuals from each of five US population groups, Caucasians (CAU), African Americans (AFA), Asians/Pacific Islanders (API), Hispanics (HIS), and Native Americans (NAT), were randomly selected from a volunteer bone marrow registry database consisting of 14,452 HLA-DRB1*11 positive individuals. This sampling provided at least an 80% probability of detecting a rare allele that occurred at 1% in the DRB1*11 positive population. Samples were typed for DRB1*11 alleles by polymerase chain reaction-sequence specific oligonucleotide probe typing (PCR-SSOP). A total of 10 DRB1*11 alleles out of 27 possible alleles were detected. The distribution and diversity of DRB1*11 alleles varied among populations although DRB1*1101 was the predominant DRB1*11 allele in all populations. Caucasians were the least diversified; only four common alleles (DRB1*1101-*1104) were observed. As well as the four common alleles, other groups also carried one or two other less frequent alleles including DRB1*1105 (API), *1106 (API), *1110 (AFA), *1114 (HIS), *1115 (NAT), and *1117 (AFA). A subset (418) of these individuals were also typed for DRB3 alleles. Most (97.6%) showed a strong association of DRB1*11 with DRB3*0202.

Optimal management of ALK-positive NSCLC progressing on crizotinib.

PubMed

Metro, Giulio; Tazza, Marco; Matocci, Roberta; Chiari, Rita; Crinò, Lucio

2017-04-01

Crizotinib is an anaplastic lymphoma kinase (ALK)-tyrosine kinase inhibitor (-TKI) that represents the standard first-line treatment of patients with ALK-rearranged (ALK-positive) advanced non-small cell lung cancer (NSCLC). In this setting, crizotinib has demonstrated a response rate of roughly 75% and a median progression-free survival just under one year. However, acquired resistance will emerge in virtually all crizotinib-treated patients, whose management may require a diversified approach according to the pace of the disease and/or the site(s) of disease progression. Crizotinib beyond disease progression is an option in patients with oligoprogressive disease, especially in presence of isolated central nervous system (CNS) relapse, provided that local ablative therapy (mainly radiotherapy) to the brain is administered. On the other hand, novel more potent and highly selective ALK-TKIs with demonstrated anti-tumor activity (CNS included) in crizotinib-refractory patients have been made available in recent years. Therefore, clinicians may well consider switching to a second-generation ALK-TKI as treatment option in case of progression on crizotinib. Therapeutic chances are more limited for patients who progress after crizotinib and a second-generation ALK-TKI, for whom both a third-generation ALK-TKI or pemetrexed-based chemotherapy could prove beneficial, while evidence in support of the use of immunotherapy in patients pretreated with ≥1 ALK-TKI is lacking. Copyright © 2017 Elsevier B.V. All rights reserved.

45 CFR 73a.735-501 - General provisions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... restrictions are placed on ownership of diversified mutual funds. (b) An FDA employee, other than a control... prohibition is not applicable to: (1) Diversified mutual funds, which are exempted from 18 U.S.C. 208 by § 73...

45 CFR 73a.735-501 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... restrictions are placed on ownership of diversified mutual funds. (b) An FDA employee, other than a control... prohibition is not applicable to: (1) Diversified mutual funds, which are exempted from 18 U.S.C. 208 by § 73...

Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.

PubMed

Farrer, Rhys A; Desjardins, Christopher A; Sakthikumar, Sharadha; Gujja, Sharvari; Saif, Sakina; Zeng, Qiandong; Chen, Yuan; Voelz, Kerstin; Heitman, Joseph; May, Robin C; Fisher, Matthew C; Cuomo, Christina A

2015-09-01

Cryptococcus gattii is a fungal pathogen of humans, causing pulmonary infections in otherwise healthy hosts. To characterize genomic variation among the four major lineages of C. gattii (VGI, -II, -III, and -IV), we generated, annotated, and compared 16 de novo genome assemblies, including the first for the rarely isolated lineages VGIII and VGIV. By identifying syntenic regions across assemblies, we found 15 structural rearrangements, which were almost exclusive to the VGI-III-IV lineages. Using synteny to inform orthology prediction, we identified a core set of 87% of C. gattii genes present as single copies in all four lineages. Remarkably, 737 genes are variably inherited across lineages and are overrepresented for response to oxidative stress, mitochondrial import, and metal binding and transport. Specifically, VGI has an expanded set of iron-binding genes thought to be important to the virulence of Cryptococcus, while VGII has expansions in the stress-related heat shock proteins relative to the other lineages. We also characterized genes uniquely absent in each lineage, including a copper transporter absent from VGIV, which influences Cryptococcus survival during pulmonary infection and the onset of meningoencephalitis. Through inclusion of population-level data for an additional 37 isolates, we identified a new transcontinental clonal group that we name VGIIx, mitochondrial recombination between VGII and VGIII, and positive selection of multidrug transporters and the iron-sulfur protein aconitase along multiple branches of the phylogenetic tree. Our results suggest that gene expansion or contraction and positive selection have introduced substantial variation with links to mechanisms of pathogenicity across this species complex. The genetic differences between phenotypically different pathogens provide clues to the underlying mechanisms of those traits and can lead to new drug targets and improved treatments for those diseases. In this paper, we compare 16 genomes belonging to four highly differentiated lineages of Cryptococcus gattii, which cause pulmonary infections in otherwise healthy humans and other animals. Half of these lineages have not had their genomes previously assembled and annotated. We identified 15 ancestral rearrangements in the genome and over 700 genes that are unique to one or more lineages, many of which are associated with virulence. In addition, we found evidence for recent transcontinental spread, mitochondrial genetic exchange, and positive selection in multidrug transporters. Our results suggest that gene expansion/contraction and positive selection are diversifying the mechanisms of pathogenicity across this species complex. Copyright © 2015 Farrer et al.

Short-term prey field lability constrains individual specialisation in resource selection and foraging site fidelity in a marine predator.

PubMed

Courbin, Nicolas; Besnard, Aurélien; Péron, Clara; Saraux, Claire; Fort, Jérôme; Perret, Samuel; Tornos, Jérémy; Grémillet, David

2018-04-16

Spatio-temporally stable prey distributions coupled with individual foraging site fidelity are predicted to favour individual resource specialisation. Conversely, predators coping with dynamic prey distributions should diversify their individual diet and/or shift foraging areas to increase net intake. We studied individual specialisation in Scopoli's shearwaters (Calonectris diomedea) from the highly dynamic Western Mediterranean, using daily prey distributions together with resource selection, site fidelity and trophic-level analyses. As hypothesised, we found dietary diversification, low foraging site fidelity and almost no individual specialisation in resource selection. Crucially, shearwaters switched daily foraging tactics, selecting areas with contrasting prey of varying trophic levels. Overall, information use and plastic resource selection of individuals with reduced short-term foraging site fidelity allow predators to overcome prey field lability. Our study is an essential step towards a better understanding of individual responses to enhanced environmental stochasticity driven by global changes, and of pathways favouring population persistence. © 2018 John Wiley & Sons Ltd/CNRS.

Invariant features of spatial inequality in consumption: The case of India

NASA Astrophysics Data System (ADS)

Chatterjee, Arnab; Chakrabarti, Anindya S.; Ghosh, Asim; Chakraborti, Anirban; Nandi, Tushar K.

2016-01-01

We study the distributional features and inequality of consumption expenditure across India, for different states, castes, religion and urban-rural divide. We find that even though the aggregate measures of inequality are fairly diversified across states, the consumption distributions show near identical statistics, once properly normalized. This feature is seen to be robust with respect to variations in sociological and economic factors. We also show that state-wise inequality seems to be positively correlated with growth which is in accord with the traditional idea of Kuznets' curve. We present a brief model to account for the invariance found empirically and show that better but riskier technology draws can create a positive correlation between inequality and growth.

The Goddard and Saturn Genes Are Essential for Drosophila Male Fertility and May Have Arisen De Novo

PubMed Central

Gubala, Anna M.; Schmitz, Jonathan F.; Kearns, Michael J.; Vinh, Tery T.; Bornberg-Bauer, Erich; Wolfner, Mariana F.

2017-01-01

New genes arise through a variety of mechanisms, including the duplication of existing genes and the de novo birth of genes from noncoding DNA sequences. While there are numerous examples of duplicated genes with important functional roles, the functions of de novo genes remain largely unexplored. Many newly evolved genes are expressed in the male reproductive tract, suggesting that these evolutionary innovations may provide advantages to males experiencing sexual selection. Using testis-specific RNA interference, we screened 11 putative de novo genes in Drosophila melanogaster for effects on male fertility and identified two, goddard and saturn, that are essential for spermatogenesis and sperm function. Goddard knockdown (KD) males fail to produce mature sperm, while saturn KD males produce few sperm, and these function inefficiently once transferred to females. Consistent with a de novo origin, both genes are identifiable only in Drosophila and are predicted to encode proteins with no sequence similarity to any annotated protein. However, since high levels of divergence prevented the unambiguous identification of the noncoding sequences from which each gene arose, we consider goddard and saturn to be putative de novo genes. Within Drosophila, both genes have been lost in certain lineages, but show conserved, male-specific patterns of expression in the species in which they are found. Goddard is consistently found in single-copy and evolves under purifying selection. In contrast, saturn has diversified through gene duplication and positive selection. These data suggest that de novo genes can acquire essential roles in male reproduction. PMID:28104747

Impact of historical founder effects and a recent bottleneck on MHC variability in Commander Arctic foxes (Vulpes lagopus)

PubMed Central

Ploshnitsa, Anna I; Goltsman, Mikhail E; Macdonald, David W; Kennedy, Lorna J; Sommer, Simone

2012-01-01

Populations of Arctic foxes (Vulpes lagopus) have been isolated on two of the Commander Islands (Bering and Mednyi) from the circumpolar distributed mainland population since the Pleistocene. In 1970–1980, an epizootic outbreak of mange caused a severe population decline on Mednyi Island. Genes of the major histocompatibility complex (MHC) play a primary role in infectious disease resistance. The main objectives of our study were to compare contemporary variation of MHC class II in mainland and island Arctic foxes, and to document the effects of the isolation and the recent bottleneck on MHC polymorphism by analyzing samples from historical and contemporary Arctic foxes. In 184 individuals, we found 25 unique MHC class II DRB and DQB alleles, and identified evidence of balancing selection maintaining allelic lineages over time at both loci. Twenty different MHC alleles were observed in mainland foxes and eight in Bering Island foxes. The historical Mednyi population contained five alleles and all contemporary individuals were monomorphic at both DRB and DQB. Our data indicate that despite positive and diversifying selection leading to elevated rates of amino acid replacement in functionally important antigen-binding sites, below a certain population size, balancing selection may not be strong enough to maintain genetic diversity in functionally important genes. This may have important fitness consequences and might explain the high pathogen susceptibility in some island populations. This is the first study that compares MHC diversity before and after a bottleneck in a wild canid population using DNA from museum samples. PMID:22408734

Research on the teaching evaluation reform of agricultural eco-environmental protection specialties under the background of deep integration of production and education

NASA Astrophysics Data System (ADS)

Ma, Guosheng

2018-02-01

With the implementation of the personnel training mode of deep integration between production and education, the original evaluation method cannot adapt to the goal of personnel training, so that the traditional teaching evaluation methods need to be reformed urgently. This paper studies and analyzes the four main problems in the teaching evaluation of agricultural eco-environmental protection specialties, and puts forward three measures to reform the teaching evaluation methods: establishing diversified evaluation indexes, establishing diversified evaluation subjects, and establishing diversified evaluation feedback mechanisms.

Psychopathology, adversity, and creativity: diversifying experiences in the development of eminent African Americans.

PubMed

Damian, Rodica Ioana; Simonton, Dean Keith

2015-04-01

Symptoms associated with mental illness have been hypothesized to relate to creative achievement because they act as diversifying experiences. However, this theory has only been tested on predominantly majority-culture samples. Do tendencies toward mental illness still predict eminent creativity when they coexist with other diversifying experiences, such as early parental death, minority-status, or poverty? These alternative diversifying experiences can be collectively referred to as examples of developmental adversity. This conjecture was tested on a significant sample of 291 eminent African Americans who, by the nature of their status as long-term minorities, would experience more developmental adversity. Replicating majority-culture patterns, African American artists showed higher mental illness rates than African American scientists. Yet the absolute percentages were significantly lower for the African Americans, regardless of profession. Furthermore, mental illness predicted higher eminence levels only for the African American artists, an effect that diminished when controlling for developmental adversity. Because the latter predicted eminence for both artists and scientists, the "madness-to-genius" link probably represents just 1 of several routes by which diversifying experiences can influence eminence. The same developmental ends can be attained by different means. This inference warrants further research using other eminent creators emerging from minority culture populations. (c) 2015 APA, all rights reserved).

Diversified management of coal enterprises in China: model selection, motivation and effect analysis

NASA Astrophysics Data System (ADS)

Lyu, Jingye; Lian, Xu; Li, Penglin

2018-01-01

In the context of promoting the new energy revolution and economic development of the new normal, the coal industry to excess production capacity is one of the important aspects of structural reform of the supply side. The purpose of diversification of coal enterprises in China is to seize historical opportunities, create new models of development and improve operational efficiency. In the research on diversification of coal enterprises, exploring the mode selection, motivation and effect from the aspects of the industry is conducive to the realization of the smooth replacement and the sustainable development of enterprises, to further enrich the strategic management of coal enterprises, to provide effective reference for the formulation of enterprise management decision-making and implementation of diversification strategy.

Rotation history effects on soybean plants and rhizosphere microbiome

USDA-ARS?s Scientific Manuscript database

Benefits of diversified cropping systems stem from the interactions between soil characteristics, crop growth patterns and physiology, and other organisms. In order to assist in the understanding and implementation of diversified rotation sequences, a long-term experiment was established to evaluate...

Aposematism increases acoustic diversification and speciation in poison frogs.

PubMed

Santos, Juan C; Baquero, Margarita; Barrio-Amorós, César; Coloma, Luis A; Erdtmann, Luciana K; Lima, Albertina P; Cannatella, David C

2014-12-07

Multimodal signals facilitate communication with conspecifics during courtship, but they can also alert eavesdropper predators. Hence, signallers face two pressures: enticing partners to mate and avoiding detection by enemies. Undefended organisms with limited escape abilities are expected to minimize predator recognition over mate attraction by limiting or modifying their signalling. Alternatively, organisms with anti-predator mechanisms such as aposematism (i.e. unprofitability signalled by warning cues) might elaborate mating signals as a consequence of reduced predation. We hypothesize that calls diversified in association with aposematism. To test this, we assembled a large acoustic signal database for a diurnal lineage of aposematic and cryptic/non-defended taxa, the poison frogs. First, we showed that aposematic and non-aposematic species share similar extinction rates, and aposematic lineages diversify more and rarely revert to the non-aposematic phenotype. We then characterized mating calls based on morphological (spectral), behavioural/physiological (temporal) and environmental traits. Of these, only spectral and temporal features were associated with aposematism. We propose that with the evolution of anti-predator defences, reduced predation facilitated the diversification of vocal signals, which then became elaborated or showy via sexual selection. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Adequately Diversified Dietary Intake and Iron and Folic Acid Supplementation during Pregnancy Is Associated with Reduced Occurrence of Symptoms Suggestive of Pre-Eclampsia or Eclampsia in Indian Women

PubMed Central

Agrawal, Sutapa; Fledderjohann, Jasmine; Vellakkal, Sukumar; Stuckler, David

2015-01-01

Background/Objective Pre-eclampsia or Eclampsia (PE or E) accounts for 25% of cases of maternal mortality worldwide. There is some evidence of a link to dietary factors, but few studies have explored this association in developing countries, where the majority of the burden falls. We examined the association between adequately diversified dietary intake, iron and folic acid supplementation during pregnancy and symptoms suggestive of PE or E in Indian women. Methods Cross-sectional data from India’s third National Family Health Survey (NFHS-3, 2005-06) was used for this study. Self-reported symptoms suggestive of PE or E during pregnancy were obtained from 39,657 women aged 15-49 years who had had a live birth in the five years preceding the survey. Multivariable logistic regression analysis was used to estimate the association between adequately diversified dietary intake, iron and folic acid supplementation during pregnancy and symptoms suggestive of PE or E after adjusting for maternal, health and lifestyle factors, and socio-demographic characteristics of the mother. Results In their most recent pregnancy, 1.2% (n=456) of the study sample experienced symptoms suggestive of PE or E. Mothers who consumed an adequately diversified diet were 34% less likely (OR: 0.66; 95% CI: 0.51-0.87) to report PE or E symptoms than mothers with inadequately diversified dietary intake. The likelihood of reporting PE or E symptoms was also 36% lower (OR: 0.64; 95% CI: 0.47-0.88) among those mothers who consumed iron and folic acid supplementation for at least 90 days during their last pregnancy. As a sensitivity analysis, we stratified our models sequentially by education, wealth, antenatal care visits, birth interval, and parity. Our results remained largely unchanged: both adequately diversified dietary intake and iron and folic acid supplementation during pregnancy were associated with a reduced occurrence of PE or E symptoms. Conclusion Having a adequately diversified dietary intake and iron and folic acid supplementation in pregnancy was associated with a reduced occurrence of symptoms suggestive of PE or E in Indian women. PMID:25785774

The Bright Side of Corporate Diversification: Evidence from Internal Labor Markets

PubMed Central

Tate, Geoffrey

2015-01-01

We document differences in human-capital deployment between diversified and focused firms. We find that diversified firms have higher labor productivity and that they redeploy labor to industries with better prospects in response to changing opportunities. The opportunities and incentives provided in internal labor markets in turn affect the development of workers' human capital. We find that workers more frequently transition to other industries in which their diversified firms operate and with smaller wage losses compared with workers in the open market, even when they leave their original firms. Overall, internal labor markets provide a bright side to corporate diversification. PMID:26924889

Testing whether Metazoan Tyrosine Loss Was Driven by Selection against Promiscuous Phosphorylation

PubMed Central

Pandya, Siddharth; Struck, Travis J.; Mannakee, Brian K.; Paniscus, Mary; Gutenkunst, Ryan N.

2015-01-01

Protein tyrosine phosphorylation is a key regulatory modification in metazoans, and the corresponding kinase enzymes have diversified dramatically. This diversification is correlated with a genome-wide reduction in protein tyrosine content, and it was recently suggested that this reduction was driven by selection to avoid promiscuous phosphorylation that might be deleterious. We tested three predictions of this intriguing hypothesis. 1) Selection should be stronger on residues that are more likely to be phosphorylated due to local solvent accessibility or structural disorder. 2) Selection should be stronger on proteins that are more likely to be promiscuously phosphorylated because they are abundant. We tested these predictions by comparing distributions of tyrosine within and among human and yeast orthologous proteins. 3) Selection should be stronger against mutations that create tyrosine versus remove tyrosine. We tested this prediction using human population genomic variation data. We found that all three predicted effects are modest for tyrosine when compared with the other amino acids, suggesting that selection against deleterious phosphorylation was not dominant in driving metazoan tyrosine loss. PMID:25312910

Geographical gradients in selection can reveal genetic constraints for evolutionary responses to ocean acidification.

PubMed

Gaitán-Espitia, Juan Diego; Marshall, Dustin; Dupont, Sam; Bacigalupe, Leonardo D; Bodrossy, Levente; Hobday, Alistair J

2017-02-01

Geographical gradients in selection can shape different genetic architectures in natural populations, reflecting potential genetic constraints for adaptive evolution under climate change. Investigation of natural pH/pCO 2 variation in upwelling regions reveals different spatio-temporal patterns of natural selection, generating genetic and phenotypic clines in populations, and potentially leading to local adaptation, relevant to understanding effects of ocean acidification (OA). Strong directional selection, associated with intense and continuous upwellings, may have depleted genetic variation in populations within these upwelling regions, favouring increased tolerances to low pH but with an associated cost in other traits. In contrast, diversifying or weak directional selection in populations with seasonal upwellings or outside major upwelling regions may have resulted in higher genetic variances and the lack of genetic correlations among traits. Testing this hypothesis in geographical regions with similar environmental conditions to those predicted under climate change will build insights into how selection may act in the future and how populations may respond to stressors such as OA. © 2017 The Author(s).

A private ultraviolet channel in visual communication.

PubMed Central

Cummings, Molly E; Rosenthal, Gil G; Ryan, Michael J

2003-01-01

Although private communication is considered an important diversifying force in evolution, there is little direct behavioural evidence to support this notion. Here, we show that ultraviolet (UV) signalling in northern swordtails (Xiphophorus) affords a channel for communication that is not accessible to their major predator, Astyanax mexicanus, the Mexican tetra. Laboratory and field behavioural experiments with swordtails (X. nigrensis) and predators (A. mexicanus) demonstrate that male UV ornamentation significantly increases their attractiveness to females but not to this predator, which is less sensitive to UV. UV reflectance among swordtail species correlates positively with tetra densities across habitats, and visual contrast estimates suggest that UV signals are highly conspicuous to swordtails in their natural environment. Cross-species comparisons also support the hypothesis that natural selection drives the use of UV communication. We compared two species, one with high (X. nigrensis) and one with low (X. malinche) Mexican tetra densities. Xiphophorus nigrensis males reflect significantly more UV than X. malinche, exhibit significant UV sexual dimorphism, and UV is a salient component of the sexual communication system. In X. malinche, however, males reflect minimally in the UV, there is no UV sexual dimorphism, and UV does not play a part in its communication system. PMID:12803903

Exploratory studies of the cruise performance of upper surface blown configurations. Experimental program: Test facilities, model design instrumentation, and lowspeed, high-lift tests

NASA Technical Reports Server (NTRS)

Braden, J. A.; Hancock, J. P.; Burdges, K. P.; Hackett, J. E.

1980-01-01

The model hardware, test facilities and instrumentation utilized in an experimental study of upper surface blown configurations at cruise is described. The high speed (subsonic) experimental work, studying the aerodynamic effects of wing nacelle geometric variations, was conducted around semispan model configurations composed of diversified, interchangeable components. Power simulation was provided by high pressure air ducted through closed forebody nacelles. Nozzle geometry was varied across size, exit aspect ratio, exit position and boattail angle. Three dimensional force and two dimensional pressure measurements were obtained at cruise Mach numbers from 0.5 to 0.8 and at nozzle pressure ratios up to about 3.0. The experimental investigation was supported by an analytical synthesis of the system using a vortex lattice representation with first order power effects. Results are also presented from a compatibility study in which a short haul transport is designed on the basis of the aerodynamic findings in the experimental study as well as acoustical data obtained in a concurrent program. High lift test data are used to substantiate the projected performance of the selected transport design.

A private ultraviolet channel in visual communication.

PubMed

Cummings, Molly E; Rosenthal, Gil G; Ryan, Michael J

2003-05-07

Although private communication is considered an important diversifying force in evolution, there is little direct behavioural evidence to support this notion. Here, we show that ultraviolet (UV) signalling in northern swordtails (Xiphophorus) affords a channel for communication that is not accessible to their major predator, Astyanax mexicanus, the Mexican tetra. Laboratory and field behavioural experiments with swordtails (X. nigrensis) and predators (A. mexicanus) demonstrate that male UV ornamentation significantly increases their attractiveness to females but not to this predator, which is less sensitive to UV. UV reflectance among swordtail species correlates positively with tetra densities across habitats, and visual contrast estimates suggest that UV signals are highly conspicuous to swordtails in their natural environment. Cross-species comparisons also support the hypothesis that natural selection drives the use of UV communication. We compared two species, one with high (X. nigrensis) and one with low (X. malinche) Mexican tetra densities. Xiphophorus nigrensis males reflect significantly more UV than X. malinche, exhibit significant UV sexual dimorphism, and UV is a salient component of the sexual communication system. In X. malinche, however, males reflect minimally in the UV, there is no UV sexual dimorphism, and UV does not play a part in its communication system.

The state of racial/ethnic diversity in North Carolina's health workforce.

PubMed

McGee, Victoria; Fraher, Erin

2012-01-01

Increasing the racial and ethnic diversity of the health care workforce is vital to achieving accessible, equitable health care. This study provides baseline data on the diversity of health care practitioners in North Carolina compared with the diversity of the state's population. We analyzed North Carolina health workforce diversity using licensure data from the respective state boards of selected professions from 1994-2009; the data are stored in the North Carolina Health Professions Data System. North Carolina's health care practitioners are less diverse than is the state's population as a whole; only 17% of the practitioners are nonwhite, compared with 33% of the state's population. Levels of diversity vary among the professions, which are diversifying slowly over time. Primary care physicians are diversifying more rapidly than are other types of practitioners; the percentage who are nonwhite increased by 14 percentage points between 1994 and 2009, a period during which 1,630 nonwhite practitioners were added to their ranks. The percentage of licensed practical nurses who are nonwhite increased by 7 percentage points over the same period with the addition of 1,542 nonwhite practitioners to their ranks. Nonwhite health professionals cluster regionally throughout the state, and 79% of them practice in metropolitan counties. This study reports on only a selected number of health professions and utilizes race/ethnicity data that were self-reported by practitioners. Tracking the diversity among North Carolina's health care practitioners provides baseline data that will facilitate future research on barriers to health workforce entry, allow assessment of diversity programs, and be useful in addressing racial and ethnic health disparities.

Thiol biochemistry of prokaryotes

NASA Technical Reports Server (NTRS)

Fahey, Robert C.

1986-01-01

The present studies have shown that GSH metabolism arose in the purple bacteria and cyanobacteria where it functions to protect against oxygen toxicity. Evidence was obtained indicating that GSH metabolism was incorporated into eucaryotes via the endosymbiosis giving rise to mitochrondria and chloroplasts. Aerobic bacteria lacking GSH utilize other thiols for apparently similar functions, the thiol being coenzyme A in Gram positive bacteria and chi-glutamylcysteine in the halobacteria. The thiol biochemistry of prokaryotes is thus seen to be much more highly diversified than that of eucaryotes and much remains to be learned about this subject.

Marine geodesy a multipurpose approach to solve oceanic problems. [including submersible navigation under iced seas, demarcation and determination of boundaries in deep ocean, tsunamis, and ecology

NASA Technical Reports Server (NTRS)

Saxena, N.

1974-01-01

Various current and future problem areas of marine geodesy are identified. These oceanic problem areas are highly diversified and include submersible navigation under ice seas, demarcation and determination of boundaries in deep ocean, tsunamis, ecology, etc., etc. Their achieved as well as desired positional accuracy estimates, based upon publications and discussions, are also given. A multipurpose approach to solve these problems is described. An optimum configuration of an ocean-bottom control-net unit is provided.

Dropout Prevention: Diversified Satellite Occupations Program and Career Development. Final Report.

ERIC Educational Resources Information Center

Jones, Hilda B.

The Diversified Satellite Occupations Program Career Development sought to prevent dropout through these strategies: registration at a school situation away from the normal school setting, creation of a close teacher-student relationship, and raise achievement levels and lower anxiety levels. Program emphases at elementary, junior and senior high…

Diversifying Fiscal Support by Pricing Public Library Services: A Policy Impact Analysis.

ERIC Educational Resources Information Center

Hicks, Donald A.

1980-01-01

Addresses the possibility of diversifying the resource base of public libraries dependent on property taxes for funding through the setting of fees for library services, and reports on a pricing policy adopted by the Dallas Public Library System. Twenty-seven references are cited. (FM)

Spring wheat production and associated pests in conventional and diversified cropping systems in north central Montana

USDA-ARS?s Scientific Manuscript database

Producers in the northern Plains are diversifying and intensifying traditional wheat-based cropping systems by reducing summer fallow and including legume and oilseed crops. This study examined the influence of diversification and intensification on spring wheat yield and quality, and associated ins...

Some Implications of a Diversifying Workforce for Governance and Management

ERIC Educational Resources Information Center

Whitchurch, Celia; Gordon, George

2011-01-01

This paper suggests that as university missions have adapted to accommodate major developments associated with, for instance, mass higher education and internationalisation agendas, university workforces have diversified. They now, for instance, incorporate practitioners in areas such as health and social care, and professional staff who support…

5 CFR 9001.104 - Prohibited financial interests.

Code of Federal Regulations, 2011 CFR

2011-01-01

... § 9001.103; and (2) An interest in a publicly-traded or publicly-available diversified mutual fund or other collective diversified investment fund, including a widely-held pension or other retirement fund... have the ability to exercise control over the financial interests held by the fund; and (ii) The fund...

Developing Cultural Intelligence and Empathy through Diversified Mentoring Relationships

ERIC Educational Resources Information Center

Young, Cheri A.; Haffejee, Badiah; Corsun, David L.

2018-01-01

Given increasing globalization and the foreign-born workforce characterizing many organizations around the world, managers are increasingly called on to effectively manage a culturally diverse workforce. One way to increase the cultural intelligence and empathy of managers was proposed by Ragins, who indicated that mentors in diversified mentoring…

Diversifying Academic and Professional Identities in Higher Education: Some Management Challenges

ERIC Educational Resources Information Center

Whitchurch, Celia; Gordon, George

2010-01-01

This paper draws on an international study of the management challenges arising from diversifying academic and professional identities in higher education. These challenges include, for instance, the introduction of practice-based disciplines with different traditions such as health and social care, the changing aspirations and expectations of…

Ceftazidime Is the Key Diversification and Selection Driver of VIM-Type Carbapenemases.

PubMed

Martínez-García, Laura; González-Alba, José M; Baquero, Fernando; Cantón, Rafael; Galán, Juan Carlos

2018-05-08

In recent decades, carbapenems have been considered the last line of antibiotic therapy for Gram-negative bacterial infections. Unfortunately, strains carrying a high diversity of β-lactamases able to hydrolyze carbapenems have emerged in the clinical setting. Among them, VIM β-lactamases have diversified in a bloom of variants. The evolutionary reconstructions performed in this work revealed that, at the end of the 1980s, two independent events involving diversification from VIM-2 and VIM-4 produced at least 25 VIM variants. Later, a third event involving diversification from VIM-1 occurred in the mid-1990s. In a second approach to understanding the emergence of VIM carbapenemases, 44 mutants derived from VIM-2 and VIM-4 were obtained by site-directed mutagenesis based on those positions predicted to be under positive selection. These variants were expressed in an isogenic context. The more-evolved variants yielded increased levels of hydrolytic efficiency toward ceftazidime to a higher degree than toward carbapenems. In fact, an antagonist effect was frequently observed. These results led us to develop an experimental-evolution step. When Escherichia coli strains carrying VIM-2 or VIM-4 were submitted to serial passages at increasing concentrations of carbapenems or ceftazidime, more-efficient new variants (such as VIM-11 and VIM-1, with N165S [bearing a change from N to S at position 165] and R228S mutations, respectively) were only obtained when ceftazidime was present. Therefore, the observed effect of ceftazidime in the diversification and selection of VIM variants might help to explain the recent bloom of carbapenemase diversity, and it also represents another example of the potential universal effect exerted by ceftazidime in the selection of more-efficient β-lactamase variants, as in TEM, CTX-M, or KPC enzymes. IMPORTANCE One of the objectives recently proposed by the World Health Organization (WHO) Assembly in the global plan on antimicrobial resistance was to improve the understanding and knowledge of antimicrobial resistance. In the present work, we paid attention to the drivers of diversification and selection of new carbapenemases in Gram-negative bacteria, which occupy one of the most critical places in the WHO priority list of antibiotic-resistant microorganisms. Based on evolutionary-reconstruction, site-directed-mutagenesis, and experimental-evolution approaches, we proposed a critical role of ceftazidime exposure in the selection of VIM carbapenemase variants. This surprising finding is also applicable to other β-lactamases, indicating that ceftazidime, and not other antibiotics, might have a universal effect in the diversification of β-lactamases. Our results might help to define future strategies to reconsider the extended use of ceftazidime. Copyright © 2018 Martínez-García et al.

AACP Special Taskforce White Paper on Diversifying Our Investment in Human Capital.

PubMed

White, Carla; Conway, Jeannine M; Davis, Paula K; Johnson-Fannin, Arcelia M; Jurkas, Jeffrey G; Murphy, Nanci L; Smith, W Thomas; Echeverri, Margarita; Youmans, Sharon L; Owings, Katie C; Adams, Jennifer L

2017-10-01

The 2015-2017 American Association of Colleges of Pharmacy (AACP) Special Taskforce on Diversifying our Investment in Human Capital was appointed for a two-year term, due to the rigors and complexities of its charges. This report serves as a white paper for academic pharmacy on diversifying our investment in human capital. The Taskforce developed and recommended a representation statement that was adapted and adopted by the AACP House of Delegates at the 2016 AACP Annual Meeting. In addition, the Taskforce developed a diversity statement for the Association that was adopted by the AACP Board of Directors in 2017. The Taskforce also provides recommendations to AACP and to academic pharmacy in this white paper.

Diversified Occupations I.

ERIC Educational Resources Information Center

Noto, Jody

This curriculum guide consists of materials for use in presenting the first year of a two-year course in diversified occupations that is designed to teach job search and job-holding skills to disadvantaged and English as a second language (ESL) students. Addressed in the 25 units included in the guide are the following topics: the purposes of…

Marginal Mentoring in the Contact Space: Diversified Mentoring Relationships at a Midsized Midwestern State University (MMSU)

ERIC Educational Resources Information Center

Meyer, Marcy; Warren-Gordon, Kiesha

2013-01-01

This study is a collaborative investigation that melds traditional qualitative social scientific and contemporary autoethnographic methods to examine diversified mentoring relationships at a midsized midwestern state university (MMSU). The first author conducted 21 semi-structured interviews with MMSU faculty members and professional personnel who…

Diversifying Curriculum as the Practice of Repressive Tolerance

ERIC Educational Resources Information Center

Brookfield, Stephen

2007-01-01

Diversifying curriculum is often assumed to be an unequivocal good in higher education--a way of opening up an educational conversation to include the widest possible diversity of perspectives and intellectual traditions. This democratic attempt to be open and inclusive springs from a humanistic concern to have all student voices heard, all…

29 CFR 2550.404c-5 - Fiduciary relief for investments in qualified default investment alternatives.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., liquidation or exchange fees, redemption fees and similar expenses charged in connection with the liquidation... accepted investment theories, is diversified so as to minimize the risk of large losses and that is... portfolio that applies generally accepted investment theories, is diversified so as to minimize the risk of...

29 CFR 2550.404c-5 - Fiduciary relief for investments in qualified default investment alternatives.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., liquidation or exchange fees, redemption fees and similar expenses charged in connection with the liquidation... accepted investment theories, is diversified so as to minimize the risk of large losses and that is... portfolio that applies generally accepted investment theories, is diversified so as to minimize the risk of...

29 CFR 2550.404c-5 - Fiduciary relief for investments in qualified default investment alternatives.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., liquidation or exchange fees, redemption fees and similar expenses charged in connection with the liquidation... accepted investment theories, is diversified so as to minimize the risk of large losses and that is... portfolio that applies generally accepted investment theories, is diversified so as to minimize the risk of...

5 CFR 2640.102 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... to paragraph (a): A mutual fund is diversified for purposes of this part if it does not have a policy... single State within the United States. Whether a mutual fund meets this standard may be determined by... is important to note that a mutual fund or employee benefit plan that is diversified for purposes of...

The Diversification of the Educational Field in Hungary.

ERIC Educational Resources Information Center

Inkei, Peter; And Others

Education throughout the world has become increasingly diversified, moving from the traditional education of children to increasingly more education of adults outside formal school settings. This case study on Hungary is one of a series of studies that were conducted to map out the different components of the diversified educational field and…

Cooperative Work Education in Diversified Occupations. General Related Curriculum Guide.

ERIC Educational Resources Information Center

Brysgel, David

This guide is intended as a working document for coordinators of cooperative work education in diversified occupations. It contains materials for use in providing students with general classroom instruction concurrent with on-the-job training. The following topics are covered in the individual units in the first-year curriculum: the cooperative…

Specificity and Evolutionary Conservation of the Escherichia coli RNA Pyrophosphohydrolase RppH*

PubMed Central

Foley, Patricia L.; Hsieh, Ping-kun; Luciano, Daniel J.; Belasco, Joel G.

2015-01-01

Bacterial RNA degradation often begins with conversion of the 5′-terminal triphosphate to a monophosphate by the RNA pyrophosphohydrolase RppH, an event that triggers rapid ribonucleolytic attack. Besides its role as the master regulator of 5′-end-dependent mRNA decay, RppH is important for the ability of pathogenic bacteria to invade host cells, yet little is known about how it chooses its targets. Here, we show that Escherichia coli RppH (EcRppH) requires at least two unpaired nucleotides at the RNA 5′ end and prefers three or more such nucleotides. It can tolerate any nucleotide at the first three positions but has a modest preference for A at the 5′ terminus and either a G or A at the second position. Mutational analysis has identified EcRppH residues crucial for substrate recognition or catalysis. The promiscuity of EcRppH differentiates it from its Bacillus subtilis counterpart, which has a strict RNA sequence requirement. EcRppH orthologs likely to share its relaxed sequence specificity are widespread in all classes of Proteobacteria, except Deltaproteobacteria, and in flowering plants. By contrast, the phylogenetic range of recognizable B. subtilis RppH orthologs appears to be restricted to the order Bacillales. These findings help to explain the selective influence of RppH on bacterial mRNA decay and show that RppH-dependent degradation has diversified significantly during the course of evolution. PMID:25657006

Specificity and evolutionary conservation of the Escherichia coli RNA pyrophosphohydrolase RppH.

PubMed

Foley, Patricia L; Hsieh, Ping-kun; Luciano, Daniel J; Belasco, Joel G

2015-04-10

Bacterial RNA degradation often begins with conversion of the 5'-terminal triphosphate to a monophosphate by the RNA pyrophosphohydrolase RppH, an event that triggers rapid ribonucleolytic attack. Besides its role as the master regulator of 5'-end-dependent mRNA decay, RppH is important for the ability of pathogenic bacteria to invade host cells, yet little is known about how it chooses its targets. Here, we show that Escherichia coli RppH (EcRppH) requires at least two unpaired nucleotides at the RNA 5' end and prefers three or more such nucleotides. It can tolerate any nucleotide at the first three positions but has a modest preference for A at the 5' terminus and either a G or A at the second position. Mutational analysis has identified EcRppH residues crucial for substrate recognition or catalysis. The promiscuity of EcRppH differentiates it from its Bacillus subtilis counterpart, which has a strict RNA sequence requirement. EcRppH orthologs likely to share its relaxed sequence specificity are widespread in all classes of Proteobacteria, except Deltaproteobacteria, and in flowering plants. By contrast, the phylogenetic range of recognizable B. subtilis RppH orthologs appears to be restricted to the order Bacillales. These findings help to explain the selective influence of RppH on bacterial mRNA decay and show that RppH-dependent degradation has diversified significantly during the course of evolution. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity.

PubMed

Krishnan, Arunkumar; Iyer, Lakshminarayan M; Holland, Stephen J; Boehm, Thomas; Aravind, L

2018-04-03

AID/APOBEC deaminases (AADs) convert cytidine to uridine in single-stranded nucleic acids. They are involved in numerous mutagenic processes, including those underpinning vertebrate innate and adaptive immunity. Using a multipronged sequence analysis strategy, we uncover several AADs across metazoa, dictyosteliida, and algae, including multiple previously unreported vertebrate clades, and versions from urochordates, nematodes, echinoderms, arthropods, lophotrochozoans, cnidarians, and porifera. Evolutionary analysis suggests a fundamental division of AADs early in metazoan evolution into secreted deaminases (SNADs) and classical AADs, followed by diversification into several clades driven by rapid-sequence evolution, gene loss, lineage-specific expansions, and lateral transfer to various algae. Most vertebrate AADs, including AID and APOBECs1-3, diversified in the vertebrates, whereas the APOBEC4-like clade has a deeper origin in metazoa. Positional entropy analysis suggests that several AAD clades are diversifying rapidly, especially in the positions predicted to interact with the nucleic acid target motif, and with potential viral inhibitors. Further, several AADs have evolved neomorphic metal-binding inserts, especially within loops predicted to interact with the target nucleic acid. We also observe polymorphisms, driven by alternative splicing, gene loss, and possibly intergenic recombination between paralogs. We propose that biological conflicts of AADs with viruses and genomic retroelements are drivers of rapid AAD evolution, suggesting a widespread presence of mutagenesis-based immune-defense systems. Deaminases like AID represent versions "institutionalized" from the broader array of AADs pitted in such arms races for mutagenesis of self-DNA, and similar recruitment might have independently occurred elsewhere in metazoa. Copyright © 2018 the Author(s). Published by PNAS.

Integrating ecosystem-service tradeoffs into land-use decisions

PubMed Central

Goldstein, Joshua H.; Caldarone, Giorgio; Duarte, Thomas Kaeo; Ennaanay, Driss; Hannahs, Neil; Mendoza, Guillermo; Polasky, Stephen; Wolny, Stacie; Daily, Gretchen C.

2012-01-01

Recent high-profile efforts have called for integrating ecosystem-service values into important societal decisions, but there are few demonstrations of this approach in practice. We quantified ecosystem-service values to help the largest private landowner in Hawaii, Kamehameha Schools, design a land-use development plan that balances multiple private and public values on its North Shore land holdings (Island of O’ahu) of ∼10,600 ha. We used the InVEST software tool to evaluate the environmental and financial implications of seven planning scenarios encompassing contrasting land-use combinations including biofuel feedstocks, food crops, forestry, livestock, and residential development. All scenarios had positive financial return relative to the status quo of negative return. However, tradeoffs existed between carbon storage and water quality as well as between environmental improvement and financial return. Based on this analysis and community input, Kamehameha Schools is implementing a plan to support diversified agriculture and forestry. This plan generates a positive financial return ($10.9 million) and improved carbon storage (0.5% increase relative to status quo) with negative relative effects on water quality (15.4% increase in potential nitrogen export relative to status quo). The effects on water quality could be mitigated partially (reduced to a 4.9% increase in potential nitrogen export) by establishing vegetation buffers on agricultural fields. This plan contributes to policy goals for climate change mitigation, food security, and diversifying rural economic opportunities. More broadly, our approach illustrates how information can help guide local land-use decisions that involve tradeoffs between private and public interests. PMID:22529388

Integrating ecosystem-service tradeoffs into land-use decisions.

PubMed

Goldstein, Joshua H; Caldarone, Giorgio; Duarte, Thomas Kaeo; Ennaanay, Driss; Hannahs, Neil; Mendoza, Guillermo; Polasky, Stephen; Wolny, Stacie; Daily, Gretchen C

2012-05-08

Recent high-profile efforts have called for integrating ecosystem-service values into important societal decisions, but there are few demonstrations of this approach in practice. We quantified ecosystem-service values to help the largest private landowner in Hawaii, Kamehameha Schools, design a land-use development plan that balances multiple private and public values on its North Shore land holdings (Island of O'ahu) of ∼10,600 ha. We used the InVEST software tool to evaluate the environmental and financial implications of seven planning scenarios encompassing contrasting land-use combinations including biofuel feedstocks, food crops, forestry, livestock, and residential development. All scenarios had positive financial return relative to the status quo of negative return. However, tradeoffs existed between carbon storage and water quality as well as between environmental improvement and financial return. Based on this analysis and community input, Kamehameha Schools is implementing a plan to support diversified agriculture and forestry. This plan generates a positive financial return ($10.9 million) and improved carbon storage (0.5% increase relative to status quo) with negative relative effects on water quality (15.4% increase in potential nitrogen export relative to status quo). The effects on water quality could be mitigated partially (reduced to a 4.9% increase in potential nitrogen export) by establishing vegetation buffers on agricultural fields. This plan contributes to policy goals for climate change mitigation, food security, and diversifying rural economic opportunities. More broadly, our approach illustrates how information can help guide local land-use decisions that involve tradeoffs between private and public interests.

Candidate loci involved in domestication and improvement detected by a published 90K wheat SNP array

PubMed Central

Gao, Lifeng; Zhao, Guangyao; Huang, Dawei; Jia, Jizeng

2017-01-01

Selection is one of the most important forces in crop evolution. Common wheat is a major world food crop and a typical allopolyploid with a huge and complex genome. We applied four approaches to detect loci selected in wheat during domestication and improvement. A total of 7,984 candidate loci were detected, accounting for 23.3% of all 34,317 SNPs analysed, a much higher proportion than estimated in previous reports. We constructed a first generation wheat selection map which revealed the following new insights on genome-wide selection: (1) diversifying selection acted by increasing, decreasing or not affecting gene frequencies; (2) the number of loci under selection during domestication was much higher than that during improvement; (3) the contribution to wheat improvement by the D sub-genome was relatively small due to the bottleneck of hexaploidisation and diversity can be expanded by using synthetic wheat and introgression lines; and (4) clustered selection regions occur throughout the wheat genome, including the centromere regions. This study will not only help future wheat breeding and evolutionary studies, but will also accelerate study of other crops, especially polyploids. PMID:28327671

Diversification of a single ancestral gene into a successful toxin superfamily in highly venomous Australian funnel-web spiders.

PubMed

Pineda, Sandy S; Sollod, Brianna L; Wilson, David; Darling, Aaron; Sunagar, Kartik; Undheim, Eivind A B; Kely, Laurence; Antunes, Agostinho; Fry, Bryan G; King, Glenn F

2014-03-05

Spiders have evolved pharmacologically complex venoms that serve to rapidly subdue prey and deter predators. The major toxic factors in most spider venoms are small, disulfide-rich peptides. While there is abundant evidence that snake venoms evolved by recruitment of genes encoding normal body proteins followed by extensive gene duplication accompanied by explosive structural and functional diversification, the evolutionary trajectory of spider-venom peptides is less clear. Here we present evidence of a spider-toxin superfamily encoding a high degree of sequence and functional diversity that has evolved via accelerated duplication and diversification of a single ancestral gene. The peptides within this toxin superfamily are translated as prepropeptides that are posttranslationally processed to yield the mature toxin. The N-terminal signal sequence, as well as the protease recognition site at the junction of the propeptide and mature toxin are conserved, whereas the remainder of the propeptide and mature toxin sequences are variable. All toxin transcripts within this superfamily exhibit a striking cysteine codon bias. We show that different pharmacological classes of toxins within this peptide superfamily evolved under different evolutionary selection pressures. Overall, this study reinforces the hypothesis that spiders use a combinatorial peptide library strategy to evolve a complex cocktail of peptide toxins that target neuronal receptors and ion channels in prey and predators. We show that the ω-hexatoxins that target insect voltage-gated calcium channels evolved under the influence of positive Darwinian selection in an episodic fashion, whereas the κ-hexatoxins that target insect calcium-activated potassium channels appear to be under negative selection. A majority of the diversifying sites in the ω-hexatoxins are concentrated on the molecular surface of the toxins, thereby facilitating neofunctionalisation leading to new toxin pharmacology.

Similar but not the same: insights into the evolutionary history of paralogous sex-determining genes of the dwarf honey bee Apis florea.

PubMed

Biewer, M; Lechner, S; Hasselmann, M

2016-01-01

Studying the fate of duplicated genes provides informative insight into the evolutionary plasticity of biological pathways to which they belong. In the paralogous sex-determining genes complementary sex determiner (csd) and feminizer (fem) of honey bee species (genus Apis), only heterozygous csd initiates female development. Here, the full-length coding sequences of the genes csd and fem of the phylogenetically basal dwarf honey bee Apis florea are characterized. Compared with other Apis species, remarkable evolutionary changes in the formation and localization of a protein-interacting (coiled-coil) motif and in the amino acids coding for the csd characteristic hypervariable region (HVR) are observed. Furthermore, functionally different csd alleles were isolated as genomic fragments from a random population sample. In the predicted potential specifying domain (PSD), a high ratio of πN/πS=1.6 indicated positive selection, whereas signs of balancing selection, commonly found in other Apis species, are missing. Low nucleotide diversity on synonymous and genome-wide, non-coding sites as well as site frequency analyses indicated a strong impact of genetic drift in A. florea, likely linked to its biology. Along the evolutionary trajectory of ~30 million years of csd evolution, episodic diversifying selection seems to have acted differently among distinct Apis branches. Consistently low amino-acid differences within the PSD among pairs of functional heterozygous csd alleles indicate that the HVR is the most important region for determining allele specificity. We propose that in the early history of the lineage-specific fem duplication giving rise to csd in Apis, A. florea csd stands as a remarkable example for the plasticity of initial sex-determining signals.

The Goddard and Saturn Genes Are Essential for Drosophila Male Fertility and May Have Arisen De Novo.

PubMed

Gubala, Anna M; Schmitz, Jonathan F; Kearns, Michael J; Vinh, Tery T; Bornberg-Bauer, Erich; Wolfner, Mariana F; Findlay, Geoffrey D

2017-05-01

New genes arise through a variety of mechanisms, including the duplication of existing genes and the de novo birth of genes from noncoding DNA sequences. While there are numerous examples of duplicated genes with important functional roles, the functions of de novo genes remain largely unexplored. Many newly evolved genes are expressed in the male reproductive tract, suggesting that these evolutionary innovations may provide advantages to males experiencing sexual selection. Using testis-specific RNA interference, we screened 11 putative de novo genes in Drosophila melanogaster for effects on male fertility and identified two, goddard and saturn, that are essential for spermatogenesis and sperm function. Goddard knockdown (KD) males fail to produce mature sperm, while saturn KD males produce few sperm, and these function inefficiently once transferred to females. Consistent with a de novo origin, both genes are identifiable only in Drosophila and are predicted to encode proteins with no sequence similarity to any annotated protein. However, since high levels of divergence prevented the unambiguous identification of the noncoding sequences from which each gene arose, we consider goddard and saturn to be putative de novo genes. Within Drosophila, both genes have been lost in certain lineages, but show conserved, male-specific patterns of expression in the species in which they are found. Goddard is consistently found in single-copy and evolves under purifying selection. In contrast, saturn has diversified through gene duplication and positive selection. These data suggest that de novo genes can acquire essential roles in male reproduction. © The Author 2017. 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.

Alternative Splicing of a Novel Inducible Exon Diversifies the CASK Guanylate Kinase Domain

PubMed Central

Dembowski, Jill A.; An, Ping; Scoulos-Hanson, Maritsa; Yeo, Gene; Han, Joonhee; Fu, Xiang-Dong; Grabowski, Paula J.

2012-01-01

Alternative pre-mRNA splicing has a major impact on cellular functions and development with the potential to fine-tune cellular localization, posttranslational modification, interaction properties, and expression levels of cognate proteins. The plasticity of regulation sets the stage for cells to adjust the relative levels of spliced mRNA isoforms in response to stress or stimulation. As part of an exon profiling analysis of mouse cortical neurons stimulated with high KCl to induce membrane depolarization, we detected a previously unrecognized exon (E24a) of the CASK gene, which encodes for a conserved peptide insertion in the guanylate kinase interaction domain. Comparative sequence analysis shows that E24a appeared selectively in mammalian CASK genes as part of a >3,000 base pair intron insertion. We demonstrate that a combination of a naturally defective 5′ splice site and negative regulation by several splicing factors, including SC35 (SRSF2) and ASF/SF2 (SRSF1), drives E24a skipping in most cell types. However, this negative regulation is countered with an observed increase in E24a inclusion after neuronal stimulation and NMDA receptor signaling. Taken together, E24a is typically a skipped exon, which awakens during neuronal stimulation with the potential to diversify the protein interaction properties of the CASK polypeptide. PMID:23008758

Assessment of Linear Finite-Difference Poisson-Boltzmann Solvers

PubMed Central

Wang, Jun; Luo, Ray

2009-01-01

CPU time and memory usage are two vital issues that any numerical solvers for the Poisson-Boltzmann equation have to face in biomolecular applications. In this study we systematically analyzed the CPU time and memory usage of five commonly used finite-difference solvers with a large and diversified set of biomolecular structures. Our comparative analysis shows that modified incomplete Cholesky conjugate gradient and geometric multigrid are the most efficient in the diversified test set. For the two efficient solvers, our test shows that their CPU times increase approximately linearly with the numbers of grids. Their CPU times also increase almost linearly with the negative logarithm of the convergence criterion at very similar rate. Our comparison further shows that geometric multigrid performs better in the large set of tested biomolecules. However, modified incomplete Cholesky conjugate gradient is superior to geometric multigrid in molecular dynamics simulations of tested molecules. We also investigated other significant components in numerical solutions of the Poisson-Boltzmann equation. It turns out that the time-limiting step is the free boundary condition setup for the linear systems for the selected proteins if the electrostatic focusing is not used. Thus, development of future numerical solvers for the Poisson-Boltzmann equation should balance all aspects of the numerical procedures in realistic biomolecular applications. PMID:20063271

Behavioral and Physiological Neural Network Analyses: A Common Pathway toward Pattern Recognition and Prediction

ERIC Educational Resources Information Center

Ninness, Chris; Lauter, Judy L.; Coffee, Michael; Clary, Logan; Kelly, Elizabeth; Rumph, Marilyn; Rumph, Robin; Kyle, Betty; Ninness, Sharon K.

2012-01-01

Using 3 diversified datasets, we explored the pattern-recognition ability of the Self-Organizing Map (SOM) artificial neural network as applied to diversified nonlinear data distributions in the areas of behavioral and physiological research. Experiment 1 employed a dataset obtained from the UCI Machine Learning Repository. Data for this study…

Cone-Deciphered Modes of Problem Solving Action (MPSA Cone): Alternative Perspectives on Diversified Professions.

ERIC Educational Resources Information Center

Lai, Su-Huei

A conceptual framework of the modes of problem-solving action has been developed on the basis of a simple relationship cone to assist individuals in diversified professions in inquiry and implementation of theory and practice in their professional development. The conceptual framework is referred to as the Cone-Deciphered Modes of Problem Solving…

Pedagogical Transaction in Religious Education: Diversified Society and John Dewey's Philosophy of Education

ERIC Educational Resources Information Center

Sutinen, Ari; Kallioniemi, Arto; Pihlström, Sami

2015-01-01

The focus of the article is on how a new approach to religious education (RE) in diversified societies can be constructed on the basis of the theory of pedagogical transaction presented by John Dewey. Reflections of developing RE are very current in Western secularized societies. We believe that Dewey's pragmatist philosophy of education and…

26 CFR 1.817-5 - Diversification requirements for variable annuity, endowment, and life insurance contracts.

Code of Federal Regulations, 2013 CFR

2013-04-01

...) and (h). Likewise, if a variable contract is not treated as an annuity contract under section 72, the... endowment contract under section 7702 (g) and (h). (2) Inadvertent failure to diversify. The investments of... considered adequately diversified for purposes of this section and section 817(h) only if— (A) No more than...

Factors Leading to Success in Diversified Occupation: A Livelihood Analysis in India

ERIC Educational Resources Information Center

Saha, Biswarup; Bahal, Ram

2015-01-01

Purpose: Livelihood diversification is a sound alternative for higher economic growth and its success or failure is conditioned by the interplay of a multitude of factors. The study of the profile of the farmers in which they operate is important to highlight the factors leading to success in diversified livelihoods. Design/Methodology/Approach: A…

Making Meaning of Work: Uncovering the Complexity of Immigrant Experience in a Multicultural Landscape

ERIC Educational Resources Information Center

Abramova, Inna

2011-01-01

Many educators draw the public's attention to the need for diversifying the teaching force. They argue that teachers from diverse cultures offer a variety of perspectives, encourage students to participate in community work, and exhibit cultural awareness and appreciation of differences. One of the ways to diversify the teaching force includes…

The Drive to Diversify the Teaching Profession: Narrow Assumptions, Hidden Complexities

ERIC Educational Resources Information Center

Santoro, Ninetta

2015-01-01

In response to increasing cultural diversity within student populations in Australia as well as Britain, Europe and North America, there have been ongoing calls to diversify the teaching profession. Such a strategy is based on assumptions that teachers who are of ethnic and racial minority are well placed to act as role models for minority…

AACP Special Taskforce White Paper on Diversifying Our Investment in Human Capital

PubMed Central

White, Carla; Conway, Jeannine M.; Davis, Paula K.; Johnson-Fannin, Arcelia M.; Jurkas, Jeffrey G.; Murphy, Nanci L.; Smith, W. Thomas; Echeverri, Margarita; Youmans, Sharon L.; Owings, Katie C.; Adams, Jennifer L.

2017-01-01

EXECUTIVE SUMMARY The 2015-2017 American Association of Colleges of Pharmacy (AACP) Special Taskforce on Diversifying our Investment in Human Capital was appointed for a two-year term, due to the rigors and complexities of its charges. This report serves as a white paper for academic pharmacy on diversifying our investment in human capital. The Taskforce developed and recommended a representation statement that was adapted and adopted by the AACP House of Delegates at the 2016 AACP Annual Meeting. In addition, the Taskforce developed a diversity statement for the Association that was adopted by the AACP Board of Directors in 2017. The Taskforce also provides recommendations to AACP and to academic pharmacy in this white paper. PMID:29200461

Phytoplankton can actively diversify their migration strategy in response to turbulent cues

NASA Astrophysics Data System (ADS)

Sengupta, Anupam; Carrara, Francesco; Stocker, Roman

2017-03-01

Marine phytoplankton inhabit a dynamic environment where turbulence, together with nutrient and light availability, shapes species fitness, succession and selection. Many species of phytoplankton are motile and undertake diel vertical migrations to gain access to nutrient-rich deeper layers at night and well-lit surface waters during the day. Disruption of this migratory strategy by turbulence is considered to be an important cause of the succession between motile and non-motile species when conditions turn turbulent. However, this classical view neglects the possibility that motile species may actively respond to turbulent cues to avoid layers of strong turbulence. Here we report that phytoplankton, including raphidophytes and dinoflagellates, can actively diversify their migratory strategy in response to hydrodynamic cues characteristic of overturning by Kolmogorov-scale eddies. Upon experiencing repeated overturning with timescales and statistics representative of ocean turbulence, an upward-swimming population rapidly (5-60 min) splits into two subpopulations, one swimming upward and one swimming downward. Quantitative morphological analysis of the harmful-algal-bloom-forming raphidophyte Heterosigma akashiwo together with a model of cell mechanics revealed that this behaviour was accompanied by a modulation of the cells’ fore-aft asymmetry. The minute magnitude of the required modulation, sufficient to invert the preferential swimming direction of the cells, highlights the advanced level of control that phytoplankton can exert on their migratory behaviour. Together with observations of enhanced cellular stress after overturning and the typically deleterious effects of strong turbulence on motile phytoplankton, these results point to an active adaptation of H. akashiwo to increase the chance of evading turbulent layers by diversifying the direction of migration within the population, in a manner suggestive of evolutionary bet-hedging. This migratory behaviour relaxes the boundaries between the fluid dynamic niches of motile and non-motile phytoplankton, and highlights that rapid responses to hydrodynamic cues are important survival strategies for phytoplankton in the ocean.

Phytoplankton can actively diversify their migration strategy in response to turbulent cues.

PubMed

Sengupta, Anupam; Carrara, Francesco; Stocker, Roman

2017-03-23

Marine phytoplankton inhabit a dynamic environment where turbulence, together with nutrient and light availability, shapes species fitness, succession and selection. Many species of phytoplankton are motile and undertake diel vertical migrations to gain access to nutrient-rich deeper layers at night and well-lit surface waters during the day. Disruption of this migratory strategy by turbulence is considered to be an important cause of the succession between motile and non-motile species when conditions turn turbulent. However, this classical view neglects the possibility that motile species may actively respond to turbulent cues to avoid layers of strong turbulence. Here we report that phytoplankton, including raphidophytes and dinoflagellates, can actively diversify their migratory strategy in response to hydrodynamic cues characteristic of overturning by Kolmogorov-scale eddies. Upon experiencing repeated overturning with timescales and statistics representative of ocean turbulence, an upward-swimming population rapidly (5-60 min) splits into two subpopulations, one swimming upward and one swimming downward. Quantitative morphological analysis of the harmful-algal-bloom-forming raphidophyte Heterosigma akashiwo together with a model of cell mechanics revealed that this behaviour was accompanied by a modulation of the cells' fore-aft asymmetry. The minute magnitude of the required modulation, sufficient to invert the preferential swimming direction of the cells, highlights the advanced level of control that phytoplankton can exert on their migratory behaviour. Together with observations of enhanced cellular stress after overturning and the typically deleterious effects of strong turbulence on motile phytoplankton, these results point to an active adaptation of H. akashiwo to increase the chance of evading turbulent layers by diversifying the direction of migration within the population, in a manner suggestive of evolutionary bet-hedging. This migratory behaviour relaxes the boundaries between the fluid dynamic niches of motile and non-motile phytoplankton, and highlights that rapid responses to hydrodynamic cues are important survival strategies for phytoplankton in the ocean.

Use of Torulaspora delbrueckii Co-fermentation With Two Saccharomyces cerevisiae Strains With Different Aromatic Characteristic to Improve the Diversity of Red Wine Aroma Profile

PubMed Central

Zhang, Bo-Qin; Luan, Yu; Duan, Chang-Qing; Yan, Guo-Liang

2018-01-01

The use of selected Saccharomyces and non-Saccharomyces strains as mixed starters has advantages over pure fermentation due to achieving wine products with distinctive and diversified aroma expected by consumers. To obtain a way to improve the aroma diversity and increase the differentiation of wine product, in this study, the aromatic effect of multi-culture of indigenous Torulaspora delbrueckii (TD12), simultaneous and sequential inoculation with two Saccharomyces strains (indigenous icewine yeast SC45 and commercial yeast BDX) with different enological characteristics were investigated in laboratory-scale 20 L fermenter, respectively. The results showed that T. delbrueckii co-fermented with different S. cerevisiae strain could generate diversified physicochemical and aromatic quality of wine as evidenced by PCA. Mixed fermentation of SC45/TD12 produced higher contents of higher alcohol (3-methyl-1-pentanol and phenylethyl alcohol), ethyl esters (ethyl decanoate and ethyl butanoate), terpenes and phenylacetaldehyde with less fatty acids (hexanoic acid, octanoic acid) and acetic acid, while BDX/TD12 generated more C6 alcohol (1-hexanol) and acetate esters (ethyl acetate and isoamyl acetate). Compared to simultaneous inoculation, sequential inoculation could achieve higher aroma diversity, and generate higher intensity of fruity, flowery and sweet attributes of wine as assessed by calculating the odor activity values. The different S. cerevisiae strain and inoculation method in alcoholic fermentation could further influence the formations of aromatic compounds in malolactic fermentation. Our results highlighted the importance of S. cerevisiae strain in shaping the aromatic quality of wine in mixed fermentation, and also suggested that using different S. cerevisiae strains with distinct aromatic characteristics co-fermentation with specific non-Saccharomyces strain is a potential way to increase the aromatic diversity and quality of wine product, which could provide an alternative way to meet the requirement of wine consumers for diversified aromatic quality. PMID:29674999

Quality assessment of the TLS data in conservation of monuments

NASA Astrophysics Data System (ADS)

Markiewicz, Jakub S.; Zawieska, Dorota

2015-06-01

Laser scanning has been recently confirming its high potential in the field of acquiring 3D data for architectural and engineering objects. The objective of this paper is to analyse the quality of the TLS data acquired for different surfaces of monumental objects, with consideration of distances and the scanning angles. Tests concerning the quality of the survey data and shapes of architectural objects, characterised by diversified curvature, structure and the uniformity of the surface, were performed. The obtained results proved that utilisation of terrestrial laser scanning techniques does not allow to achieve expected accuracy for some historical surfaces and it should be substituted by alternative, photogrammetric techniques. Therefore, the typology of constructions of historical objects is important not only for selection of the optimum technique of surveys, but also for its appropriate utilisation. The test objects were architectural details of the Main Hall of the Warsaw University of Technology. Scans were acquired using the 5006h scanner. Diversified geometry of scans was tested, and the relations between the distance and obtained accuracy were specified. In the case of numerous conservational works the precise surface reconstruction is often important, in order to specify damages. Therefore, the repeatability of obtained TLS results for selected surfaces was also tested. Different surfaces were analysed, which are composed of different materials having glittery elements and inhomogeneous structure. The obtained results and performed analyses revealed the high imperfections of the TLS technique applied for measuring surfaces of historical objects. The presented accuracy of measurements of projection of historical surfaces, obtained using the TLS technique may be applied by art conservators, museum professionals, archaeologists and other specialists, to perform wide analyses of historical heritage objects.

Successful refolding and NMR structure of rMagi3: A disulfide-rich insecticidal spider toxin.

PubMed

Titaux-Delgado, Gustavo; Carrillo, Elisa; Mendoza, Angeles; Mayorga-Flores, Marlen; Escobedo-González, Fátima C; Cano-Sánchez, Patricia; López-Vera, Estuardo; Corzo, Gerardo; Del Rio-Portilla, Federico

2018-03-01

The need for molecules with high specificity against noxious insects leads the search towards spider venoms that have evolved highly selective toxins for insect preys. In this respect, spiders as a highly diversified group of almost exclusive insect predators appear to possess infinite potential for the discovery of novel insect-selective toxins. In 2003, a group of toxins was isolated from the spider Macrothele gigas and the amino acid sequence was reported. We obtained, by molecular biology techniques in a heterologous system, one of these toxins. Purification process was optimized by chromatographic methods to determine the three-dimensional structure by nuclear magnetic resonance in solution, and, finally, their biological activity was tested. rMagi3 resulted to be a specific insect toxin with no effect on mice. © 2017 The Protein Society.

Soil carbon fractions in response to long-term crop rotations in the Loess Plateau of China

USDA-ARS?s Scientific Manuscript database

Diversified crop rotations may enhance C fractions and soil quality by affecting the quality and quantity of crop residue returned to the soil compared with monocropping and fallow. We evaluated the effect of 30-yr-old diversified crop rotations on soil C fractions at 0- to 15- and 15- to 30-cm dept...

Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses

USDA-ARS?s Scientific Manuscript database

Two opposing evolutionary constraints exert pressure on pathogens: one to diversify virulence factors in order to evade host defenses, and the other to retain virulence factors critical for maintaining a compatible interaction. To better understand how the diversified arsenals of fungal genes promot...

The Ideological Dilemma in Teaching Literature: Moral Conflicts in a Diversified Society--An Israeli Teacher Case Study

ERIC Educational Resources Information Center

Baratz, Lea; Reingold, Roni

2010-01-01

The current study examines the implications of literary teaching material in a national diversified society in which the governmental educational policy separates between two national educational systems, and controls both of these separate systems. We set out to examine whether, in such realty, teachers are willing to teach texts, not formally…

East and central farming and forest region and Atlantic basin diversified farming region: LRRs N and S

Treesearch

Brad D. Lee; John M. Kabrick

2017-01-01

The central, unglaciated US east of the Great Plains to the Atlantic coast corresponds to the area covered by LRR N (East and Central Farming and Forest Region) and S (Atlantic Basin Diversified Farming Region). These regions roughly correspond to the Interior Highlands, Interior Plains, Appalachian Highlands, and the Northern Coastal Plains.

The relative contribution of drift and selection to phenotypic divergence: A test case using the horseshoe bats Rhinolophus simulator and Rhinolophus swinnyi.

PubMed

Mutumi, Gregory L; Jacobs, David S; Winker, Henning

2017-06-01

Natural selection and drift can act on populations individually, simultaneously or in tandem and our understanding of phenotypic divergence depends on our ability to recognize the contribution of each. According to the quantitative theory of evolution, if an organism has diversified through neutral evolutionary processes (mutation and drift), variation of phenotypic characteristics between different geographic localities ( B ) should be directly proportional to the variation within localities ( W ), that is, B  ∝  W . Significant deviations from this null model imply that non-neutral forces such as natural selection are acting on a phenotype. We investigated the relative contributions of drift and selection to intraspecific diversity using southern African horseshoe bats as a test case. We characterized phenotypic diversity across the distributional range of Rhinolophus simulator ( n =  101) and Rhinolophus swinnyi ( n =  125) using several traits associated with flight and echolocation. Our results suggest that geographic variation in both species was predominantly caused by disruptive natural selection ( B was not directly proportional to W ). Evidence for correlated selection (co-selection) among traits further confirmed that our results were not compatible with drift. Selection rather than drift is likely the predominant evolutionary process shaping intraspecific variation in traits that strongly impact fitness.

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

PubMed Central

Barbe, Valérie; Baeriswyl, Simon; Bidet, Philippe; Bingen, Edouard; Bonacorsi, Stéphane; Bouchier, Christiane; Bouvet, Odile; Calteau, Alexandra; Chiapello, Hélène; Clermont, Olivier; Cruveiller, Stéphane; Danchin, Antoine; Diard, Médéric; Dossat, Carole; Karoui, Meriem El; Frapy, Eric; Garry, Louis; Ghigo, Jean Marc; Gilles, Anne Marie; Johnson, James; Le Bouguénec, Chantal; Lescat, Mathilde; Mangenot, Sophie; Martinez-Jéhanne, Vanessa; Matic, Ivan; Nassif, Xavier; Oztas, Sophie; Petit, Marie Agnès; Pichon, Christophe; Rouy, Zoé; Ruf, Claude Saint; Schneider, Dominique; Tourret, Jérôme; Vacherie, Benoit; Vallenet, David; Médigue, Claudine; Rocha, Eduardo P. C.; Denamur, Erick

2009-01-01

The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome. PMID:19165319

Site-selective protein-modification chemistry for basic biology and drug development

NASA Astrophysics Data System (ADS)

Krall, Nikolaus; da Cruz, Filipa P.; Boutureira, Omar; Bernardes, Gonçalo J. L.

2016-02-01

Nature has produced intricate machinery to covalently diversify the structure of proteins after their synthesis in the ribosome. In an attempt to mimic nature, chemists have developed a large set of reactions that enable post-expression modification of proteins at pre-determined sites. These reactions are now used to selectively install particular modifications on proteins for many biological and therapeutic applications. For example, they provide an opportunity to install post-translational modifications on proteins to determine their exact biological roles. Labelling of proteins in live cells with fluorescent dyes allows protein uptake and intracellular trafficking to be tracked and also enables physiological parameters to be measured optically. Through the conjugation of potent cytotoxicants to antibodies, novel anti-cancer drugs with improved efficacy and reduced side effects may be obtained. In this Perspective, we highlight the most exciting current and future applications of chemical site-selective protein modification and consider which hurdles still need to be overcome for more widespread use.

Site-selective protein-modification chemistry for basic biology and drug development.

PubMed

Krall, Nikolaus; da Cruz, Filipa P; Boutureira, Omar; Bernardes, Gonçalo J L

2016-02-01

Nature has produced intricate machinery to covalently diversify the structure of proteins after their synthesis in the ribosome. In an attempt to mimic nature, chemists have developed a large set of reactions that enable post-expression modification of proteins at pre-determined sites. These reactions are now used to selectively install particular modifications on proteins for many biological and therapeutic applications. For example, they provide an opportunity to install post-translational modifications on proteins to determine their exact biological roles. Labelling of proteins in live cells with fluorescent dyes allows protein uptake and intracellular trafficking to be tracked and also enables physiological parameters to be measured optically. Through the conjugation of potent cytotoxicants to antibodies, novel anti-cancer drugs with improved efficacy and reduced side effects may be obtained. In this Perspective, we highlight the most exciting current and future applications of chemical site-selective protein modification and consider which hurdles still need to be overcome for more widespread use.

What's wrong with hazard-ranking systems? An expository note.

PubMed

Cox, Louis Anthony Tony

2009-07-01

Two commonly recommended principles for allocating risk management resources to remediate uncertain hazards are: (1) select a subset to maximize risk-reduction benefits (e.g., maximize the von Neumann-Morgenstern expected utility of the selected risk-reducing activities), and (2) assign priorities to risk-reducing opportunities and then select activities from the top of the priority list down until no more can be afforded. When different activities create uncertain but correlated risk reductions, as is often the case in practice, then these principles are inconsistent: priority scoring and ranking fails to maximize risk-reduction benefits. Real-world risk priority scoring systems used in homeland security and terrorism risk assessment, environmental risk management, information system vulnerability rating, business risk matrices, and many other important applications do not exploit correlations among risk-reducing opportunities or optimally diversify risk-reducing investments. As a result, they generally make suboptimal risk management recommendations. Applying portfolio optimization methods instead of risk prioritization ranking, rating, or scoring methods can achieve greater risk-reduction value for resources spent.

Heterogeneous Diversity of Spacers within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)

NASA Astrophysics Data System (ADS)

He, Jiankui; Deem, Michael W.

2010-09-01

Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of antiviral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face.

Heterogeneous diversity of spacers within CRISPR (clustered regularly interspaced short palindromic repeats).

PubMed

He, Jiankui; Deem, Michael W

2010-09-17

Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of antiviral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face.

The effect of a VR exercise program on falls and depression in the elderly with mild depression in the local community.

PubMed

Yang, Jong-Eun; Lee, Tac-Young; Kim, Jin-Kyung

2017-12-01

[Purpose] The purpose of this study is to explore the effect of a VR exercise program on falls and depression in the elderly with mild depression who reside in the local community. [Subjects and Methods] This study was performed by targeting 15 elderly subjects with mild depression who resided in the local community. The targeted subjects voluntarily selected 3 VR exercise programs (each lasting 10 minutes) among 4 activities, and a resting time of 5 minutes was given for an interval after each activity. The VR exercise program was performed for total 12 weeks (36 times), 3 times a week, 45 minutes per session. [Results] After exercise, scores of static balance test (anteroposterior), Falls Efficacy Scale, and the Activities-specific Balance Confidence Scale in the test subjects were improved and depression and internal stress scores were significantly decreased after the intervention. [Conclusion] It can be concluded that the VR exercise program exerts a positive effect not only on the physical factor but also on the mental factor of the elderly subjects with mild depression who reside in the local community. It is expected that based on the VR exercise program, diversified home programs for the elderly should be developed in the future.

Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles.

PubMed

Mustafin, Zakhar Sergeevich; Lashin, Sergey Alexandrovich; Matushkin, Yury Georgievich; Gunbin, Konstantin Vladimirovich; Afonnikov, Dmitry Arkadievich

2017-01-27

There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape ( http://cytoscape.org/ ) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged 'network evolution' found in Cytoscape official app store and in literature. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results. Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes; (2) the evolutionary origin of gene network components; (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface. Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation.

Building uncertainty into cost-effectiveness rankings: portfolio risk-return tradeoffs and implications for decision rules.

PubMed

O'Brien, B J; Sculpher, M J

2000-05-01

Current principles of cost-effectiveness analysis emphasize the rank ordering of programs by expected economic return (eg, quality-adjusted life-years gained per dollar expended). This criterion ignores the variance associated with the cost-effectiveness of a program, yet variance is a common measure of risk when financial investment options are appraised. Variation in health care program return is likely to be a criterion of program selection for health care managers with fixed budgets and outcome performance targets. Characterizing health care resource allocation as a risky investment problem, we show how concepts of portfolio analysis from financial economics can be adopted as a conceptual framework for presenting cost-effectiveness data from multiple programs as mean-variance data. Two specific propositions emerge: (1) the current convention of ranking programs by expected return is a special case of the portfolio selection problem in which the decision maker is assumed to be indifferent to risk, and (2) for risk-averse decision makers, the degree of joint risk or covariation in cost-effectiveness between programs will create incentives to diversify an investment portfolio. The conventional normative assumption of risk neutrality for social-level public investment decisions does not apply to a large number of health care resource allocation decisions in which health care managers seek to maximize returns subject to budget constraints and performance targets. Portfolio theory offers a useful framework for studying mean-variance tradeoffs in cost-effectiveness and offers some positive predictions (and explanations) of actual decision making in the health care sector.

Ethnic Education Should Undertake the Major Historic Task of Ethnic Unity and the Possibility of and Explorations into the Localization of Diversified Education

ERIC Educational Resources Information Center

Minhui, Qian

2010-01-01

This article argues that the choice of cultures by ethnic education was determined by a given form of elitist ideology and a power agency. After the conversion of China's society from a planned economy to a market economy, this elitist ideology and power agency has become diversified and includes the elitist ideology of statism. Empowerment has…

Sálvese Quien Pueda: Structural Adjustment and Emigration from Lima

PubMed Central

MASSEY, DOUGLAS S.; CAPOFERRO, CHIARA

2010-01-01

Beginning in 1987, Peru imposed a regime of structural adjustment to transform its economy along neoliberal lines. This analysis suggests that a shift resulted in the odds of international migration and the motivations for leaving among inhabitants of Peru’s largest labor market. Before 1987, under the regime of import substitution industrialization, jobs at wages capable of sustaining a basic standard of living were widely available; those few who left the country self-selected for higher human capital and moved abroad to improve their earnings. Under neoliberalism, however, both employment and wages fell to levels that made it difficult for families to sustain themselves. In response, households—with the assistance of friends and relatives with foreign experience—diversified their labor portfolios away from the local job market structural adjustment zones. The number of migrants then rose, the diversity of foreign destinations increased, and migration became less selective with respect to human capital. PMID:20824152

Evolutionary engineering for industrial microbiology.

PubMed

Vanee, Niti; Fisher, Adam B; Fong, Stephen S

2012-01-01

Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors.

PubMed

Whitmer, Shannon L M; Ladner, Jason T; Wiley, Michael R; Patel, Ketan; Dudas, Gytis; Rambaut, Andrew; Sahr, Foday; Prieto, Karla; Shepard, Samuel S; Carmody, Ellie; Knust, Barbara; Naidoo, Dhamari; Deen, Gibrilla; Formenty, Pierre; Nichol, Stuart T; Palacios, Gustavo; Ströher, Ute

2018-01-30

Following cessation of continuous Ebola virus (EBOV) transmission within Western Africa, sporadic EBOV disease (EVD) cases continued to re-emerge beyond the viral incubation period. Epidemiological and genomic evidence strongly suggests that this represented transmission from EVD survivors. To investigate whether persistent infections are characterized by ongoing viral replication, we sequenced EBOV from the semen of nine EVD survivors and a subset of corresponding acute specimens. EBOV evolutionary rates during persistence were either similar to or reduced relative to acute infection rates. Active EBOV replication/transcription continued during convalescence, but decreased over time, consistent with viral persistence rather than viral latency. Patterns of genetic divergence suggest a moderate relaxation of selective constraints within the sGP carboxy-terminal tail during persistent infections, but do not support widespread diversifying selection. Altogether, our data illustrate that EBOV persistence in semen, urine, and aqueous humor is not a quiescent or latent infection. Published by Elsevier Inc.

Effect of Growth Mindset on School Engagement and Psychological Well-Being of Chinese Primary and Middle School Students: The Mediating Role of Resilience

PubMed Central

Zeng, Guang; Hou, Hanchao; Peng, Kaiping

2016-01-01

The objective of positive education is not only to improve students’ well-being but also their academic performance. As an important concept in positive education, growth mindset refers to core assumptions about the malleability of a person’s intellectual abilities. The present study investigates the relation of growth mindsets to psychological well-being and school engagement. The study also explores the mediating function of resilience in this relation. We recruited a total of 1260 (658 males and 602 females) Chinese students from five diversified primary and middle schools. Results from the structural equation model show that the development of high levels of growth mindsets in students predicts higher psychological well-being and school engagement through the enhancement of resilience. The current study contributes to our understanding of the potential mechanisms by which positive education (e.g., altering the mindset of students) can impact psychological well-being and school engagement. PMID:28018251

Effect of Growth Mindset on School Engagement and Psychological Well-Being of Chinese Primary and Middle School Students: The Mediating Role of Resilience.

PubMed

Zeng, Guang; Hou, Hanchao; Peng, Kaiping

2016-01-01

The objective of positive education is not only to improve students' well-being but also their academic performance. As an important concept in positive education, growth mindset refers to core assumptions about the malleability of a person's intellectual abilities. The present study investigates the relation of growth mindsets to psychological well-being and school engagement. The study also explores the mediating function of resilience in this relation. We recruited a total of 1260 (658 males and 602 females) Chinese students from five diversified primary and middle schools. Results from the structural equation model show that the development of high levels of growth mindsets in students predicts higher psychological well-being and school engagement through the enhancement of resilience. The current study contributes to our understanding of the potential mechanisms by which positive education (e.g., altering the mindset of students) can impact psychological well-being and school engagement.

Evaluation of P1'-diversified phosphinic peptides leads to the development of highly selective inhibitors of MMP-11.

PubMed

Matziari, Magdalini; Beau, Fabrice; Cuniasse, Philippe; Dive, Vincent; Yiotakis, Athanasios

2004-01-15

Phosphinic peptides were previously reported to be potent inhibitors of several matrixins (MMPs). To identify more selective inhibitors of MMP-11, a matrixin overexpressed in breast cancer, a series of phosphinic pseudopeptides bearing a variety of P(1)'-side chains has been synthesized, by parallel diversification of a phosphinic template. The potencies of these compounds were evaluated against a set of seven MMPs (MMP-2, MMP-7, MMP-8, MMP-9, MMP-11, MMP-13, and MMP-14). The chemical strategy applied led to the identification of several phosphinic inhibitors displaying high selectivity toward MMP-11. One of the most selective inhibitors of MMP-11 in this series, compound 22, exhibits a K(i) value of 0.23 microM toward MMP-11, while its potency toward the other MMPs tested is 2 orders of magnitude lower. This remarkable selectivity may rely on interactions of the P(1)'-side chain atoms of these inhibitors with residues located at the entrance of the S(1)'-cavity of MMP-11. The design of inhibitors able to interact with residues located at the entrance of MMPs' S(1)'-cavity might represent an alternative strategy to identify selective inhibitors that will fully differentiate one MMP among the others.

The nature of selection on the major histocompatibility complex.

PubMed

Apanius, V; Penn, D; Slev, P R; Ruff, L R; Potts, W K

1997-01-01

Only natural selection can account for the extreme genetic diversity of genes of the major histocompatibility complex (MHC). Although the structure and function of classic MHC genes is well understood at the molecular and cellular levels, there is controversy about how MHC diversity is selectively maintained. The diversifying selection can be driven by pathogen interactions and inbreeding avoidance mechanisms. Pathogen-driven selection can maintain MHC polymorphism based on heterozygote advantage or frequency-dependent selection due to pathogen evasion of MHC-dependent immune recognition. Empirical evidence demonstrates that specific MHC haplotypes are resistant to certain infectious agents, while susceptible to others. These data are consistent with both heterozygote advantage and frequency-dependent models. Additional research is needed to discriminate between these mechanisms. Infectious agents can precipitate autoimmunity and can potentially contribute to MHC diversity through molecular mimicry and by favoring immunodominance. MHC-dependent abortion and mate choice, based on olfaction, can also maintain MHC diversity and probably functions both to avoid genome-wide inbreeding and produce MHC-heterozygous offspring with increased immune responsiveness. Although this diverse set of hypotheses are often treated as competing alternatives, we believe that they all fit into a coherent, internally consistent thesis. It is likely that at least in some species, all of these mechanisms operate, leading to the extreme diversification found in MHC genes.

How does male–male competition generate negative frequency-dependent selection and disruptive selection during speciation?

PubMed Central

Border, Shana E

2018-01-01

Abstract Natural selection has been shown to drive population differentiation and speciation. The role of sexual selection in this process is controversial; however, most of the work has centered on mate choice while the role of male–male competition in speciation is relatively understudied. Here, we outline how male–male competition can be a source of diversifying selection on male competitive phenotypes, and how this can contribute to the evolution of reproductive isolation. We highlight how negative frequency-dependent selection (advantage of rare phenotype arising from stronger male–male competition between similar male phenotypes compared with dissimilar male phenotypes) and disruptive selection (advantage of extreme phenotypes) drives the evolution of diversity in competitive traits such as weapon size, nuptial coloration, or aggressiveness. We underscore that male–male competition interacts with other life-history functions and that variable male competitive phenotypes may represent alternative adaptive options. In addition to competition for mates, aggressive interference competition for ecological resources can exert selection on competitor signals. We call for a better integration of male–male competition with ecological interference competition since both can influence the process of speciation via comparable but distinct mechanisms. Altogether, we present a more comprehensive framework for studying the role of male–male competition in speciation, and emphasize the need for better integration of insights gained from other fields studying the evolutionary, behavioral, and physiological consequences of agonistic interactions. PMID:29492042

Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification.

PubMed

Covain, Raphaël; Fisch-Muller, Sonia; Oliveira, Claudio; Mol, Jan H; Montoya-Burgos, Juan I; Dray, Stéphane

2016-01-01

The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with Rineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria. Copyright © 2015 Elsevier Inc. All rights reserved.

Functional diversification of sea urchin ABCC1 (MRP1) by alternative splicing.

PubMed

Gökirmak, Tufan; Campanale, Joseph P; Reitzel, Adam M; Shipp, Lauren E; Moy, Gary W; Hamdoun, Amro

2016-06-01

The multidrug resistance protein (MRP) family encodes a diverse repertoire of ATP-binding cassette (ABC) transporters with multiple roles in development, disease, and homeostasis. Understanding MRP evolution is central to unraveling their roles in these diverse processes. Sea urchins occupy an important phylogenetic position for understanding the evolution of vertebrate proteins and have been an important invertebrate model system for study of ABC transporters. We used phylogenetic analyses to examine the evolution of MRP transporters and functional approaches to identify functional forms of sea urchin MRP1 (also known as SpABCC1). SpABCC1, the only MRP homolog in sea urchins, is co-orthologous to human MRP1, MRP3, and MRP6 (ABCC1, ABCC3, and ABCC6) transporters. However, efflux assays revealed that alternative splicing of exon 22, a region critical for substrate interactions, could diversify functions of sea urchin MRP1. Phylogenetic comparisons also indicate that while MRP1, MRP3, and MRP6 transporters potentially arose from a single transporter in basal deuterostomes, alternative splicing appears to have been the major mode of functional diversification in invertebrates, while duplication may have served a more important role in vertebrates. These results provide a deeper understanding of the evolutionary origins of MRP transporters and the potential mechanisms used to diversify their functions in different groups of animals. Copyright © 2016 the American Physiological Society.

Functional diversification of sea urchin ABCC1 (MRP1) by alternative splicing

PubMed Central

Gökirmak, Tufan; Campanale, Joseph P.; Reitzel, Adam M.; Shipp, Lauren E.; Moy, Gary W.

2016-01-01

The multidrug resistance protein (MRP) family encodes a diverse repertoire of ATP-binding cassette (ABC) transporters with multiple roles in development, disease, and homeostasis. Understanding MRP evolution is central to unraveling their roles in these diverse processes. Sea urchins occupy an important phylogenetic position for understanding the evolution of vertebrate proteins and have been an important invertebrate model system for study of ABC transporters. We used phylogenetic analyses to examine the evolution of MRP transporters and functional approaches to identify functional forms of sea urchin MRP1 (also known as SpABCC1). SpABCC1, the only MRP homolog in sea urchins, is co-orthologous to human MRP1, MRP3, and MRP6 (ABCC1, ABCC3, and ABCC6) transporters. However, efflux assays revealed that alternative splicing of exon 22, a region critical for substrate interactions, could diversify functions of sea urchin MRP1. Phylogenetic comparisons also indicate that while MRP1, MRP3, and MRP6 transporters potentially arose from a single transporter in basal deuterostomes, alternative splicing appears to have been the major mode of functional diversification in invertebrates, while duplication may have served a more important role in vertebrates. These results provide a deeper understanding of the evolutionary origins of MRP transporters and the potential mechanisms used to diversify their functions in different groups of animals. PMID:27053522

Clinical disease registries in acute myocardial infarction.

PubMed

Ashrafi, Reza; Hussain, Hussain; Brisk, Robert; Boardman, Leanne; Weston, Clive

2014-06-26

Disease registries, containing systematic records of cases, have for nearly 100 years been valuable in exploring and understanding various aspects of cardiology. This is particularly true for myocardial infarction, where such registries have provided both epidemiological and clinical information that was not readily available from randomised controlled trials in highly-selected populations. Registries, whether mandated or voluntary, prospective or retrospective in their analysis, have at their core a common study population and common data definitions. In this review we highlight how registries have diversified to offer information on epidemiology, risk modelling, quality assurance/improvement and original research-through data mining, transnational comparisons and the facilitation of enrolment in, and follow-up during registry-based randomised clinical trials.

Heterogeneous diversity of spacers within CRISPR

NASA Astrophysics Data System (ADS)

Deem, Michael; He, Jiankui

2011-03-01

Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of anti-viral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face. 1) J. He and M. W. Deem, Phys. Rev. Lett. 105 (2010) 128102

A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties

PubMed Central

Tiller, Thomas; Schuster, Ingrid; Deppe, Dorothée; Siegers, Katja; Strohner, Ralf; Herrmann, Tanja; Berenguer, Marion; Poujol, Dominique; Stehle, Jennifer; Stark, Yvonne; Heßling, Martin; Daubert, Daniela; Felderer, Karin; Kaden, Stefan; Kölln, Johanna; Enzelberger, Markus; Urlinger, Stefanie

2013-01-01

This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds. PMID:23571156

A two-locus model of spatially varying stabilizing or directional selection on a quantitative trait

PubMed Central

Geroldinger, Ludwig; Bürger, Reinhard

2014-01-01

The consequences of spatially varying, stabilizing or directional selection on a quantitative trait in a subdivided population are studied. A deterministic two-locus two-deme model is employed to explore the effects of migration, the degree of divergent selection, and the genetic architecture, i.e., the recombination rate and ratio of locus effects, on the maintenance of genetic variation. The possible equilibrium configurations are determined as functions of the migration rate. They depend crucially on the strength of divergent selection and the genetic architecture. The maximum migration rates are investigated below which a stable fully polymorphic equilibrium or a stable single-locus polymorphism can exist. Under stabilizing selection, but with different optima in the demes, strong recombination may facilitate the maintenance of polymorphism. However usually, and in particular with directional selection in opposite direction, the critical migration rates are maximized by a concentrated genetic architecture, i.e., by a major locus and a tightly linked minor one. Thus, complementing previous work on the evolution of genetic architectures in subdivided populations subject to diversifying selection, it is shown that concentrated architectures may aid the maintenance of polymorphism. Conditions are obtained when this is the case. Finally, the dependence of the phenotypic variance, linkage disequilibrium, and various measures of local adaptation and differentiation on the parameters is elaborated. PMID:24726489

A two-locus model of spatially varying stabilizing or directional selection on a quantitative trait.

PubMed

Geroldinger, Ludwig; Bürger, Reinhard

2014-06-01

The consequences of spatially varying, stabilizing or directional selection on a quantitative trait in a subdivided population are studied. A deterministic two-locus two-deme model is employed to explore the effects of migration, the degree of divergent selection, and the genetic architecture, i.e., the recombination rate and ratio of locus effects, on the maintenance of genetic variation. The possible equilibrium configurations are determined as functions of the migration rate. They depend crucially on the strength of divergent selection and the genetic architecture. The maximum migration rates are investigated below which a stable fully polymorphic equilibrium or a stable single-locus polymorphism can exist. Under stabilizing selection, but with different optima in the demes, strong recombination may facilitate the maintenance of polymorphism. However usually, and in particular with directional selection in opposite direction, the critical migration rates are maximized by a concentrated genetic architecture, i.e., by a major locus and a tightly linked minor one. Thus, complementing previous work on the evolution of genetic architectures in subdivided populations subject to diversifying selection, it is shown that concentrated architectures may aid the maintenance of polymorphism. Conditions are obtained when this is the case. Finally, the dependence of the phenotypic variance, linkage disequilibrium, and various measures of local adaptation and differentiation on the parameters is elaborated. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Analysis of Pvama1 genes from China-Myanmar border reveals little regional genetic differentiation of Plasmodium vivax populations.

PubMed

Zhu, Xiaotong; Zhao, Pan; Wang, Si; Liu, Fei; Liu, Jun; Wang, Jian; Yang, Zhaoqing; Yan, Guiyun; Fan, Qi; Cao, Yaming; Cui, Liwang

2016-11-29

With the premise of diminishing parasite genetic diversity following the reduction of malaria incidence, the analysis of polymorphic antigenic markers may provide important information about the impact of malaria control on local parasite populations. Here we evaluated the genetic diversity of Plasmodium vivax apical membrane antigen 1 (Pvama1) gene in a parasite population from the China-Myanmar border and compared it with global P. vivax populations. We performed evolutionary analysis to examine the genetic diversity, natural selection, and population differentiation of 73 Pvama1 sequences acquired from the China-Myanmar border as well as 615 publically available Pvama1 sequences from seven global P. vivax populations. A total of 308 Pvama1 haplotypes were identified among the global P. vivax isolates. The overall nucleotide diversity of Pvama1 gene among the 73 China-Myanmar border parasite isolates was 0.008 with 41 haplotypes being identified (Hd = 0.958). Domain I (DI) harbored the majority (26/33) of the polymorphic sites. The McDonald Kreitman test showed a significant positive selection across the ectodomain and the DI of Pvama1. The fixation index (F ST ) estimation between the China-Myanmar border, Thailand (0.01) and Myanmar (0.10) showed only slight geographical genetic differentiation. Notably, the Sal-I haplotype was not detected in any of the analyzed global isolates, whereas the Belem strain was restricted to the Thai population. The detected mutations are mapped outside the overlapped region of the predicted B-cell epitopes and intrinsically unstructured/disordered regions. This study revealed high levels of genetic diversity of Pvama1 in the P. vivax parasite population from the China-Myanmar border with DI displaying stronger diversifying selection than other domains. There were low levels of population subdivision among parasite populations from the Greater Mekong Subregion.

Speciation genes in plants

PubMed Central

Rieseberg, Loren H.; Blackman, Benjamin K.

2010-01-01

Background Analyses of speciation genes – genes that contribute to the cessation of gene flow between populations – can offer clues regarding the ecological settings, evolutionary forces and molecular mechanisms that drive the divergence of populations and species. This review discusses the identities and attributes of genes that contribute to reproductive isolation (RI) in plants, compares them with animal speciation genes and investigates what these genes can tell us about speciation. Scope Forty-one candidate speciation genes were identified in the plant literature. Of these, seven contributed to pre-pollination RI, one to post-pollination, prezygotic RI, eight to hybrid inviability, and 25 to hybrid sterility. Genes, gene families and genetic pathways that were frequently found to underlie the evolution of RI in different plant groups include the anthocyanin pathway and its regulators (pollinator isolation), S RNase-SI genes (unilateral incompatibility), disease resistance genes (hybrid necrosis), chimeric mitochondrial genes (cytoplasmic male sterility), and pentatricopeptide repeat family genes (cytoplasmic male sterility). Conclusions The most surprising conclusion from this review is that identities of genes underlying both prezygotic and postzygotic RI are often predictable in a broad sense from the phenotype of the reproductive barrier. Regulatory changes (both cis and trans) dominate the evolution of pre-pollination RI in plants, whereas a mix of regulatory mutations and changes in protein-coding genes underlie intrinsic postzygotic barriers. Also, loss-of-function mutations and copy number variation frequently contribute to RI. Although direct evidence of positive selection on speciation genes is surprisingly scarce in plants, analyses of gene family evolution, along with theoretical considerations, imply an important role for diversifying selection and genetic conflict in the evolution of RI. Unlike in animals, however, most candidate speciation genes in plants exhibit intraspecific polymorphism, consistent with an important role for stochastic forces and/or balancing selection in development of RI in plants. PMID:20576737

Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies

PubMed Central

Chen, Jun; Källman, Thomas; Ma, Xiao-Fei; Zaina, Giusi; Morgante, Michele; Lascoux, Martin

2016-01-01

The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower FST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both FST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI. PMID:27172202

Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies.

PubMed

Chen, Jun; Källman, Thomas; Ma, Xiao-Fei; Zaina, Giusi; Morgante, Michele; Lascoux, Martin

2016-07-07

The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower FST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both FST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI. Copyright © 2016 Chen et al.

[Single-nucleotide polymorphism in populations of sockeye salmon Oncorhynchus nerka from Kamchatka Peninsula].

PubMed

Khrustaleva, A M; Gritsenko, O F; Klovach, N V

2013-11-01

The genetic polymorphism of 45 single-nucleotide polymorphism loci was examined in the four largest wild populations of sockeye salmon Oncorhynchusnerka from drainages of the Asian coast of the Pacific Ocean (Eastern and Western Kamchatka). It was demonstrated that sockeye salmon from the Palana River were considerably different from all other populations examined. The most probable explanation of the observed differences is the suggestion on possible demographic events in the history of this population associated with the decrease in its effective number. To study the origin, colonization patterns, and evolution of Asian sockeye salmon, as well as to resolve some of the applied tasks, like population assignment and genetic identification, a differentiation approach to SNP-marker selection was suggested. Adaptively important loci that evolve under the pressure of balancing (stabilizing) selection were identified, thanks to which the number of loci that provide the baseline classification error rates in the population assignment tests was reduced to 30. It was demonstrated that SNPs located in the MHC2 and GPH genes were affected by diversifying selection. Procedures for selecting single-nucleotide polymorphisms for phylogenetic studies of Asian sockeye salmon were suggested. Using principal-component analysis, 17 loci that adequately reproduce genetic differentiation within arid among the regions of the origin of Kamchatka sockeye salmon, were selected.

Endocrine regulation and sexual differentiation of avian copulatory sexually selected characters.

PubMed

Brennan, Patricia L R; Adkins-Regan, Elizabeth

2014-10-01

Reproductive specializations in birds have provided intriguing model systems to better understand the role of endocrine mechanisms that regulate phenotype expression and the action of sexual selection. A comparative approach can elucidate how endocrine systems associated with control of sexual differentiation, sexual maturation, and reproductive physiology and behavior have diversified. Here we compare the copulatory sexually selected traits of two members of the galloanseriform superfamily: quail and ducks. Japanese quail have a non-intromittent penis, and they have evolved a unique foam gland that is known to be involved in post-copulatory sexual selection. In contrast, ducks have maintained a large intromittent penis that has evolved via copulatory male-male competition and has been elaborated in a sexually antagonistic race due to sexual conflict with females over mating. These adaptations function in concert with sex-specific and, in part, species-specific behaviors. Although the approaches to study these traits have been different, exploring the differences in neuroendocrine regulation of sexual behavior, development and seasonality of the foam gland and the penis side by side, allow us to suggest some areas where future research would be productive to better understand the evolution of novelty in sexually selected traits. Copyright © 2014 Elsevier Ltd. All rights reserved.

Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes

PubMed Central

Norman, Paul J.; Abi-Rached, Laurent; Gendzekhadze, Ketevan; Hammond, John A.; Moesta, Achim K.; Sharma, Deepti; Graef, Thorsten; McQueen, Karina L.; Guethlein, Lisbeth A.; Carrington, Christine V.F.; Chandanayingyong, Dasdayanee; Chang, Yih-Hsin; Crespí, Catalina; Saruhan-Direskeneli, Güher; Hameed, Kamran; Kamkamidze, Giorgi; Koram, Kwadwo A.; Layrisse, Zulay; Matamoros, Nuria; Milà, Joan; Park, Myoung Hee; Pitchappan, Ramasamy M.; Ramdath, D. Dan; Shiau, Ming-Yuh; Stephens, Henry A.F.; Struik, Siske; Tyan, Dolly; Verity, David H.; Vaughan, Robert W.; Davis, Ronald W.; Fraser, Patricia A.; Riley, Eleanor M.; Ronaghi, Mostafa; Parham, Peter

2009-01-01

Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed by other cells. For primate NK cells, the killer-cell immunoglobulin-like receptors (KIR) are a variable and rapidly evolving family of MHC Class I receptors. Studied here is KIR3DL1/S1, which encodes receptors for highly polymorphic human HLA-A and -B and comprises three ancient allelic lineages that have been preserved by balancing selection throughout human evolution. While the 3DS1 lineage of activating receptors has been conserved, the two 3DL1 lineages of inhibitory receptors were diversified through inter-lineage recombination with each other and with 3DS1. Prominent targets for recombination were D0-domain polymorphisms, which modulate enhancer function, and dimorphism at position 283 in the D2 domain, which influences inhibitory function. In African populations, unequal crossing over between the 3DL1 and 3DL2 genes produced a deleted KIR haplotype in which the telomeric “half” was reduced to a single fusion gene with functional properties distinct from its 3DL1 and 3DL2 parents. Conversely, in Eurasian populations, duplication of the KIR3DL1/S1 locus by unequal crossing over has enabled individuals to carry and express alleles of all three KIR3DL1/S1 lineages. These results demonstrate how meiotic recombination combines with an ancient, preserved diversity to create new KIR phenotypes upon which natural selection acts. A consequence of such recombination is to blur the distinction between alleles and loci in the rapidly evolving human KIR gene family. PMID:19411600

The evolutionary implications of knox-I gene duplications in conifers: correlated evidence from phylogeny, gene mapping, and analysis of functional divergence.

PubMed

Guillet-Claude, Carine; Isabel, Nathalie; Pelgas, Betty; Bousquet, Jean

2004-12-01

Class I knox genes code for transcription factors that play an essential role in plant growth and development as central regulators of meristem cell identity. Based on the analysis of new cDNA sequences from various tissues and genomic DNA sequences, we identified a highly diversified group of class I knox genes in conifers. Phylogenetic analyses of complete amino acid sequences from various seed plants indicated that all conifer sequences formed a monophyletic group. Within conifers, four subgroups here named genes KN1 to KN4 were well delineated, each regrouping pine and spruce sequences. KN4 was sister group to KN3, which was sister group to KN1 and KN2. Genetic mapping on the genomes of two divergent Picea species indicated that KN1 and KN2 are located close to each other on the same linkage group, whereas KN3 and KN4 mapped on different linkage groups, correlating the more ancient divergence of these two genes. The proportion of synonymous and nonsynonymous substitutions suggested intense purifying selection for the four genes. However, rates of substitution per year indicated an evolution in two steps: faster rates were noted after gene duplications, followed subsequently by lower rates. Positive directional selection was detected for most of the internal branches harboring an accelerated rate of evolution. In addition, many sites with highly significant amino acid rate shift were identified between these branches. However, the tightly linked KN1 and KN2 did not diverge as much from each other. The implications of the correlation between phylogenetic, structural, and functional information are discussed in relation to the diversification of the knox-I gene family in conifers.

An Evolutionary Analysis of the Secoviridae Family of Viruses

PubMed Central

Thompson, Jeremy R.; Kamath, Nitin; Perry, Keith L.

2014-01-01

The plant-infecting Secoviridae family of viruses forms part of the Picornavirales order, an important group of non-enveloped viruses that infect vertebrates, arthropods, plants and algae. The impact of the secovirids on cultivated crops is significant, infecting a wide range of plants from grapevine to rice. The overwhelming majority are transmitted by ecdysozoan vectors such as nematodes, beetles and aphids. In this study, we have applied a variety of computational methods to examine the evolutionary traits of these viruses. Strong purifying selection pressures were calculated for the coat protein (CP) sequences of nine species, although for two species evidence of both codon specific and episodic diversifying selection were found. By using Bayesian phylogenetic reconstruction methods CP nucleotide substitution rates for four species were estimated to range from between 9.29×10−3 to 2.74×10−3 (subs/site/year), values which are comparable with the short-term estimates of other related plant- and animal-infecting virus species. From these data, we were able to construct a time-measured phylogeny of the subfamily Comovirinae that estimated divergence of ninety-four extant sequences occurred less than 1,000 years ago with present virus species diversifying between 50 and 250 years ago; a period coinciding with the intensification of agricultural practices in industrial societies. Although recombination (modularity) was limited to closely related taxa, significant and often unique similarities in the protein domains between secovirid and animal infecting picorna-like viruses, especially for the protease and coat protein, suggested a shared ancestry. We discuss our results in a wider context and find tentative evidence to indicate that some members of the Secoviridae might have their origins in insects, possibly colonizing plants in a number of founding events that have led to speciation. Such a scenario; virus infection between species of different taxonomic kingdoms, has significant implications for virus emergence. PMID:25180860

Burnout in Female Faculty Members.

PubMed

Cassidy-Vu, Lisa; Beck, Keli; Moore, Justin B

2017-04-01

Despite approximately equal numbers of male and female medical school graduates, women are entering academic medicine at a lower rate than their male colleagues. Of those who do assume a faculty position, female faculty members report higher levels of burnout, often attributable to gender-specific difficulties in clinical expectations and maintenance of work-life balance. Many of these struggles are attributable to issues that are amenable to supportive policies, but these policies are inconsistent in their availability and practice. This commentary presents evidence for inconsistencies in the day-to-day experience of female faculty members, and proposes solutions for the mitigation of the challenges experienced more often by female faculty members with the goal of diversifying and strengthening academic medicine.

Burnout in Female Faculty Members

PubMed Central

Cassidy-Vu, Lisa; Beck, Keli; Moore, Justin B.

2016-01-01

Despite approximately equal numbers of male and female medical school graduates, women are entering academic medicine at a lower rate than their male colleagues. Of those who do assume a faculty position, female faculty members report higher levels of burnout, often attributable to gender-specific difficulties in clinical expectations and maintenance of work-life balance. Many of these struggles are attributable to issues that are amenable to supportive policies, but these policies are inconsistent in their availability and practice. This commentary presents evidence for inconsistencies in the day-to-day experience of female faculty members, and proposes solutions for the mitigation of the challenges experienced more often by female faculty members with the goal of diversifying and strengthening academic medicine. PMID:27650035

Technology Maturity for the Habitable-zone Exoplanet Imaging Mission (HabEx) Concept

NASA Astrophysics Data System (ADS)

Morgan, Rhonda; Warfield, Keith R.; Stahl, H. Philip; Mennesson, Bertrand; Nikzad, Shouleh; nissen, joel; Balasubramanian, Kunjithapatham; Krist, John; Mawet, Dimitri; Stapelfeldt, Karl; warwick, Steve

2018-01-01

HabEx Architecture A is a 4m unobscured telescope optimized for direct imaging and spectroscopy of potentially habitable exoplanets, and also enables a wide range of general astrophysics science. The exoplanet detection and characterization drives the enabling core technologies. A hybrid starlight suppression approach of a starshade and coronagraph diversifies technology maturation risk. In this poster we assess these exoplanet-driven technologies, including elements of coronagraphs, starshades, mirrors, jitter mitigation, wavefront control, and detectors. By utilizing high technology readiness solutions where feasible, and identifying required technology development that can begin early, HabEx will be well positioned for assessment by the community in 2020 Astrophysics Decadal Survey.

Diversification of Processors Based on Redundancy in Instruction Set

NASA Astrophysics Data System (ADS)

Ichikawa, Shuichi; Sawada, Takashi; Hata, Hisashi

By diversifying processor architecture, computer software is expected to be more resistant to plagiarism, analysis, and attacks. This study presents a new method to diversify instruction set architecture (ISA) by utilizing the redundancy in the instruction set. Our method is particularly suited for embedded systems implemented with FPGA technology, and realizes a genuine instruction set randomization, which has not been provided by the preceding studies. The evaluation results on four typical ISAs indicate that our scheme can provide a far larger degree of freedom than the preceding studies. Diversified processors based on MIPS architecture were actually implemented and evaluated with Xilinx Spartan-3 FPGA. The increase of logic scale was modest: 5.1% in Specialized design and 3.6% in RAM-mapped design. The performance overhead was also modest: 3.4% in Specialized design and 11.6% in RAM-mapped design. From these results, our scheme is regarded as a practical and promising way to secure FPGA-based embedded systems.

Diversifying the Geosciences: Examples from the Arctic

NASA Astrophysics Data System (ADS)

Holmes, R. M.

2017-12-01

Like other realms of the geosciences, the scientists who comprise the Arctic research community tends to be white and male. For example, a survey of grants awarded over a 5-year period beginning in 2010 by NSF's Arctic System Science and Arctic Natural Sciences programs showed that over 90% of PIs were white whereas African Americans, Hispanics, and Native Americans together accounted for only about 1% of PIs. Over 70% of the PIs were male. I will suggest that involving diverse upper-level undergraduate students in authentic field research experiences may be one of the shortest and surest routes to diversifying the Arctic research community, and by extension, the geoscientific research community overall. Upper-level undergraduate students are still open to multiple possibilities, but an immersive field research experience often helps solidify graduate school and career trajectories. Though an all-of-the-above strategy is needed, focusing on engaging a diverse cohort of upper-level undergraduate students may provide one of the most efficient means of diversifying the geosciences over the coming years and decades.

Rewiring protein synthesis: From natural to synthetic amino acids.

PubMed

Fan, Yongqiang; Evans, Christopher R; Ling, Jiqiang

2017-11-01

The protein synthesis machinery uses 22 natural amino acids as building blocks that faithfully decode the genetic information. Such fidelity is controlled at multiple steps and can be compromised in nature and in the laboratory to rewire protein synthesis with natural and synthetic amino acids. This review summarizes the major quality control mechanisms during protein synthesis, including aminoacyl-tRNA synthetases, elongation factors, and the ribosome. We will discuss evolution and engineering of such components that allow incorporation of natural and synthetic amino acids at positions that deviate from the standard genetic code. The protein synthesis machinery is highly selective, yet not fixed, for the correct amino acids that match the mRNA codons. Ambiguous translation of a codon with multiple amino acids or complete reassignment of a codon with a synthetic amino acid diversifies the proteome. Expanding the genetic code with synthetic amino acids through rewiring protein synthesis has broad applications in synthetic biology and chemical biology. Biochemical, structural, and genetic studies of the translational quality control mechanisms are not only crucial to understand the physiological role of translational fidelity and evolution of the genetic code, but also enable us to better design biological parts to expand the proteomes of synthetic organisms. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

Scalariform-to-simple transition in vessel perforation plates triggered by differences in climate during the evolution of Adoxaceae

PubMed Central

Lens, Frederic; Vos, Rutger A.; Charrier, Guillaume; van der Niet, Timo; Merckx, Vincent; Baas, Pieter; Aguirre Gutierrez, Jesus; Jacobs, Bart; Chacon Dória, Larissa; Smets, Erik; Delzon, Sylvain; Janssens, Steven B.

2016-01-01

Background and Aims Angiosperms with simple vessel perforations have evolved many times independently of species having scalariform perforations, but detailed studies to understand why these transitions in wood evolution have happened are lacking. We focus on the striking difference in wood anatomy between two closely related genera of Adoxaceae, Viburnum and Sambucus, and link the anatomical divergence with climatic and physiological insights. Methods After performing wood anatomical observations, we used a molecular phylogenetic framework to estimate divergence times for 127 Adoxaceae species. The conditions under which the genera diversified were estimated using ancestral area reconstruction and optimization of ancestral climates, and xylem-specific conductivity measurements were performed. Key Results Viburnum, characterized by scalariform vessel perforations (ancestral), diversified earlier than Sambucus, having simple perforations (derived). Ancestral climate reconstruction analyses point to cold temperate preference for Viburnum and warm temperate for Sambucus. This is reflected in the xylem-specific conductivity rates of the co-occurring species investigated, showing that Viburnum lantana has rates much lower than Sambucus nigra. Conclusions The lack of selective pressure for high conductive efficiency during early diversification of Viburnum and the potentially adaptive value of scalariform perforations in frost-prone cold temperate climates have led to retention of the ancestral vessel perforation type, while higher temperatures during early diversification of Sambucus have triggered the evolution of simple vessel perforations, allowing more efficient long-distance water transport. PMID:27498812

Mitochondrial genome diversity in the Tubalar, Even, and Ulchi: contribution to prehistory of native Siberians and their affinities to Native Americans.

PubMed

Sukernik, Rem I; Volodko, Natalia V; Mazunin, Ilya O; Eltsov, Nikolai P; Dryomov, Stanislav V; Starikovskaya, Elena B

2012-05-01

To fill remaining gaps in mitochondrial DNA diversity in the least surveyed eastern and western flanks of Siberia, 391 mtDNA samples (144 Tubalar from Altai, 87 Even from northeastern Siberia, and 160 Ulchi from the Russian Far East) were characterized via high-resolution restriction fragment length polymorphism/single nucleotide polymorphisms analysis. The subhaplogroup structure was extended through complete sequencing of 67 mtDNA samples selected from these and other related native Siberians. Specifically, we have focused on the evolutionary histories of the derivatives of M and N haplogroups, putatively reflecting different phases of settling Siberia by early modern humans. Population history and phylogeography of the resulting mtDNA genomes, combined with those from previously published data sets, revealed a wide range of tribal- and region-specific mtDNA haplotypes that emerged or diversified in Siberia before or after the last glacial maximum, ∼18 kya. Spatial distribution and ages of the "east" and "west" Eurasian mtDNA haploclusters suggest that anatomically modern humans that originally colonized Altai derived from macrohaplogroup N and came from Southwest Asia around 38,000 years ago. The derivatives of macrohaplogroup M, which largely emerged or diversified within the Russian Far East, came along with subsequent migrations to West Siberia millennia later. The last glacial maximum played a critical role in the timing and character of the settlement of the Siberian subcontinent. Copyright © 2012 Wiley Periodicals, Inc.

Evolutionary diversification of the auditory organ sensilla in Neoconocephalus katydids (Orthoptera: Tettigoniidae) correlates with acoustic signal diversification over phylogenetic relatedness and life history.

PubMed

Strauß, J; Alt, J A; Ekschmitt, K; Schul, J; Lakes-Harlan, R

2017-06-01

Neoconocephalus Tettigoniidae are a model for the evolution of acoustic signals as male calls have diversified in temporal structure during the radiation of the genus. The call divergence and phylogeny in Neoconocephalus are established, but in tettigoniids in general, accompanying evolutionary changes in hearing organs are not studied. We investigated anatomical changes of the tympanal hearing organs during the evolutionary radiation and divergence of intraspecific acoustic signals. We compared the neuroanatomy of auditory sensilla (crista acustica) from nine Neoconocephalus species for the number of auditory sensilla and the crista acustica length. These parameters were correlated with differences in temporal call features, body size, life histories and different phylogenetic positions. By this, adaptive responses to shifting frequencies of male calls and changes in their temporal patterns can be evaluated against phylogenetic constraints and allometry. All species showed well-developed auditory sensilla, on average 32-35 between species. Crista acustica length and sensillum numbers correlated with body size, but not with phylogenetic position or life history. Statistically significant correlations existed also with specific call patterns: a higher number of auditory sensilla occurred in species with continuous calls or slow pulse rates, and a longer crista acustica occurred in species with double pulses or slow pulse rates. The auditory sensilla show significant differences between species despite their recent radiation, and morphological and ecological similarities. This indicates the responses to natural and sexual selection, including divergence of temporal and spectral signal properties. Phylogenetic constraints are unlikely to limit these changes of the auditory systems. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

[Estimation of activity of pharmakopeal disinfectants and antiseptics against Gram-negative and Gram-positive bacteria isolated from clinical specimens, drugs and environment].

PubMed

Grzybowska, Wanda; Młynarczyk, Grazyna; Młynarczyk, Andrzej; Bocian, Ewa; Luczak, Mirosław; Tyski, Stefan

2007-01-01

The MIC of nine different disinfectants and antiseptics were determined for the Gram-negative and Gram-positive bacteria. Strains originated from clinical specimens, drugs and environment. A sensitivity was determined against chlorhexidinum digluconate (Gram-negative: 0,625-80 mg/L, Gram-positive: 0,3-10 mg/L), benzalconium chloride (Gram-negative: 2,5-1280 mg/L, Gram-positive: 1,25-20 mg/L), salicilic acid (Gram-negative and Gram-positive: 400-1600 mg/L), benzoic acid (Gram-negative: 800-1600 mg/L, Gram-positive: 400-1 600 mg/L), boric acid (Gram-negative: 800-12 800 mg/L, Gram-positive: 1 600-6400 mg/L), chloramine B (Gram-negative: 1600-6400 mg/L, Gram-positive:800- 6400 mg/L), jodine (Gram-negative: 200-1600 mg/L, Gram-positive: 200-1600 mg/L), etacridine lactate (Gram-negative: 40 do > 20480 mg/L, Gram-positive: 40-1280 mg/L) and resorcine (Gram-negative: 1600-6400 mg/L, Gram-positive: 800-6400 mg/L). Diversified values of MIC for different strains were obtained, especially in the case of benzalconium chloride, etacridine lactate, chlorhexidinum digluconate, boric acid and iodine. Strains isolated from environment were usually more susceptible to examined compounds than clinical strains. The biggest diversification of sensitivity was observed among strains originated from drugs where besides sensitive appeared strains characterizing by very high MIC values of some substances, eg. boric acid.

Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe.

PubMed

Iso-Touru, T; Tapio, M; Vilkki, J; Kiseleva, T; Ammosov, I; Ivanova, Z; Popov, R; Ozerov, M; Kantanen, J

2016-12-01

Domestication in the near eastern region had a major impact on the gene pool of humpless taurine cattle (Bos taurus). As a result of subsequent natural and artificial selection, hundreds of different breeds have evolved, displaying a broad range of phenotypic traits. Here, 10 Eurasian B. taurus breeds from different biogeographic and production conditions, which exhibit different demographic histories and have been under artificial selection at various intensities, were investigated using the Illumina BovineSNP50 panel to understand their genetic diversity and population structure. In addition, we scanned genomes from eight breeds for signatures of diversifying selection. Our population structure analysis indicated six distinct breed groups, the most divergent being the Yakutian cattle from Siberia. Selection signals were shared (experimental P-value < 0.01) with more than four breeds on chromosomes 6, 7, 13, 16 and 22. The strongest selection signals in the Yakutian cattle were found on chromosomes 7 and 21, where a miRNA gene and genes related to immune system processes are respectively located. In general, genomic regions indicating selection overlapped with known QTL associated with milk production (e.g. on chromosome 19), reproduction (e.g. on chromosome 24) and meat quality (e.g. on chromosome 7). The selection map created in this study shows that native cattle breeds and their genetic resources represent unique material for future breeding. © 2016 Stichting International Foundation for Animal Genetics.

Postcopulatory sexual selection generates speciation phenotypes in Drosophila.

PubMed

Manier, Mollie K; Lüpold, Stefan; Belote, John M; Starmer, William T; Berben, Kirstin S; Ala-Honkola, Outi; Collins, William F; Pitnick, Scott

2013-10-07

Identifying traits that reproductively isolate species, and the selective forces underlying their divergence, is a central goal of evolutionary biology and speciation research. There is growing recognition that postcopulatory sexual selection, which can drive rapid diversification of interacting ejaculate and female reproductive tract traits that mediate sperm competition, may be an engine of speciation. Conspecific sperm precedence (CSP) is a taxonomically widespread form of reproductive isolation, but the selective causes and divergent traits responsible for CSP are poorly understood. To test the hypothesis that postcopulatory sexual selection can generate reproductive isolation, we expressed GFP or RFP in sperm heads of recently diverged sister species, Drosophila simulans and D. mauritiana, to enable detailed resolution of species-specific sperm precedence mechanisms. Between-species divergence in sperm competition traits and mechanisms prompted six a priori predictions regarding mechanisms of CSP and degree of cross asymmetry in reproductive isolation. We resolved four distinct mechanisms of CSP that were highly consistent with predictions. These comprise interactions between multiple sex-specific traits, including two independent mechanisms by which females exert sophisticated control over sperm fate to favor the conspecific male. Our results confirm that reproductive isolation can quickly arise from diversifying (allopatric) postcopulatory sexual selection. This experimental approach to "speciation phenotypes" illustrates how knowledge of sperm precedence mechanisms can be used to predict the mechanisms and extent of reproductive isolation between populations and species. Copyright © 2013 Elsevier Ltd. All rights reserved.

Variation under domestication in plants: 1859 and today

PubMed Central

Brown, Anthony H. D.

2010-01-01

Charles Darwin began The Origin of Species with a chapter entitled variation under domestication, which encapsulated decades of his research on a diverse array of animal and plant domesticated species. Variation in these species compared with that in their wild relatives, their origins and their selection by humans, formed a paradigm for his theory of the evolutionary origin of species by means of natural selection. This chapter, its subsequent expansion into a two-volume monograph, together with the rediscovery of Mendel's laws, later became the foundation of scientific plant breeding. In the period up to the present, several advances in genetics (such as artificial mutation, polyploidy, adaptation and genetic markers) have amplified the discipline with concepts and questions, the seeds of which are in Darwin's original words. Today, we are witnessing a flowering of genomic research into the process of domestication itself, particularly the specific major and minor genes involved. In one striking way, our view of domestic diversity contrasts with that in Darwin's writing. He stressed the abundance of diversity and the diversifying power of artificial selection, whereas we are concerned about dwindling genetic diversity that attends modern agriculture and development. In this context, it is paramount to strive for a deeper understanding of how farmer selection including both deliberate selection and unconscious selection, might generate and retain diversity. This knowledge is essential for devising in situ conservation measures. PMID:20643742

Peripheral blood lymphocytes express recombination-activating genes 1 and 2 during Epstein-Barr virus-induced infectious mononucleosis.

PubMed

Wagner, Hans-Joachim; Scott, Rona S; Buchwald, Dedra; Sixbey, John W

2004-09-01

Implicit in the persistence of Epstein-Barr virus (EBV) in B lymphocytes is the successful circumvention of ongoing cell selection for competence of B cell receptors (BCRs). Because the EBV infection of B cells in vitro induces enzymatic machinery that is responsible for secondary immunoglobulin gene rearrangement, we examined the expression of the recombination-activating genes (RAGs) in peripheral blood mononuclear cells (PBMCs) from 26 patients with infectious mononucleosis (IM). RAG1 and/or RAG2 RNA was detected in PBMCs from 42% of patients with IM but not from healthy control subjects. EBV may usurp the cellular mechanism that diversifies the BCR, to guarantee a level of survival signaling sufficient for its own persistence.

Uncovering the information core in recommender systems

NASA Astrophysics Data System (ADS)

Zeng, Wei; Zeng, An; Liu, Hao; Shang, Ming-Sheng; Zhou, Tao

2014-08-01

With the rapid growth of the Internet and overwhelming amount of information that people are confronted with, recommender systems have been developed to effectively support users' decision-making process in online systems. So far, much attention has been paid to designing new recommendation algorithms and improving existent ones. However, few works considered the different contributions from different users to the performance of a recommender system. Such studies can help us improve the recommendation efficiency by excluding irrelevant users. In this paper, we argue that in each online system there exists a group of core users who carry most of the information for recommendation. With them, the recommender systems can already generate satisfactory recommendation. Our core user extraction method enables the recommender systems to achieve 90% of the accuracy of the top-L recommendation by taking only 20% of the users into account. A detailed investigation reveals that these core users are not necessarily the large-degree users. Moreover, they tend to select high quality objects and their selections are well diversified.

Adaptability of non-genetic diversity in bacterial chemotaxis

PubMed Central

Frankel, Nicholas W; Pontius, William; Dufour, Yann S; Long, Junjiajia; Hernandez-Nunez, Luis; Emonet, Thierry

2014-01-01

Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an alternative, or even evolutionary stepping-stone, to switching between multiple systems. We hypothesized that mutations in gene regulation could lead to heritable control of chemotactic diversity. By simulating foraging and colonization of E. coli using a single-cell chemotaxis model, we found that different environments selected for different behaviors. The resulting trade-offs show that populations facing diverse environments would ideally diversify behaviors when time for navigation is limited. We show that advantageous diversity can arise from changes in the distribution of protein levels among individuals, which could occur through mutations in gene regulation. We propose experiments to test our prediction that chemotactic diversity in a clonal population could be a selectable trait that enables adaptation to environmental variability. DOI: http://dx.doi.org/10.7554/eLife.03526.001 PMID:25279698

Temperature-Centric Evaluation of Sensor Transients

NASA Astrophysics Data System (ADS)

Ayhan, Tuba; Muezzinoglu, Kerem; Vergara, Alexander; Yalcin, Mustak

2011-09-01

Controllable sensing conditions provide the means for diversifying sensor response and achieving better selectivity. Modulating the sensing layer temperature of metal-oxide sensors is a popular method for multiplexing the limited number of sensing elements that can be employed in a practical array. Time limitations in many applications, however, cannot tolerate an ad-hoc, one-size-fits-all modulation pattern. When the response pattern is itself non-stationary, as in the transient phase, a temperature program also becomes infeasible. We consider the problem of determining and tuning into a fixed optimum temperature in a sensor array. For this purpose, we present an empirical analysis of the temperature's role on the performance of a metal-oxide gas sensor array in the identification of odorants along the response transient. We show that the optimal temperature in this sense depends heavily on the selection of (i) the set of candidate analytes, (ii) the time-window of the analysis, (iii) the feature extracted from the sensor response, and (iv) the computational identification method used.

Evolution and Diversity of the Human Hepatitis D Virus Genome

PubMed Central

Huang, Chi-Ruei; Lo, Szecheng J.

2010-01-01

Human hepatitis delta virus (HDV) is the smallest RNA virus in genome. HDV genome is divided into a viroid-like sequence and a protein-coding sequence which could have originated from different resources and the HDV genome was eventually constituted through RNA recombination. The genome subsequently diversified through accumulation of mutations selected by interactions between the mutated RNA and proteins with host factors to successfully form the infectious virions. Therefore, we propose that the conservation of HDV nucleotide sequence is highly related with its functionality. Genome analysis of known HDV isolates shows that the C-terminal coding sequences of large delta antigen (LDAg) are the highest diversity than other regions of protein-coding sequences but they still retain biological functionality to interact with the heavy chain of clathrin can be selected and maintained. Since viruses interact with many host factors, including escaping the host immune response, how to design a program to predict RNA genome evolution is a great challenging work. PMID:20204073

Homeotic Evolution in the Mammalia: Diversification of Therian Axial Seriation and the Morphogenetic Basis of Human Origins

PubMed Central

Filler, Aaron G.

2007-01-01

Background Despite the rising interest in homeotic genes, little has been known about the course and pattern of evolution of homeotic traits across the mammalian radiation. An array of emerging and diversifying homeotic gradients revealed by this study appear to generate new body plans and drive evolution at a large scale. Methodology/Principal Findings This study identifies and evaluates a set of homeotic gradients across 250 extant and fossil mammalian species and their antecedents over a period of 220 million years. These traits are generally expressed as co-linear gradients along the body axis rather than as distinct segmental identities. Relative position or occurrence sequence vary independently and are subject to polarity reversal and mirroring. Five major gradient modification sets are identified: (1)–quantitative changes of primary segmental identity pattern that appeared at the origin of the tetrapods ; (2)–frame shift relation of costal and vertebral identity which diversifies from the time of amniote origins; (3)–duplication, mirroring, splitting and diversification of the neomorphic laminar process first commencing at the dawn of mammals; (4)–emergence of homologically variable lumbar lateral processes upon commencement of the radiation of therian mammals and ; (5)–inflexions and transpositions of the relative position of the horizontal septum of the body and the neuraxis at the emergence of various orders of therian mammals. Convergent functional changes under homeotic control include laminar articular engagement with septo-neural transposition and ventrally arrayed lumbar transverse process support systems. Conclusion/Significance Clusters of homeotic transformations mark the emergence point of mammals in the Triassic and the radiation of therians in the Cretaceous. A cluster of homeotic changes in the Miocene hominoid Morotopithecus that are still seen in humans supports establishment of a new “hominiform” clade and suggests a homeotic origin for the human upright body plan. PMID:17925867

Post-Miocene expansion, colonization, and host switching drove speciation among extant nematodes of the archaic genus Trichinella

PubMed Central

Zarlenga, D. S.; Rosenthal, B. M.; La Rosa, G.; Pozio, E.; Hoberg, E. P.

2006-01-01

Parasitic nematodes of the genus Trichinella cause significant food-borne illness and occupy a unique evolutionary position at the base of the phylum Nematoda, unlike the free-living nematode Caenorhabditis elegans. Although the forthcoming genome sequence of Trichinella spiralis can provide invaluable comparative information about nematode biology, a basic framework for understanding the history of the genus Trichinella is needed to maximize its utility. We therefore developed the first robust and comprehensive analysis of the phylogeny and biogeographic history of Trichinella using the variation in three genes (nuclear small-subunit rDNA, and second internal transcribed spacer, mitochondrial large-subunit rDNA, and cytochrome oxidase I DNA) from all 11 recognized taxa. We conclude that (i) although Trichinellidae may have diverged from their closest extant relatives during the Paleozoic, all contemporary species of Trichinella diversified within the last 20 million years through geographic colonization and pervasive host switching among foraging guilds of obligate carnivores; (ii) mammalian carnivores disseminated encapsulated forms from Eurasia to Africa during the late Miocene and Pliocene, and to the Nearctic across the Bering Land Bridge during the Pliocene and Pleistocene, when crown species ultimately diversified; (iii) the greatest risk to human health is posed by those species retaining an ancestral capacity to parasitize a wide range of hosts; and (iv) early hominids may have first acquired Trichinella on the African savannah several million years before swine domestication as their diets shifted from herbivory to facultative carnivory. PMID:16651518

The Impacts of Wind Speed Trends and Long-term Variability in Relation to Hydroelectric Reservoir Inflows on Wind Power in the Pacific Northwest

NASA Astrophysics Data System (ADS)

Cross, B.; Kohfeld, K. E.; Cooper, A.; Bailey, H. J.; Rucker, M.

2013-12-01

The use of wind power is growing rapidly in the Pacific Northwest (PNW ) due to environmental concerns, decreasing costs of implementation, strong wind speeds, and a desire to diversify electricity sources to minimize the impacts of streamflow variability on electricity prices and system flexibility. In hydroelectric dominated systems, like the PNW, the benefits of wind power can be maximized by accounting for the relationship between long term variability in wind speeds and reservoir inflows. Clean energy policies in British Columbia make the benefits of increased wind power generation during low streamflow periods particularly large, by preventing the overbuilding of marginal hydroelectric projects. The goal of this work was to quantify long-term relationships between wind speed and streamflow behavior in British Columbia. Wind speed data from the North American Regional Reanalysis (NARR) and cumulative usable inflows (CUI) from BC Hydro were used to analyze 10m wind speed and density (WD) trends, WD-CUI correlations, and WD anomalies during low and high inflow periods in the PNW (40°N to 65°N, 110°W to 135°W) from 1979-2010. Statistically significant positive wind speed and density trends were found for most of the PNW, with the largest increases along the Pacific Coast. CUI-WD correlations were weakly positive for most regions, with the highest values along the US coast (r ~0.55), generally weaker correlations to the north, and negative correlations (r ~ -0.25) along BC's North Coast. When considering seasonal relationships, the Spring freshet was coincident with lower WD anomalies west of the Rocky Mountains and higher WDs to the east. A similar but opposite pattern was observed for low inflow winter months. When considering interannual variability, lowest inflow years experienced positive WD anomalies (up to 40% increases) for the North Coast. In highest inflow years, positive WD anomalies were widespread in the US and for smaller patches of central BC. By accounting for regional and temporal differences in the relationship between wind (WD) and streamflow (CUI) behaviour during wind farm site selection, the benefits of energy diversification can be maximized.

Frequency dependence limits divergent evolution by favouring rare immigrants over residents.

PubMed

Bolnick, Daniel I; Stutz, William E

2017-06-08

Two distinct forms of natural selection promote adaptive biological diversity. Divergent selection occurs when different environments favour different phenotypes, leading to increased differences between populations. Negative frequency-dependent selection occurs when rare variants within a population are favoured over common ones, increasing diversity within populations. These two diversifying forces promote genetic variation at different spatial scales, and may act in opposition, but their relative effects remain unclear because they are rarely measured concurrently. Here we show that negative frequency-dependent selection within populations can favor rare immigrants over locally adapted residents. We reciprocally transplanted lake and stream ecotypes of threespine stickleback into lake and stream habitats, while manipulating the relative abundance of residents versus immigrants. We found negative frequency-dependence: survival was highest for the locally rare ecotype, rather than natives. Also, individuals with locally rare major histocompatibility complex (MHC) class IIb genotypes were infected by fewer parasites. This negative frequency-dependent selection will tend to favour rare immigrants over common residents, amplifying the effect of migration and undermining the efficacy of divergent natural selection to drive population differences. The only signal of divergent selection was a tendency for foreign fish to have higher parasite loads than residents, after controlling for MHC genotype rarity. Frequency-dependent ecological interactions have long been thought to promote speciation. Our results suggest a more nuanced view in which negative frequency dependence alters the fate of migrants to promote or constrain evolutionary divergence between populations.

Decentralizing conservation and diversifying livelihoods within Kanchenjunga Conservation Area, Nepal.

PubMed

Parker, Pete; Thapa, Brijesh; Jacob, Aerin

2015-12-01

To alleviate poverty and enhance conservation in resource dependent communities, managers must identify existing livelihood strategies and the associated factors that impede household access to livelihood assets. Researchers increasingly advocate reallocating management power from exclusionary central institutions to a decentralized system of management based on local and inclusive participation. However, it is yet to be shown if decentralizing conservation leads to diversified livelihoods within a protected area. The purpose of this study was to identify and assess factors affecting household livelihood diversification within Nepal's Kanchenjunga Conservation Area Project, the first protected area in Asia to decentralize conservation. We randomly surveyed 25% of Kanchenjunga households to assess household socioeconomic and demographic characteristics and access to livelihood assets. We used a cluster analysis with the ten most common income generating activities (both on- and off-farm) to group the strategies households use to diversify livelihoods, and a multinomial logistic regression to identify predictors of livelihood diversification. We found four distinct groups of household livelihood strategies with a range of diversification that directly corresponded to household income. The predictors of livelihood diversification were more related to pre-existing socioeconomic and demographic factors (e.g., more landholdings and livestock, fewer dependents, receiving remittances) than activities sponsored by decentralizing conservation (e.g., microcredit, training, education, interaction with project staff). Taken together, our findings indicate that without direct policies to target marginalized groups, decentralized conservation in Kanchenjunga will continue to exclude marginalized groups, limiting a household's ability to diversify their livelihood and perpetuating their dependence on natural resources. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evidence-based protocol for structural rehabilitation of the spine and posture: review of clinical biomechanics of posture (CBP®) publications

PubMed Central

Oakley, Paul A.; Harrison, Donald D.; Harrison, Deed E.; Haas, Jason W.

2005-01-01

BACKGROUND Although practice protocols exist for SMT and functional rehabilitation, no practice protocols exist for structural rehabilitation. Traditional chiropractic practice guidelines have been limited to acute and chronic pain treatment, with limited inclusion of functional and exclusion of structural rehabilitation procedures. OBJECTIVE (1) To derive an evidence-based practice protocol for structural rehabilitation from publications on Clinical Biomechanics of Posture (CBP®) methods, and (2) to compare the evidence for Diversified, SMT, and CBP®. METHODS Clinical control trials utilizing CBP® methods and spinal manipulative therapy (SMT) were obtained from searches in Mantis, CINAHL, and Index Medicus. Using data from SMT review articles, evidence for Diversified Technique (as taught in chiropractic colleges), SMT, and CBP® were rated and compared. RESULTS From the evidence from Clinical Control Trials on SMT and CBP®, there is very little evidence support for Diversified (our rating = 18), as taught in chiropractic colleges, for the treatment of pain subjects, while CBP® (our rating = 46) and SMT for neck pain (rating = 58) and low back pain (our rating = 202) have evidence-based support. CONCLUSIONS While CBP® Technique has approximately as much evidence-based support as SMT for neck pain, CBP® has more evidence to support its methods than the Diversified technique taught in chiropractic colleges, but not as much as SMT for low back pain. The evolution of chiropractic specialization has occurred, and doctors providing structural-based chiropractic care require protocol guidelines for patient quality assurance and standardization. A structural rehabilitation protocol was developed based on evidence from CBP® publications. PMID:17549209

Sexual differences in telomere selection in the wild.

PubMed

Olsson, Mats; Pauliny, Angela; Wapstra, Erik; Uller, Tobias; Schwartz, Tonia; Miller, Emily; Blomqvist, Donald

2011-05-01

Telomere length is restored primarily through the action of the reverse transcriptase telomerase, which may contribute to a prolonged lifespan in some but not all species and may result in longer telomeres in one sex than the other. To what extent this is an effect of proximate mechanisms (e.g. higher stress in males, higher oestradiol/oestrogen levels in females), or is an evolved adaptation (stronger selection for telomere length in one sex), usually remains unknown. Sand lizard (Lacerta agilis) females have longer telomeres than males and better maintain telomere length through life than males do. We also show that telomere length more strongly contributes to life span and lifetime reproductive success in females than males and that telomere length is under sexually diversifying selection in the wild. Finally, we performed a selection analysis with number of recruited offspring into the adult population as a response variable with telomere length, life span and body size as predictor variables. This showed significant differences in selection pressures between the sexes with strong ongoing selection in females, with these three predictors explaining 63% of the variation in recruitment. Thus, the sexually dimorphic telomere dynamics with longer telomeres in females is a result of past and ongoing selection in sand lizards. Finally, we compared the results from our selection analyses based on Telometric-derived data to the results based on data generated by the software ImageJ. ImageJ resulted in shorter average telomere length, but this difference had virtually no qualitative effect on the patterns of ongoing selection. © 2011 Blackwell Publishing Ltd.

Case studies of orthopedic surgery in California: the virtues of care coordination versus specialization.

PubMed

Robinson, James C

2013-05-01

Two overarching frameworks compete to address the organizational ills of the health care system. One framework diagnoses lack of coordination and prescribes integration and global payment. The other diagnoses loss of focus and prescribes specialization and episode payment. This article, based on research and interviews, assesses how the two frameworks manifest themselves at two high-volume orthopedic hospitals in Irvine, California. The Kaiser Permanente Irvine Medical Center is part of a large and diversified health system. The Hoag Orthopedic Institute is a single-specialty facility jointly owned by the physicians and the hospital. Market outcomes, such as the merger of the Hoag specialty hospital into a larger diversified health system, suggest that Kaiser's focus on coordination of patient care from preadmission to postdischarge is a key factor in its success. But Hoag's specialization also leads to improved efficiencies. The integrated approach appears to be prevailing. At the same time, large diversified organizations might obtain further efficiencies by pursuing service-line strategies as described in this article--for instance, by providing incentives for efficiency and quality for each specialty and type of care.

Two-faced property of a market factor in asset pricing and diversification effect

NASA Astrophysics Data System (ADS)

Eom, Cheoljun

2017-04-01

This study empirically investigates the test hypothesis that a market factor acting as a representative common factor in the pricing models has a negative influence on constructing a well-diversified portfolio from the Markowitz mean-variance optimization function (MVOF). We use the comparative correlation matrix (C-CM) method to control a single eigenvalue among all eigenvalues included in the sample correlation matrix (S-CM), through the random matrix theory (RMT). In particular, this study observes the effect of the largest eigenvalue that has the property of the market factor. According to the results, the largest eigenvalue has the highest explanatory power on the stock return changes. The C-CM without the largest eigenvalue in the S-CM constructs a more diversified portfolio capable of improving the practical applicability of the MVOF. Moreover, the more diversified portfolio constructed from this C-CM has better out-of-sample performance in the future period. These results support the test hypothesis for the two-faced property of the market factor, defined by the largest eigenvalue.

Specification Patent Management for Web Application Platform Ecosystem

NASA Astrophysics Data System (ADS)

Fukami, Yoshiaki; Isshiki, Masao; Takeda, Hideaki; Ohmukai, Ikki; Kokuryo, Jiro

Diversified usage of web applications has encouraged disintegration of web platform into management of identification and applications. Users make use of various kinds of data linked to their identity with multiple applications on certain social web platforms such as Facebook or MySpace. There has emerged competition among web application platforms. Platformers can design relationship with developers by controlling patent of their own specification and adopt open technologies developed external organizations. Platformers choose a way to open according to feature of the specification and their position. Patent management of specification come to be a key success factor to build competitive web application platforms. Each way to attract external developers such as standardization, open source has not discussed and analyzed all together.

Isomorphism and external support in conflicting institutional environments: a study of drug abuse treatment units.

PubMed

D'Aunno, T; Sutton, R I; Price, R H

1991-09-01

Using institutional theory, we developed predictions about organizational units that moved from an environment making consistent demands to one making conflicting demands. Many community mental health centers have diversified into drug abuse treatment. The units providing those services face conflicting demands from the traditional mental health sector and the new drug abuse treatment sector about which clients to serve, how to assess their problems, and who should provide treatment. We propose that in response to such demands these units will adopt apparently conflicting practices. Also, isomorphism with the traditional sector will be positively associated with external support from parent mental health centers and other actors in the mental health sector. Results generally support those predictions.

Methods and practices to diversify cell-based products.

PubMed

Vertès, Alain A

2017-12-15

Medicinal signaling cell (MSC)-based products represent emerging treatments in various therapeutic areas including cardiometabolic, inflammation, autoimmunity, orthopedics, wound healing and oncology. Exploring innovation beyond minimally manipulated plastic-adherent ex vivo expanded allogeneic MSCs enables product delineation. Product delineation is on the critical path to maximize clinical benefits and market access. An innovation framework is presented here along various innovation dimensions comprising composition-of-matter by means of positive cell surface markers, formulation varying for example the cell dose or the preservation mode and medium, manufacturing to adapt the secretome of MSCs to the condition of interest, the mode of delivery and corresponding delivery devices, as well as molecular engineering and biomarkers. The rationale of the innovation space thus described applies generally to all cell-based therapies.

Selective Recovery of Critical Materials from Geothermal Fluid

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

Mayes, Richard T.; Halstenberg, Phillip W.; Moyer, Bruce A.

This project, funded by the DOE Small Business Voucher program, assisted the partner with the development of ion-imprinted adsorbents for the selective extraction of rare earth elements (REE) from geothermal brines. This effort seeks to utilize a currently untapped resource thus diversifying the U. S. REE market. The initial stage of the program focused on the adsorbent developed by partner and optimization of the adsorbent. The adsorbent was based upon an ion imprinted ligand that was copolymerized with a crosslinker to generate the REE selectivity. During this task, the adsorbents were irradiated via electron beam at the NEO Beam Electronmore » Beam Crosslinking Facility (Mercury Plastics, Middlefield, OH) to induce further crosslinking. The irradiation crosslinked adsorbents exhibited no difference in the Fourier transform infrared spectroscopic (FTIR) analysis suggesting inefficiency in the crosslinking. In the later stage of the effort, a new method was proposed and studied at ORNL involving a new partnership between the partner and a commercial polymer vender. This resulted in a new material being developed which allows the partner to utilize a commercial support and integrate the synthesis into a production-ready product stream. This will enhance the route to commercialization for the partner resulting in a quicker market penetration for the product. The new adsorbent exhibits selectivity for REE over transition metals commonly found within geothermal brines. Further optimization is required for enhanced selectivity, capacity, and intra-lanthanide separations.« less

Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection

PubMed Central

Silva, Inês N.; Santos, Mário R.; Zlosnik, James E. A.; Speert, David P.; Buskirk, Sean W.; Bruger, Eric L.; Waters, Christopher M.

2016-01-01

ABSTRACT Burkholderia multivorans is an opportunistic pathogen capable of causing severe disease in patients with cystic fibrosis (CF). Patients may be chronically infected for years, during which the bacterial population evolves in response to unknown forces. Here we analyze the genomic and functional evolution of a B. multivorans infection that was sequentially sampled from a CF patient over 20 years. The population diversified into at least four primary, coexisting clades with distinct evolutionary dynamics. The average substitution rate was only 2.4 mutations/year, but notably, some lineages evolved more slowly, whereas one diversified more rapidly by mostly nonsynonymous mutations. Ten loci, mostly involved in gene expression regulation and lipid metabolism, acquired three or more independent mutations and define likely targets of selection. Further, a broad range of phenotypes changed in association with the evolved mutations; they included antimicrobial resistance, biofilm regulation, and the presentation of lipopolysaccharide O-antigen repeats, which was directly caused by evolved mutations. Additionally, early isolates acquired mutations in genes involved in cyclic di-GMP (c-di-GMP) metabolism that associated with increased c-di-GMP intracellular levels. Accordingly, these isolates showed lower motility and increased biofilm formation and adhesion to CFBE41o− epithelial cells than the initial isolate, and each of these phenotypes is an important trait for bacterial persistence. The timing of the emergence of this clade of more adherent genotypes correlated with the period of greatest decline in the patient’s lung function. All together, our observations suggest that selection on B. multivorans populations during long-term colonization of CF patient lungs either directly or indirectly targets adherence, metabolism, and changes in the cell envelope related to adaptation to the biofilm lifestyle. IMPORTANCE Bacteria may become genetically and phenotypically diverse during long-term colonization of cystic fibrosis (CF) patient lungs, yet our understanding of within-host evolutionary processes during these infections is lacking. Here we combined current genome sequencing technologies and detailed phenotypic profiling of the opportunistic pathogen Burkholderia multivorans using sequential isolates sampled from a CF patient over 20 years. The evolutionary history of these isolates highlighted bacterial genes and pathways that were likely subject to strong selection within the host and were associated with altered phenotypes, such as biofilm production, motility, and antimicrobial resistance. Importantly, multiple lineages coexisted for years or even decades within the infection, and the period of diversification within the dominant lineage was associated with deterioration of the patient’s lung function. Identifying traits under strong selection during chronic infection not only sheds new light onto Burkholderia evolution but also sets the stage for tailored therapeutics targeting the prevailing lineages associated with disease progression. PMID:27822534

Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals

PubMed Central

Shabalina, Svetlana A.; Ogurtsov, Aleksey Y.; Spiridonov, Nikolay A.; Koonin, Eugene V.

2014-01-01

Alternative splicing (AS), alternative transcription initiation (ATI) and alternative transcription termination (ATT) create the extraordinary complexity of transcriptomes and make key contributions to the structural and functional diversity of mammalian proteomes. Analysis of mammalian genomic and transcriptomic data shows that contrary to the traditional view, the joint contribution of ATI and ATT to the transcriptome and proteome diversity is quantitatively greater than the contribution of AS. Although the mean numbers of protein-coding constitutive and alternative nucleotides in gene loci are nearly identical, their distribution along the transcripts is highly non-uniform. On average, coding exons in the variable 5′ and 3′ transcript ends that are created by ATI and ATT contain approximately four times more alternative nucleotides than core protein-coding regions that diversify exclusively via AS. Short upstream exons that encompass alternative 5′-untranslated regions and N-termini of proteins evolve under strong nucleotide-level selection whereas in 3′-terminal exons that encode protein C-termini, protein-level selection is significantly stronger. The groups of genes that are subject to ATI and ATT show major differences in biological roles, expression and selection patterns. PMID:24792168

Individual-based models for adaptive diversification in high-dimensional phenotype spaces.

PubMed

Ispolatov, Iaroslav; Madhok, Vaibhav; Doebeli, Michael

2016-02-07

Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state before diversification occurs, as exemplified by the concept of evolutionary branching points in adaptive dynamics theory. Recent results indicate that adaptive dynamics may often not converge to equilibrium points and instead generate complicated trajectories if evolution takes place in high-dimensional phenotype spaces. Even though some analytical results on diversification in complex phenotype spaces are available, to study this problem in general we need to reconstruct individual-based models from the adaptive dynamics generating the non-equilibrium dynamics. Here we first provide a method to construct individual-based models such that they faithfully reproduce the given adaptive dynamics attractor without diversification. We then show that a propensity to diversify can be introduced by adding Gaussian competition terms that generate frequency dependence while still preserving the same adaptive dynamics. For sufficiently strong competition, the disruptive selection generated by frequency-dependence overcomes the directional evolution along the selection gradient and leads to diversification in phenotypic directions that are orthogonal to the selection gradient. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

A Diversified Investment Strategy Using Autonomous Agents

NASA Astrophysics Data System (ADS)

Barbosa, Rui Pedro; Belo, Orlando

In a previously published article, we presented an architecture for implementing agents with the ability to trade autonomously in the Forex market. At the core of this architecture is an ensemble of classification and regression models that is used to predict the direction of the price of a currency pair. In this paper, we will describe a diversified investment strategy consisting of five agents which were implemented using that architecture. By simulating trades with 18 months of out-of-sample data, we will demonstrate that data mining models can produce profitable predictions, and that the trading risk can be diminished through investment diversification.

New era / new solutions: The role of alternative tariff structures in water supply projects.

PubMed

Pinto, F Silva; Marques, R Cunha

2017-12-01

Water utilities face different challenges that may force them to seek prioritized objectives. When doing so, particular projects may have to be developed, being important to understand their impact on water tariffs, and thus, on customers. Such consequences may bear an increased relevance in cases stressed with, e.g., resource scarcity, poverty, and the need for infrastructure investments. The resulting cost and revenue variability demand a comprehensive study. If the first may require a stochastic modeling (in major cost components) in order to consider its inherent uncertainty, the second needs to be modeled following context-specific objectives set by the relevant stakeholders. The solutions achieved will likely promote distinct revenue sources, as well as diversified water tariff structures. A multi-objective optimization model (i.e., a Framework for Suitable Prices) is built to deal with those diversified requirements (e.g., stochastic energy costs, affordability, cost recovery, or administrative simplicity). The model is solved through achievement scalarizing functions with several weighting coefficients for a reference point, so as to provide a significant perception of possible revenue options (and their impact) to the decision makers. The proposed method is applied to a case study, Boa Vista Island in Cabo Verde, in which the background characteristics, namely water sources availability (e.g., the adoption of desalination technologies), economic development and other contextual factors were considered. The key role of tariff structure selection is displayed, instead of assuming it a priori, giving important insights regarding project feasibility. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Ternary Brain-Computer Interface Based on Single-Trial Readiness Potentials of Self-initiated Fine Movements: A Diversified Classification Scheme

PubMed Central

Abou Zeid, Elias; Rezazadeh Sereshkeh, Alborz; Schultz, Benjamin; Chau, Tom

2017-01-01

In recent years, the readiness potential (RP), a type of pre-movement neural activity, has been investigated for asynchronous electroencephalogram (EEG)-based brain-computer interfaces (BCIs). Since the RP is attenuated for involuntary movements, a BCI driven by RP alone could facilitate intentional control amid a plethora of unintentional movements. Previous studies have mainly attempted binary single-trial classification of RP. An RP-based BCI with three or more states would expand the options for functional control. Here, we propose a ternary BCI based on single-trial RPs. This BCI classifies amongst an idle state, a left hand and a right hand self-initiated fine movement. A pipeline of spatio-temporal filtering with per participant parameter optimization was used for feature extraction. The ternary classification was decomposed into binary classifications using a decision-directed acyclic graph (DDAG). For each class pair in the DDAG structure, an ordered diversified classifier system (ODCS-DDAG) was used to select the best among various classification algorithms or to combine the results of different classification algorithms. Using EEG data from 14 participants performing self-initiated left or right key presses, punctuated with rest periods, we compared the performance of ODCS-DDAG to a ternary classifier and four popular multiclass decomposition methods using only a single classification algorithm. ODCS-DDAG had the highest performance (0.769 Cohen's Kappa score) and was significantly better than the ternary classifier and two of the four multiclass decomposition methods. Our work supports further study of RP-based BCI for intuitive asynchronous environmental control or augmentative communication. PMID:28596725

Large-scale diversification without genetic isolation in nematode symbionts of figs

PubMed Central

Susoy, Vladislav; Herrmann, Matthias; Kanzaki, Natsumi; Kruger, Meike; Nguyen, Chau N.; Rödelsperger, Christian; Röseler, Waltraud; Weiler, Christian; Giblin-Davis, Robin M.; Ragsdale, Erik J.; Sommer, Ralf J.

2016-01-01

Diversification is commonly understood to be the divergence of phenotypes accompanying that of lineages. In contrast, alternative phenotypes arising from a single genotype are almost exclusively limited to dimorphism in nature. We report a remarkable case of macroevolutionary-scale diversification without genetic divergence. Upon colonizing the island-like microecosystem of individual figs, symbiotic nematodes of the genus Pristionchus accumulated a polyphenism with up to five discrete adult morphotypes per species. By integrating laboratory and field experiments with extensive genotyping of individuals, including the analysis of 49 genomes from a single species, we show that rapid filling of potential ecological niches is possible without diversifying selection on genotypes. This uncoupling of morphological diversification and speciation in fig-associated nematodes has resulted from a remarkable expansion of discontinuous developmental plasticity. PMID:26824073

Structure and function of polyketide biosynthetic enzymes: various strategies for production of structurally diverse polyketides.

PubMed

Miyanaga, Akimasa

2017-12-01

Polyketides constitute a large family of natural products that display various biological activities. Polyketides exhibit a high degree of structural diversity, although they are synthesized from simple acyl building blocks. Recent biochemical and structural studies provide a better understanding of the biosynthetic logic of polyketide diversity. This review highlights the biosynthetic mechanisms of structurally unique polyketides, β-amino acid-containing macrolactams, enterocin, and phenolic lipids. Functional and structural studies of macrolactam biosynthetic enzymes have revealed the unique biosynthetic machinery used for selective incorporation of a rare β-amino acid starter unit into the polyketide skeleton. Biochemical and structural studies of cyclization enzymes involved in the biosynthesis of enterocin and phenolic lipids provide mechanistic insights into how these enzymes diversify the carbon skeletons of their products.

Competition-colonization dynamics: An ecology approach to quasispecies dynamics and virulence evolution in RNA viruses.

PubMed

Ojosnegros, Samuel; Beerenwinkel, Niko; Domingo, Esteban

2010-07-01

A single and purified clone of foot-and-mouth disease virus diversified in cell culture into two subpopulations that were genetically distinct. The subpopulation with higher virulence was a minority and was suppressed by the dominant but less virulent one. These two populations follow the competitioncolonization dynamics described in ecology. Virulent viruses can be regarded as colonizers because they killed the cells faster and they spread faster. The attenuated subpopulation resembles competitors because of its higher replication efficiency in coinfected cells. Our results suggest a new model for the evolution of virulence which is based on interactions between components of the quasispecies. Competition between viral mutants takes place at two levels, intracellular competition and competition for new cells. The two strategies are subjected to densitydependent selection.

Diversified cropping systems support greater microbial cycling and retention of carbon and nitrogen

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

King, Alison E.; Hofmockel, Kirsten S.

2017-03-01

Diversifying biologically simple cropping systems often entails altering other management practices, such as tillage regime or nitrogen (N) source. We hypothesized that the interaction of crop rotation, N source, and tillage in diversified cropping systems would promote microbially-mediated soil C and N cycling while attenuating inorganic N pools. We studied a cropping systems trial in its 10th year in Iowa, USA, which tested a 2-yr cropping system of corn (Zea mays L.)/soybean [Glycine max (L.) Merr.] managed with conventional fertilizer N inputs and conservation tillage, a 3-yr cropping system of corn/soybean/small grain + red clover (Trifolium pratense L.), and amore » 4-yr cropping system of corn/soybean/small grain + alfalfa (Medicago sativa L.)/alfalfa. Three year and 4-yr cropping systems were managed with composted manure, reduced N fertilizer inputs, and periodic moldboard ploughing. We assayed soil microbial biomass carbon (MBC) and N (MBN), soil extractable NH4 and NO3, gross proteolytic activity of native soil, and potential activity of six hydrolytic enzymes eight times during the growing season. At the 0-20cm depth, native protease activity in the 4-yr cropping system was greater than in the 2-yr cropping system by a factor of 7.9, whereas dissolved inorganic N pools did not differ between cropping systems (P = 0.292). At the 0-20cm depth, MBC and MBN the 4-yr cropping system exceeded those in the 2-yr cropping system by factors of 1.51 and 1.57. Our findings suggest that diversified crop cropping systems, even when periodically moldboard ploughed, support higher levels of microbial biomass, greater production of bioavailable N from SOM, and a deeper microbially active layer than less diverse cropping systems.« less

The Genome of the “Great Speciator” Provides Insights into Bird Diversification

PubMed Central

Cornetti, Luca; Valente, Luis M.; Dunning, Luke T.; Quan, Xueping; Black, Richard A.; Hébert, Olivier; Savolainen, Vincent

2015-01-01

Among birds, white-eyes (genus Zosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the “great speciator.” The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation. PMID:26338191

Manipulation for the control of back pain and curve progression in patients with skeletally mature idiopathic scoliosis: two cases.

PubMed

Tarola, G A

1994-05-01

This report of two cases illustrates the potential effect of chiropractic manipulative therapy on back pain and curve progression in the at-risk, skeletally mature patient with adolescent idiopathic scoliosis. Two patients suffering from lumbar scoliosis and chronic back pain. Both had scoliosis that had progressed after skeletal maturity. Diversified type chiropractic manipulative therapy was used palliatively for back pain relief in one case, and routinely 1-2 times per month in the other case. The manipulation was applied manually, with the patients in the prone and side-posture positions. Vertebral levels manipulated were identified as fixated/dysfunctional segments based on static and/or motion palpation. They were generally applied to areas above and/or below the curve apex. When applied at the apex, cavitation was more easily achieved when the direction of thrust was into the concave side. This was also tolerated better by the patient. No attempt was made to "straighten the curve" by thrusting into the convex side. Gentle manual intersegmental mobilization, stretching and muscle massage techniques were also applied. The case treated palliatively had curve progression consistent with the literature over an 8-yr period. The case treated routinely did not. The procedure was effective in both cases for subjective relief of back pain. Diversified-type CMT has a favorable effect on acute back pain when used palliatively. The procedure may also have a favorable long term effect of preventing recurrence of back pain and on retarding curve progression when used routinely 1-2 times per month.

Evidence of late Palaeocene-early Eocene equatorial rain forest refugia in southern Western Ghats, India.

PubMed

Prasad, V; Farooqui, A; Tripathi, S K M; Garg, R; Thakur, B

2009-11-01

Equatorial rain forests that maintain a balance between speciation and extinction are hot-spots for studies of biodiversity. Western Ghats in southern India have gained attention due to high tropical biodiversity and endemism in their southern most area. We attempted to track the affinities of the pollen fl ora of the endemic plants of Western Ghat area within the fossil palynoflora of late Palaeocene-early Eocene (approximately 55-50 Ma) sedimentary deposits of western and northeastern Indian region. The study shows striking similarity of extant pollen with twenty eight most common fossil pollen taxa of the early Palaeogene. Widespread occurrences of coal and lignite deposits during early Palaeogene provide evidence of existence of well diversified rain forest community and swampy vegetation in the coastal low lying areas all along the western and northeastern margins of the Indian subcontinent. Prevalence of excessive humid climate during this period has been seen as a result of equatorial positioning of Indian subcontinent, superimposed by a long term global warming phase (PETM and EECO) during the early Palaeogene. The study presents clear evidence that highly diversifi ed equatorial rain forest vegetation once widespread in the Indian subcontinent during early Palaeogene times, are now restricted in a small area as a refugia in the southernmost part of the Western Ghat area. High precipitation and shorter periods of dry months seem to have provided suitable environment to sustain lineages of ancient tropical vegetation in this area of Western Ghats in spite of dramatic climatic changes subsequent to the post India-Asia collision and during the Quaternary and Recent times.

Testing for the Occurrence of Selective Episodes During the Divergence of Otophysan Fishes: Insights from Mitogenomics.

PubMed

D'Anatro, Alejandro; Giorello, Facundo; Feijoo, Matías; Lessa, Enrique P

2017-04-01

How natural selection shapes biodiversity constitutes a topic of renewed interest during the last few decades. The division Otophysi comprises approximately two-thirds of freshwater fish diversity and probably underwent an extensive adaptive radiation derived from a single invasion of the supercontinent Pangaea, giving place to the evolution of the main five Otophysan lineages during a short period of time. Little is known about the factors involved in the processes that lead to lineage diversification among this group of fishes and identifying directional selection acting over protein-coding genes could offer clues about the processes acting on species diversification. The main objective of this study was to explore the otophysan mitochondrial genome evolution, in order to account for the possible signatures of selective events in this lineage, and to explore for the functional connotations of these molecular substitutions. Mainly, three different approaches were used: the "ω-based" BS-REL and MEME methods, implemented in the DATAMONKEY web server, and analysis of selection on amino acid properties, implemented in the software TreeSAAP. We found evidence of selective episodes along several branches of the evolutionary history of othophysan fishes. Analyses carried out using the BS-REL algorithm suggest episodic diversifying selection at basal branches of the otophysan lineage, which was also supported by analyses implemented in MEME and TreeSAAP. These results suggest that throughout the Siluriformes radiation, an important number of adaptive changes occurred in their mitochondrial genome. The metabolic consequences and ecological correlates of these molecular substitutions should be addressed in future studies.

Variable Selection through Correlation Sifting

NASA Astrophysics Data System (ADS)

Huang, Jim C.; Jojic, Nebojsa

Many applications of computational biology require a variable selection procedure to sift through a large number of input variables and select some smaller number that influence a target variable of interest. For example, in virology, only some small number of viral protein fragments influence the nature of the immune response during viral infection. Due to the large number of variables to be considered, a brute-force search for the subset of variables is in general intractable. To approximate this, methods based on ℓ1-regularized linear regression have been proposed and have been found to be particularly successful. It is well understood however that such methods fail to choose the correct subset of variables if these are highly correlated with other "decoy" variables. We present a method for sifting through sets of highly correlated variables which leads to higher accuracy in selecting the correct variables. The main innovation is a filtering step that reduces correlations among variables to be selected, making the ℓ1-regularization effective for datasets on which many methods for variable selection fail. The filtering step changes both the values of the predictor variables and output values by projections onto components obtained through a computationally-inexpensive principal components analysis. In this paper we demonstrate the usefulness of our method on synthetic datasets and on novel applications in virology. These include HIV viral load analysis based on patients' HIV sequences and immune types, as well as the analysis of seasonal variation in influenza death rates based on the regions of the influenza genome that undergo diversifying selection in the previous season.

[Recruiting and Personal Development in Surgical Departments of Large Referral Centers - Current Practice and Options for Improvement from Industry and Service Business].

PubMed

Homayounfar, K; König, S; Rabe, C; Beck-Broichsitter, B; Lützen, U; Ghadimi, M B; Schmidt, C

2017-12-01

Background Cut-throat competition, cost pressure, generation Y, shortage of qualified staff and feminisation influence human resources management in visceral surgery. The assessment of the current situation by chief surgeons (CS) as well as proof of transferability of strategies from industry and service business (ISB) have not yet been investigated. Material and Methods The CS of university hospitals and large referral centres (> 800 beds) were interviewed (n = 100) on the basis of a standardised questionnaire including 43 items. Closed questions were designed with a 5-point Likert scale and their analysis was presented as means (MW) and standard deviations (±). Ten human resources manager (HMR) of ISB were invited to participate in 45-minute telephone interviews. Results Thirty-seven CS participated in the survey, 15 of whom were full professors. Unsolicited applications (100%), job advertisements (78%) and direct approaches to final year students (78%) were the most common ways of recruitment. Only 17% of CS used a standardised form for preparation. Professional expertise (MW 2.2 ± 0.9), social skills (MW 1.9 ± 0.6) and excellent German language skills (MW 1.8 ± 0.8) were named as important qualifications for employment, while references and certificates were regarded as being less important (MW 3.2 ± 0.9). Personal development was regarded as important (MW 1.1 ± 0.2), but a defined period for residency was not guaranteed (MW 3.0 ± 1.5). Transparent selection criteria for career opportunities (MW 2.5 ± 1.1) and different career models (MW 2.7 ± 1.2) were only rarely available. Six HRM participated in the interviews. Active head-hunting (75%), Internet platforms (75%), presentations at conferences (75%), as well as hiring trainees (50%), job advertisements (50%) and social media (50%) were established options to find qualified employees. Professional and management careers were often separate career paths, while social expertise was regarded as being crucial for filling management positions. Conclusion In visceral surgery, unsolicited applications, job advertisements and direct approaches to final year students are the most common ways for recruitment. Diversified professional and management careers are not yet established. Recruiting strategies that are successful in ISB - such as active scouting and use of social media - should be evaluated for visceral surgery, as well as diversified career models. Georg Thieme Verlag KG Stuttgart · New York.

Enhancing Scheduling Performance for a Wafer Fabrication Factory: The Biobjective Slack-Diversifying Nonlinear Fluctuation-Smoothing Rule

PubMed Central

Chen, Toly; Wang, Yu Cheng

2012-01-01

A biobjective slack-diversifying nonlinear fluctuation-smoothing rule (biSDNFS) is proposed in the present work to improve the scheduling performance of a wafer fabrication factory. This rule was derived from a one-factor bi-objective nonlinear fluctuation-smoothing rule (1f-biNFS) by dynamically maximizing the standard deviation of the slack, which has been shown to benefit scheduling performance by several previous studies. The efficacy of the biSDNFS was validated with a simulated case; evidence was found to support its effectiveness. We also suggested several directions in which it can be exploited in the future. PMID:23509446

SEXUAL SPECIES ARE SEPARATED BY LARGER GENETIC GAPS THAN ASEXUAL SPECIES IN ROTIFERS

PubMed Central

Tang, Cuong Q; Obertegger, Ulrike; Fontaneto, Diego; Barraclough, Timothy G

2014-01-01

Why organisms diversify into discrete species instead of showing a continuum of genotypic and phenotypic forms is an important yet rarely studied question in speciation biology. Does species discreteness come from adaptation to fill discrete niches or from interspecific gaps generated by reproductive isolation? We investigate the importance of reproductive isolation by comparing genetic discreteness, in terms of intra- and interspecific variation, between facultatively sexual monogonont rotifers and obligately asexual bdelloid rotifers. We calculated the age (phylogenetic distance) and average pairwise genetic distance (raw distance) within and among evolutionarily significant units of diversity in six bdelloid clades and seven monogonont clades sampled for 4211 individuals in total. We find that monogonont species are more discrete than bdelloid species with respect to divergence between species but exhibit similar levels of intraspecific variation (species cohesiveness). This pattern arises because bdelloids have diversified into discrete genetic clusters at a faster net rate than monogononts. Although sampling biases or differences in ecology that are independent of sexuality might also affect these patterns, the results are consistent with the hypothesis that bdelloids diversified at a faster rate into less discrete species because their diversification does not depend on the evolution of reproductive isolation. PMID:24975991

Pollination Reservoirs in Lowbush Blueberry (Ericales: Ericaceae)

PubMed Central

Drummond, F. A.; Hoshide, A. K.; Dibble, A. C.; Stack, L. B.

2017-01-01

Abstract Pollinator-dependent agriculture heavily relies upon a single pollinator—the honey bee. To diversify pollination strategies, growers are turning to alternatives. Densely planted reservoirs of pollen- and nectar-rich flowers (pollination reservoirs, hereafter “PRs”) may improve pollination services provided by wild bees. Our focal agroecosystem, lowbush blueberry (Vaccinium angustifolium Aiton), exists in a simple landscape uniquely positioned to benefit from PRs. First, we contrast bee visitation rates and use of three types of PR. We consider the effects of PRs on wild bee diversity and the composition of bumble bee pollen loads. We contrast field-level crop pollination services between PRs and controls four years postestablishment. Last, we calculate the time to pay for PR investment. Social bees preferentially used clover plantings; solitary bees preferentially used wildflower plantings. On average, bumble bee pollen loads in treatment fields contained 37% PR pollen. PRs significantly increased visitation rates to the crop in year 4, and exerted a marginally significant positive influence on fruit set. The annualized costs of PRs were covered by the fourth year using the measured increase in pollination services. Our findings provide evidence of the positive impact of PRs on crop pollination services. PMID:28069631

CONSTRUCTING AND DERIVING RECIPROCAL TRIGONOMETRIC RELATIONS: A FUNCTIONAL ANALYTIC APPROACH

PubMed Central

Ninness, Chris; Dixon, Mark; Barnes-Holmes, Dermot; Rehfeldt, Ruth Anne; Rumph, Robin; McCuller, Glen; Holland, James; Smith, Ronald; Ninness, Sharon K; McGinty, Jennifer

2009-01-01

Participants were pretrained and tested on mutually entailed trigonometric relations and combinatorially entailed relations as they pertained to positive and negative forms of sine, cosine, secant, and cosecant. Experiment 1 focused on training and testing transformations of these mathematical functions in terms of amplitude and frequency followed by tests of novel relations. Experiment 2 addressed training in accordance with frames of coordination (same as) and frames of opposition (reciprocal of) followed by more tests of novel relations. All assessments of derived and novel formula-to-graph relations, including reciprocal functions with diversified amplitude and frequency transformations, indicated that all 4 participants demonstrated substantial improvement in their ability to identify increasingly complex trigonometric formula-to-graph relations pertaining to same as and reciprocal of to establish mathematically complex repertoires. PMID:19949509

Constructing and deriving reciprocal trigonometric relations: a functional analytic approach.

PubMed

Ninness, Chris; Dixon, Mark; Barnes-Holmes, Dermot; Rehfeldt, Ruth Anne; Rumph, Robin; McCuller, Glen; Holland, James; Smith, Ronald; Ninness, Sharon K; McGinty, Jennifer

2009-01-01

Participants were pretrained and tested on mutually entailed trigonometric relations and combinatorially entailed relations as they pertained to positive and negative forms of sine, cosine, secant, and cosecant. Experiment 1 focused on training and testing transformations of these mathematical functions in terms of amplitude and frequency followed by tests of novel relations. Experiment 2 addressed training in accordance with frames of coordination (same as) and frames of opposition (reciprocal of) followed by more tests of novel relations. All assessments of derived and novel formula-to-graph relations, including reciprocal functions with diversified amplitude and frequency transformations, indicated that all 4 participants demonstrated substantial improvement in their ability to identify increasingly complex trigonometric formula-to-graph relations pertaining to same as and reciprocal of to establish mathematically complex repertoires.

Shark Attack: high affinity binding proteins derived from shark vNAR domains by stepwise in vitro affinity maturation.

PubMed

Zielonka, Stefan; Weber, Niklas; Becker, Stefan; Doerner, Achim; Christmann, Andreas; Christmann, Christine; Uth, Christina; Fritz, Janine; Schäfer, Elena; Steinmann, Björn; Empting, Martin; Ockelmann, Pia; Lierz, Michael; Kolmar, Harald

2014-12-10

A novel method for stepwise in vitro affinity maturation of antigen-specific shark vNAR domains is described that exclusively relies on semi-synthetic repertoires derived from non-immunized sharks. Target-specific molecules were selected from a CDR3-randomized bamboo shark (Chiloscyllium plagiosum) vNAR library using yeast surface display as platform technology. Various antigen-binding vNAR domains were easily isolated by screening against several therapeutically relevant antigens, including the epithelial cell adhesion molecule (EpCAM), the Ephrin type-A receptor 2 (EphA2), and the human serine protease HTRA1. Affinity maturation was demonstrated for EpCAM and HTRA1 by diversifying CDR1 of target-enriched populations which allowed for the rapid selection of nanomolar binders. EpCAM-specific vNAR molecules were produced as soluble proteins and more extensively characterized via thermal shift assays and biolayer interferometry. Essentially, we demonstrate that high-affinity binders can be generated in vitro without largely compromising the desirable high thermostability of the vNAR scaffold. Copyright © 2014 Elsevier B.V. All rights reserved.

Macroevolution of perfume signalling in orchid bees.

PubMed

Weber, Marjorie G; Mitko, Lukasz; Eltz, Thomas; Ramírez, Santiago R

2016-11-01

Theory predicts that both stabilising selection and diversifying selection jointly contribute to the evolution of sexual signalling traits by (1) maintaining the integrity of communication signals within species and (2) promoting the diversification of traits among lineages. However, for many important signalling traits, little is known about whether these dynamics translate into predictable macroevolutionary signatures. Here, we test for macroevolutionary patterns consistent with sexual signalling theory in the perfume signals of neotropical orchid bees, a group well studied for their chemical sexual communication. Our results revealed both high species-specificity and elevated rates of evolution in perfume signals compared to nonsignalling traits. Perfume complexity was correlated with the number of congeners in a species' range, suggesting that perfume evolution may be tied to the remarkably high number of orchid bee species coexisting together in some neotropical communities. Finally, sister-pair comparisons were consistent with both rapid divergence at speciation and character displacement upon secondary contact. Together, our results provide new insight into the macroevolution of sexual signalling in insects. © 2016 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Ecological genomics of natural plant populations: the Israeli perspective.

PubMed

Nevo, Eviatar

2009-01-01

The genomic era revolutionized evolutionary population biology. The ecological genomics of the wild progenitors of wheat and barley reviewed here was central in the research program of the Institute of Evolution, University of Haifa, since 1975 ( http://evolution.haifa.ac.il ). We explored the following questions: (1) How much of the genomic and phenomic diversity of wild progenitors of cultivars (wild emmer wheat, Triticum dicoccoides, the progenitor of most wheat, plus wild relatives of the Aegilops species; wild barley, Hordeum spontaneum, the progenitor of cultivated barley; wild oat, Avena sterilis, the progenitor of cultivated oats; and wild lettuce species, Lactuca, the progenitor and relatives of cultivated lettuce) are adaptive and processed by natural selection at both coding and noncoding genomic regions? (2) What is the origin and evolution of genomic adaptation and speciation processes and their regulation by mutation, recombination, and transposons under spatiotemporal variables and stressful macrogeographic and microgeographic environments? (3) How much genetic resources are harbored in the wild progenitors for crop improvement? We advanced ecological genetics into ecological genomics and analyzed (regionally across Israel and the entire Near East Fertile Crescent and locally at microsites, focusing on the "Evolution Canyon" model) hundreds of populations and thousands of genotypes for protein (allozyme) and deoxyribonucleic acid (DNA) (coding and noncoding) diversity, partly combined with phenotypic diversity. The environmental stresses analyzed included abiotic (climatic and microclimatic, edaphic) and biotic (pathogens, demographic) stresses. Recently, we introduced genetic maps, cloning, and transformation of candidate genes. Our results indicate abundant genotypic and phenotypic diversity in natural plant populations. The organization and evolution of molecular and organismal diversity in plant populations, at all genomic regions and geographical scales, are nonrandom and are positively correlated with, and partly predictable by, abiotic and biotic environmental heterogeneity and stress. Biodiversity evolution, even in small isolated populations, is primarily driven by natural selection including diversifying, balancing, cyclical, and purifying selection regimes interacting with, but, ultimately, overriding the effects of mutation, migration, and stochasticity. The progenitors of cultivated plants harbor rich genetic resources and are the best hope for crop improvement by both classical and modern biotechnological methods. Future studies should focus on the interplay between structural and functional genome organization focusing on gene regulation.

Embryonic lethality is not sufficient to explain hourglass-like conservation of vertebrate embryos.

PubMed

Uchida, Yui; Uesaka, Masahiro; Yamamoto, Takayoshi; Takeda, Hiroyuki; Irie, Naoki

2018-01-01

Understanding the general trends in developmental changes during animal evolution, which are often associated with morphological diversification, has long been a central issue in evolutionary developmental biology. Recent comparative transcriptomic studies revealed that gene expression profiles of mid-embryonic period tend to be more evolutionarily conserved than those in earlier or later periods. While the hourglass-like divergence of developmental processes has been demonstrated in a variety of animal groups such as vertebrates, arthropods, and nematodes, the exact mechanism leading to this mid-embryonic conservation remains to be clarified. One possibility is that the mid-embryonic period (pharyngula period in vertebrates) is highly prone to embryonic lethality, and the resulting negative selections lead to evolutionary conservation of this phase. Here, we tested this "mid-embryonic lethality hypothesis" by measuring the rate of lethal phenotypes of three different species of vertebrate embryos subjected to two kinds of perturbations: transient perturbations and genetic mutations. By subjecting zebrafish ( Danio rerio ), African clawed frog ( Xenopus laevis ), and chicken ( Gallus gallus ) embryos to transient perturbations, namely heat shock and inhibitor treatments during three developmental periods [early (represented by blastula and gastrula), pharyngula, and late], we found that the early stages showed the highest rate of lethal phenotypes in all three species. This result was corroborated by perturbation with genetic mutations. By tracking the survival rate of wild-type embryos and embryos with genetic mutations induced by UV irradiation in zebrafish and African clawed frogs, we found that the highest decrease in survival rate was at the early stages particularly around gastrulation in both these species. In opposition to the "mid-embryonic lethality hypothesis," our results consistently showed that the stage with the highest lethality was not around the conserved pharyngula period, but rather around the early period in all the vertebrate species tested. These results suggest that negative selection by embryonic lethality could not explain hourglass-like conservation of animal embryos. This highlights the potential contribution of alternative mechanisms such as the diversifying effect of positive selections against earlier and later stages, and developmental constraints which lead to conservation of mid-embryonic stages.

Usefulness of a Darwinian System in a Biotechnological Application: Evolution of Optical Window Fluorescent Protein Variants under Selective Pressure

PubMed Central

Ng, David; Pauli, Jutta; Resch-Genger, Ute; Kühn, Enrico; Heuer, Steffen; Beisker, Wolfgang; Köster, Reinhard W.; Zitzelsberger, Horst; Caldwell, Randolph B

2014-01-01

With rare exceptions, natural evolution is an extremely slow process. One particularly striking exception in the case of protein evolution is in the natural production of antibodies. Developing B cells activate and diversify their immunoglobulin (Ig) genes by recombination, gene conversion (GC) and somatic hypermutation (SHM). Iterative cycles of hypermutation and selection continue until antibodies of high antigen binding specificity emerge (affinity maturation). The avian B cell line DT40, a cell line which is highly amenable to genetic manipulation and exhibits a high rate of targeted integration, utilizes both GC and SHM. Targeting the DT40's diversification machinery onto transgenes of interest inserted into the Ig loci and coupling selective pressure based on the desired outcome mimics evolution. Here we further demonstrate the usefulness of this platform technology by selectively pressuring a large shift in the spectral properties of the fluorescent protein eqFP615 into the highly stable and advanced optical imaging expediting fluorescent protein Amrose. The method is advantageous as it is time and cost effective and no prior knowledge of the outcome protein's structure is necessary. Amrose was evolved to have high excitation at 633 nm and excitation/emission into the far-red, which is optimal for whole-body and deep tissue imaging as we demonstrate in the zebrafish and mouse model. PMID:25192257

Usefulness of a Darwinian system in a biotechnological application: evolution of optical window fluorescent protein variants under selective pressure.

PubMed

Schoetz, Ulrike; Deliolanis, Nikolaos C; Ng, David; Pauli, Jutta; Resch-Genger, Ute; Kühn, Enrico; Heuer, Steffen; Beisker, Wolfgang; Köster, Reinhard W; Zitzelsberger, Horst; Caldwell, Randolph B

2014-01-01

With rare exceptions, natural evolution is an extremely slow process. One particularly striking exception in the case of protein evolution is in the natural production of antibodies. Developing B cells activate and diversify their immunoglobulin (Ig) genes by recombination, gene conversion (GC) and somatic hypermutation (SHM). Iterative cycles of hypermutation and selection continue until antibodies of high antigen binding specificity emerge (affinity maturation). The avian B cell line DT40, a cell line which is highly amenable to genetic manipulation and exhibits a high rate of targeted integration, utilizes both GC and SHM. Targeting the DT40's diversification machinery onto transgenes of interest inserted into the Ig loci and coupling selective pressure based on the desired outcome mimics evolution. Here we further demonstrate the usefulness of this platform technology by selectively pressuring a large shift in the spectral properties of the fluorescent protein eqFP615 into the highly stable and advanced optical imaging expediting fluorescent protein Amrose. The method is advantageous as it is time and cost effective and no prior knowledge of the outcome protein's structure is necessary. Amrose was evolved to have high excitation at 633 nm and excitation/emission into the far-red, which is optimal for whole-body and deep tissue imaging as we demonstrate in the zebrafish and mouse model.

Diversity, cellular origin and autoreactivity of antibody-secreting cell expansions in acute Systemic Lupus Erythematosus

PubMed Central

Tipton, Christopher M; Fucile, Christopher F; Darce, Jaime; Chida, Asiya; Ichikawa, Travis; Gregoretti, Ivan; Schieferl, Sandra; Hom, Jennifer; Jenks, Scott; Feldman, Ron J; Mehr, Ramit; Wei, Chungwen; Lee, F. Eun-Hyung; Cheung, Wan Cheung; Rosenberg, Alexander F; Sanz, Iñaki

2015-01-01

Acute SLE courses with antibody-secreting cells (ASC) surges whose origin, diversity, and contribution to serum autoantibodies remain unknown. Deep sequencing, autoantibody proteome and single-cell analysis demonstrated highly diversified ASC punctuated by VH4-34 clones that produce dominant serum autoantibodies. A fraction of ASC clones contained unmutated autoantibodies, a finding consistent with differentiation outside the germinal centers. A substantial ASC segment derived from a distinct subset of newly activated naïve cells of significant clonality that persist in the circulation for several months. Thus, selection of SLE autoreactivities occurred during polyclonal activation with prolonged recruitment of recently activated naïve B cells. These findings shed light into SLE pathogenesis, help explain the benefit of anti-B cell agents and facilitate the design of future therapies. PMID:26006014

Development of biosensors and their application in metabolic engineering.

PubMed

Zhang, Jie; Jensen, Michael K; Keasling, Jay D

2015-10-01

In a sustainable bioeconomy, many commodities and high value chemicals, including pharmaceuticals, will be manufactured using microbial cell factories from renewable feedstocks. These cell factories can be efficiently generated by constructing libraries of diversified genomes followed by screening for the desired phenotypes. However, methods available for microbial genome diversification far exceed our ability to screen and select for those variants with optimal performance. Genetically encoded biosensors have shown the potential to address this gap, given their ability to respond to small molecule binding and ease of implementation with high-throughput analysis. Here we describe recent progress in biosensor development and their applications in a metabolic engineering context. We also highlight examples of how biosensors can be integrated with synthetic circuits to exert feedback regulation on the metabolism for improved performance of cell factories. Copyright © 2015 Elsevier Ltd. All rights reserved.

The protein cofactor allows the sequence of an RNase P ribozyme to diversify by maintaining the catalytically active structure of the enzyme.

PubMed Central

Kim, J J; Kilani, A F; Zhan, X; Altman, S; Liu, F

1997-01-01

To study the effect proteins have on the catalysis and evolution of RNA enzymes, we simulated evolution of RNase P catalytic M1 RNA in vitro, in the presence and absence of its C5 protein cofactor. In the presence of C5, functional M1 sequence variants (not catalytically active in the absence of C5) were selected in addition to those identical to M1. C5 maintains the catalytically active structure of the variants and allows for an enhanced spectrum of M1 molecules to function in the context of a ribonucleoprotein (RNP) complex. The generation of an RNP enzyme, requiring both RNA and protein components, from a catalytically active RNA molecule has implications for how modern RNP complexes evolved from ancestral RNAs. PMID:9174096

The emperor's new wardrobe: Rebalancing diversity of animal models in neuroscience research.

PubMed

Yartsev, Michael M

2017-10-27

The neuroscience field is steaming ahead, fueled by a revolution in cutting-edge technologies. Concurrently, another revolution has been underway-the diversity of species utilized for neuroscience research is sharply declining, as the field converges on a few selected model organisms. Here, from the perspective of a young scientist, I naively ask: Is the great diversity of questions in neuroscience best studied in only a handful of animal models? I review some of the limitations the field is facing following this convergence and how these can be rectified by increasing the diversity of appropriate model species. I propose that at this exciting time of revolution in genetics and device technologies, neuroscience might be ready to diversify again, if provided the appropriate support. Copyright © 2017, American Association for the Advancement of Science.

Trafficking arms: oomycete effectors enter host plant cells.

PubMed

Birch, Paul R J; Rehmany, Anne P; Pritchard, Leighton; Kamoun, Sophien; Beynon, Jim L

2006-01-01

Oomycetes cause devastating plant diseases of global importance, yet little is known about the molecular basis of their pathogenicity. Recently, the first oomycete effector genes with cultivar-specific avirulence (AVR) functions were identified. Evidence of diversifying selection in these genes and their cognate plant host resistance genes suggests a molecular "arms race" as plants and oomycetes attempt to achieve and evade detection, respectively. AVR proteins from Hyaloperonospora parasitica and Phytophthora infestans are detected in the plant host cytoplasm, consistent with the hypothesis that oomycetes, as is the case with bacteria and fungi, actively deliver effectors inside host cells. The RXLR amino acid motif, which is present in these AVR proteins and other secreted oomycete proteins, is similar to a host-cell-targeting signal in virulence proteins of malaria parasites (Plasmodium species), suggesting a conserved role in pathogenicity.

Atlantic forests to the all Americas: Biogeographical history and divergence times of Neotropical Ficus (Moraceae).

PubMed

Machado, Anderson Ferreira Pinto; Rønsted, Nina; Bruun-Lund, Sam; Pereira, Rodrigo Augusto Santinelo; Paganucci de Queiroz, Luciano

2018-05-01

Ficus (Moraceae) is well diversified in the Neotropics with two lineages inhabiting the wet forests of this region. The hemiepiphytes of section Americanae are the most diversified with c. 120 species, whereas section Pharmacosycea includes about 20 species mostly with a terrestrial habit. To reconstruct the biogeographical history and diversification of Ficus in the Americas, we produced a dated Bayesian phylogenetic hypothesis of Neotropical Ficus including two thirds of the species sequenced for five nuclear regions (At103, ETS, G3pdh, ITS/5.8S and Tpi). Ancestral range was estimated using all models available in Biogeobears and Binary State Speciation and Extinction analysis was used to evaluate the role of the initial habit and propagule size in diversification. The phylogenetic analyses resolved both Neotropical sections as monophyletic but the internal relationships between species in section Americanae remain unclear. Ficus started their diversification in the Neotropics between the Oligocene and Miocene. The genus experienced two bursts of diversification: in the middle Miocene and the Pliocene. Colonization events from the Amazon to adjacent areas coincide with the end of the Pebas system (10 Mya) and the connection of landmasses. Divergence of endemic species in the Atlantic forest is inferred to have happened after its isolation and the opening and consolidation of the Cerrado. Our results suggest a complex diversification in the Atlantic forest differing between postulated refuges and more instable areas in the South distribution of the forest. Finally the selection for initial hemiepiphytic habit and small to medium propagule size influenced the diversification and current distribution of the species at Neotropical forests marked by the historical instability and long-distance dispersal. Copyright © 2018 Elsevier Inc. All rights reserved.

Correlation between nuptial colors and visual sensitivities tuned by opsins leads to species richness in sympatric Lake Victoria cichlid fishes.

PubMed

Miyagi, Ryutaro; Terai, Yohey; Aibara, Mitsuto; Sugawara, Tohru; Imai, Hiroo; Tachida, Hidenori; Mzighani, Semvua Isa; Okitsu, Takashi; Wada, Akimori; Okada, Norihiro

2012-11-01

Reproductive isolation that prevents interspecific hybridization between closely related coexisting species maintains sympatric species diversity. One of the reproductive isolations is mate choice based on color signals (breeding color perceived by color vision). This is well known in several animal taxa, yet little is known about its genetic and molecular mechanism. Lake Victoria cichlid fishes are thought to be an example of sympatric species diversity. In the species inhabiting different light environments in rocky shore, speciation by sensory drive through color signals has been proposed by analyses of the long wavelength-sensitive (LWS) opsin gene and the male nuptial coloration. However, the genetic and molecular mechanism of how diversity of sympatric species occurring in the same habitat is maintained remains unknown. To address this issue, we determined nucleotide sequences of eight opsins of six sympatric species collected from a sandy-muddy shore--an ideal model system for studying sympatric species. Among eight opsins, the LWS and RH1 alleles were diversified and one particular allele is dominant or fixed in each species, and we propose that this is due to natural selection. The functions of their LWS alleles were also diversified as shown by absorption measurements of reconstituted visual pigments. To analyze the relationship between nuptial coloration and the absorption of LWS pigments, we systematically evaluated and defined nuptial coloration. We showed that the coloration was species specific with respect to hue and significantly differentiated by the index values of hue (dominant wavelength: λ(d)). The λ(d) value of the male nuptial coloration correlated with the absorption of LWS pigments from all the species, suggesting that reproductive isolation through mate choice using color signals may prevent sympatric interspecific hybridization, thereby maintaining the species diversity in sympatric species in Lake Victoria.

Diverse mechanisms shape the evolution of virulence factors in the potato late blight pathogen Phytophthora infestans sampled from China

PubMed Central

Wu, E-Jiao; Yang, Li-Na; Zhu, Wen; Chen, Xiao-Mei; Shang, Li-Ping; Zhan, Jiasui

2016-01-01

Evolution of virulence in plant pathogens is still poorly understood but the knowledge is important for the effective use of plant resistance and sustainable disease management. Spatial population dynamics of virulence, race and SSR markers in 140 genotypes sampled from seven geographic locations in China were compared to infer the mechanisms driving the evolution of virulence in Phytophthora infestans (P. infestans). All virulence types and a full spectrum of race complexity, ranging from the race able to infect the universally susceptible cultivar only to all differentials, were detected. Eight and two virulence factors were under diversifying and constraining selection respectively while no natural selection was detected in one of the virulence types. Further analyses revealed excesses in simple and complex races but deficiency in intermediate race and negative associations of annual mean temperature at the site from which pathogen isolates were collected with frequency of virulence to differentials and race complexity in the pathogen populations. These results suggest that host selection may interact with other factors such as climatic conditions in determining the evolutionary trajectory of virulence and race structure in P. infestans and global warming may slow down the emergence of new virulence in the pathogen. PMID:27193142

Use of Mature miRNA Strand Selection in miRNAs Families in Cervical Cancer Development

PubMed Central

Granados-López, Angelica Judith; Ruiz-Carrillo, José Luis; Servín-González, Luis Steven; Martínez-Rodríguez, José Luis; Reyes-Estrada, Claudia Araceli; Gutiérrez-Hernández, Rosalinda; López, Jesús Adrián

2017-01-01

Aberrant miRNA expression is well recognized as a cancer hallmark, nevertheless miRNA function and expression does not always correlate in patients tissues and cell lines studies. In addition to this issue, miRNA strand usage conduces to increased cell signaling pathways modulation diversifying cellular processes regulation. In cervical cancer, 20 miRNA families are involved in carcinogenesis induction and development to this moment. These families have 5p and 3p strands with different nucleotide (nt) chain sizes. In general, mature 5p strands are larger: two miRNAs of 24 nt, 24 miRNAs of 23 nt, 35 miRNAs of 22 nt and three miRNAs of 21 nt. On the other hand, the 3p strands lengths observed are: seven miRNAs of 23 nt, 50 miRNAs of 22 nt, six miRNAs of 21 nt and four miRNAs of 20 nt. Based on the analysis of the 20 miRNA families associated with cervical cancer, 67 3p strands and 65 5p strands are selected suggesting selectivity and specificity mechanisms regulating cell processes like proliferation, apoptosis, migration, invasion, metabolism and Warburg effect. The insight reviewed here could be used in the miRNA based therapy, diagnosis and prognosis approaches. PMID:28216603

Use of Mature miRNA Strand Selection in miRNAs Families in Cervical Cancer Development.

PubMed

Granados-López, Angelica Judith; Ruiz-Carrillo, José Luis; Servín-González, Luis Steven; Martínez-Rodríguez, José Luis; Reyes-Estrada, Claudia Araceli; Gutiérrez-Hernández, Rosalinda; López, Jesús Adrián

2017-02-14

Aberrant miRNA expression is well recognized as a cancer hallmark, nevertheless miRNA function and expression does not always correlate in patients tissues and cell lines studies. In addition to this issue, miRNA strand usage conduces to increased cell signaling pathways modulation diversifying cellular processes regulation. In cervical cancer, 20 miRNA families are involved in carcinogenesis induction and development to this moment. These families have 5p and 3p strands with different nucleotide (nt) chain sizes. In general, mature 5p strands are larger: two miRNAs of 24 nt, 24 miRNAs of 23 nt, 35 miRNAs of 22 nt and three miRNAs of 21 nt. On the other hand, the 3p strands lengths observed are: seven miRNAs of 23 nt, 50 miRNAs of 22 nt, six miRNAs of 21 nt and four miRNAs of 20 nt. Based on the analysis of the 20 miRNA families associated with cervical cancer, 67 3p strands and 65 5p strands are selected suggesting selectivity and specificity mechanisms regulating cell processes like proliferation, apoptosis, migration, invasion, metabolism and Warburg effect. The insight reviewed here could be used in the miRNA based therapy, diagnosis and prognosis approaches.

Genetic diversity of the merozoite surface protein-3 gene in Plasmodium falciparum populations in Thailand.

PubMed

Pattaradilokrat, Sittiporn; Sawaswong, Vorthon; Simpalipan, Phumin; Kaewthamasorn, Morakot; Siripoon, Napaporn; Harnyuttanakorn, Pongchai

2016-10-21

An effective malaria vaccine is an urgently needed tool to fight against human malaria, the most deadly parasitic disease of humans. One promising candidate is the merozoite surface protein-3 (MSP-3) of Plasmodium falciparum. This antigenic protein, encoded by the merozoite surface protein (msp-3) gene, is polymorphic and classified according to size into the two allelic types of K1 and 3D7. A recent study revealed that both the K1 and 3D7 alleles co-circulated within P. falciparum populations in Thailand, but the extent of the sequence diversity and variation within each allelic type remains largely unknown. The msp-3 gene was sequenced from 59 P. falciparum samples collected from five endemic areas (Mae Hong Son, Kanchanaburi, Ranong, Trat and Ubon Ratchathani) in Thailand and analysed for nucleotide sequence diversity, haplotype diversity and deduced amino acid sequence diversity. The gene was also subject to population genetic analysis (F st ) and neutrality tests (Tajima's D, Fu and Li D* and Fu and Li' F* tests) to determine any signature of selection. The sequence analyses revealed eight unique DNA haplotypes and seven amino acid sequence variants, with a haplotype and nucleotide diversity of 0.828 and 0.049, respectively. Neutrality tests indicated that the polymorphism detected in the alanine heptad repeat region of MSP-3 was maintained by positive diversifying selection, suggesting its role as a potential target of protective immune responses and supporting its role as a vaccine candidate. Comparison of MSP-3 variants among parasite populations in Thailand, India and Nigeria also inferred a close genetic relationship between P. falciparum populations in Asia. This study revealed the extent of the msp-3 gene diversity in P. falciparum in Thailand, providing the fundamental basis for the better design of future blood stage malaria vaccines against P. falciparum.

Evolutionary History of Lagomorphs in Response to Global Environmental Change

PubMed Central

Ge, Deyan; Wen, Zhixin; Xia, Lin; Zhang, Zhaoqun; Erbajeva, Margarita; Huang, Chengming; Yang, Qisen

2013-01-01

Although species within Lagomorpha are derived from a common ancestor, the distribution range and body size of its two extant groups, ochotonids and leporids, are quite differentiated. It is unclear what has driven their disparate evolutionary history. In this study, we compile and update all fossil records of Lagomorpha for the first time, to trace the evolutionary processes and infer their evolutionary history using mitochondrial genes, body length and distribution of extant species. We also compare the forage selection of extant species, which offers an insight into their future prospects. The earliest lagomorphs originated in Asia and later diversified in different continents. Within ochotonids, more than 20 genera occupied the period from the early Miocene to middle Miocene, whereas most of them became extinct during the transition from the Miocene to Pliocene. The peak diversity of the leporids occurred during the Miocene to Pliocene transition, while their diversity dramatically decreased in the late Quaternary. Mantel tests identified a positive correlation between body length and phylogenetic distance of lagomorphs. The body length of extant ochotonids shows a normal distribution, while the body length of extant leporids displays a non-normal pattern. We also find that the forage selection of extant pikas features a strong preference for C3 plants, while for the diet of leporids, more than 16% of plant species are identified as C4 (31% species are from Poaceae). The ability of several leporid species to consume C4 plants is likely to result in their size increase and range expansion, most notably in Lepus. Expansion of C4 plants in the late Miocene, the so-called ‘nature’s green revolution’, induced by global environmental change, is suggested to be one of the major ‘ecological opportunities’, which probably drove large-scale extinction and range contraction of ochotonids, but inversely promoted diversification and range expansion of leporids. PMID:23573205

The impacts of different expansion modes on performance of small solar energy firms: perspectives of absorptive capacity.

PubMed

Chen, Hsing Hung; Shen, Tao; Xu, Xin-Long; Ma, Chao

2013-01-01

The characteristics of firm's expansion by differentiated products and diversified products are quite different. However, the study employing absorptive capacity to examine the impacts of different modes of expansion on performance of small solar energy firms has never been discussed before. Then, a conceptual model to analyze the tension between strategies and corporate performance is proposed to filling the vacancy. After practical investigation, the results show that stronger organizational institutions help small solar energy firms expanded by differentiated products increase consistency between strategies and corporate performance; oppositely, stronger working attitudes with weak management controls help small solar energy firms expanded by diversified products reduce variance between strategies and corporate performance.

Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3

PubMed Central

Alcaide, Miguel; Liu, Mark

2013-01-01

Genes of the Major Histocompatibility Complex (MHC) have become an important marker for the investigation of adaptive genetic variation in vertebrates because of their critical role in pathogen resistance. However, despite significant advances in the last few years the characterization of MHC variation in non-model species still remains a challenging task due to the redundancy and high variation of this gene complex. Here we report the utility of a single pair of primers for the cross-amplification of the third exon of MHC class I genes, which encodes the more polymorphic half of the peptide-binding region (PBR), in oscine passerines (songbirds; Aves: Passeriformes), a group especially challenging for MHC characterization due to the presence of large and complex MHC multigene families. In our survey, although the primers failed to amplify exon 3 from two suboscine passerine birds, they amplified exon 3 of multiple MHC class I genes in all 16 species of oscine songbirds tested, yielding a total of 120 sequences. The 16 songbird species belong to 14 different families, primarily within the Passerida, but also in the Corvida. Using a conservative approach based on the analysis of cloned amplicons (n = 16) from each species, we found between 3 and 10 MHC sequences per individual. Each allele repertoire was highly divergent, with the overall number of polymorphic sites per species ranging from 33 to 108 (out of 264 sites) and the average number of nucleotide differences between alleles ranging from 14.67 to 43.67. Our survey in songbirds allowed us to compare macroevolutionary dynamics of exon 3 between songbirds and non-passerine birds. We found compelling evidence of positive selection acting specifically upon peptide-binding codons across birds, and we estimate the strength of diversifying selection in songbirds to be about twice that in non-passerines. Analysis using comparative methods suggest weaker evidence for a higher GC content in the 3rd codon position of exon 3 in non-passerine birds, a pattern that contrasts with among-clade GC patterns found in other avian studies and may suggests different mutational mechanisms. Our primers represent a useful tool for the characterization of functional and evolutionarily relevant MHC variation across the hyperdiverse songbirds. PMID:23781408

Survival relative to new and ancestral host plants, phytoplasma infection, and genetic constitution in host races of a polyphagous insect disease vector

PubMed Central

Maixner, Michael; Albert, Andreas; Johannesen, Jes

2014-01-01

Dissemination of vectorborne diseases depends strongly on the vector's host range and the pathogen's reservoir range. Because vectors interact with pathogens, the direction and strength of a vector's host shift is vital for understanding epidemiology and is embedded in the framework of ecological specialization. This study investigates survival in host-race evolution of a polyphagous insect disease vector, Hyalesthes obsoletus, whether survival is related to the direction of the host shift (from field bindweed to stinging nettle), the interaction with plant-specific strains of obligate vectored pathogens/symbionts (stolbur phytoplasma), and whether survival is related to genetic differentiation between the host races. We used a twice repeated, identical nested experimental design to study survival of the vector on alternative hosts and relative to infection status. Survival was tested with Kaplan–Meier analyses, while genetic differentiation between vector populations was quantified with microsatellite allele frequencies. We found significant direct effects of host plant (reduced survival on wrong hosts) and sex (males survive longer than females) in both host races and relative effects of host (nettle animals more affected than bindweed animals) and sex (males more affected than females). Survival of bindweed animals was significantly higher on symptomatic than nonsymptomatic field bindweed, but in the second experiment only. Infection potentially had a positive effect on survival in nettle animals but due to low infection rates the results remain suggestive. Genetic differentiation was not related to survival. Greater negative plant-transfer effect but no negative effect of stolbur in the derived host race suggests preadaptation to the new pathogen/symbiont strain before strong diversifying selection during the specialization process. Physiological maladaptation or failure to accept the ancestral plant will have similar consequences, namely positive assortative mating within host races and a reduction in the likelihood of oviposition on the alternative plant and thus the acquisition of alternative stolbur strains. PMID:25247065

Survival relative to new and ancestral host plants, phytoplasma infection, and genetic constitution in host races of a polyphagous insect disease vector.

PubMed

Maixner, Michael; Albert, Andreas; Johannesen, Jes

2014-08-01

Dissemination of vectorborne diseases depends strongly on the vector's host range and the pathogen's reservoir range. Because vectors interact with pathogens, the direction and strength of a vector's host shift is vital for understanding epidemiology and is embedded in the framework of ecological specialization. This study investigates survival in host-race evolution of a polyphagous insect disease vector, Hyalesthes obsoletus, whether survival is related to the direction of the host shift (from field bindweed to stinging nettle), the interaction with plant-specific strains of obligate vectored pathogens/symbionts (stolbur phytoplasma), and whether survival is related to genetic differentiation between the host races. We used a twice repeated, identical nested experimental design to study survival of the vector on alternative hosts and relative to infection status. Survival was tested with Kaplan-Meier analyses, while genetic differentiation between vector populations was quantified with microsatellite allele frequencies. We found significant direct effects of host plant (reduced survival on wrong hosts) and sex (males survive longer than females) in both host races and relative effects of host (nettle animals more affected than bindweed animals) and sex (males more affected than females). Survival of bindweed animals was significantly higher on symptomatic than nonsymptomatic field bindweed, but in the second experiment only. Infection potentially had a positive effect on survival in nettle animals but due to low infection rates the results remain suggestive. Genetic differentiation was not related to survival. Greater negative plant-transfer effect but no negative effect of stolbur in the derived host race suggests preadaptation to the new pathogen/symbiont strain before strong diversifying selection during the specialization process. Physiological maladaptation or failure to accept the ancestral plant will have similar consequences, namely positive assortative mating within host races and a reduction in the likelihood of oviposition on the alternative plant and thus the acquisition of alternative stolbur strains.

Diversified Control Paths: A Significant Way Disease Genes Perturb the Human Regulatory Network

PubMed Central

Wang, Bingbo; Gao, Lin; Zhang, Qingfang; Li, Aimin; Deng, Yue; Guo, Xingli

2015-01-01

Background The complexity of biological systems motivates us to use the underlying networks to provide deep understanding of disease etiology and the human diseases are viewed as perturbations of dynamic properties of networks. Control theory that deals with dynamic systems has been successfully used to capture systems-level knowledge in large amount of quantitative biological interactions. But from the perspective of system control, the ways by which multiple genetic factors jointly perturb a disease phenotype still remain. Results In this work, we combine tools from control theory and network science to address the diversified control paths in complex networks. Then the ways by which the disease genes perturb biological systems are identified and quantified by the control paths in a human regulatory network. Furthermore, as an application, prioritization of candidate genes is presented by use of control path analysis and gene ontology annotation for definition of similarities. We use leave-one-out cross-validation to evaluate the ability of finding the gene-disease relationship. Results have shown compatible performance with previous sophisticated works, especially in directed systems. Conclusions Our results inspire a deeper understanding of molecular mechanisms that drive pathological processes. Diversified control paths offer a basis for integrated intervention techniques which will ultimately lead to the development of novel therapeutic strategies. PMID:26284649

Archaea: The First Domain of Diversified Life

PubMed Central

Caetano-Anollés, Gustavo; Nasir, Arshan; Zhou, Kaiyue; Caetano-Anollés, Derek; Mittenthal, Jay E.; Sun, Feng-Jie; Kim, Kyung Mo

2014-01-01

The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea. PMID:24987307

Diversification of both KIR and NKG2 natural killer cell receptor genes in macaques - implications for highly complex MHC-dependent regulation of natural killer cells.

PubMed

Walter, Lutz; Petersen, Beatrix

2017-02-01

The killer immunoglobulin-like receptors (KIR) as well as their MHC class I ligands display enormous genetic diversity and polymorphism in macaque species. Signals resulting from interaction between KIR or CD94/NKG2 receptors and their cognate MHC class I proteins essentially regulate the activity of natural killer (NK) cells. Macaque and human KIR share many features, such as clonal expression patterns, gene copy number variations, specificity for particular MHC class I allotypes, or epistasis between KIR and MHC class I genes that influence susceptibility and resistance to immunodeficiency virus infection. In this review article we also annotated publicly available rhesus macaque BAC clone sequences and provide the first description of the CD94-NKG2 genomic region. Besides the presence of genes that are orthologous to human NKG2A and NKG2F, this region contains three NKG2C paralogues. Hence, the genome of rhesus macaques contains moderately expanded and diversified NKG2 genes in addition to highly diversified KIR genes. The presence of two diversified NK cell receptor families in one species has not been described before and is expected to require a complex MHC-dependent regulation of NK cells. © 2016 John Wiley & Sons Ltd.

FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants1

PubMed Central

Tohge, Takayuki; Klie, Sebastian; Fernie, Alisdair R.

2016-01-01

Gene duplications generate new genes that can acquire similar but often diversified functions. Recent studies of gene coexpression networks have indicated that, not only genes, but also pathways can be multiplied and diversified to perform related functions in different parts of an organism. Identification of such diversified pathways, or modules, is needed to expand our knowledge of biological processes in plants and to understand how biological functions evolve. However, systematic explorations of modules remain scarce, and no user-friendly platform to identify them exists. We have established a statistical framework to identify modules and show that approximately one-third of the genes of a plant’s genome participate in hundreds of multiplied modules. Using this framework as a basis, we implemented a platform that can explore and visualize multiplied modules in coexpression networks of eight plant species. To validate the usefulness of the platform, we identified and functionally characterized pollen- and root-specific cell wall modules that multiplied to confer tip growth in pollen tubes and root hairs, respectively. Furthermore, we identified multiplied modules involved in secondary metabolite synthesis and corroborated them by metabolite profiling of tobacco (Nicotiana tabacum) tissues. The interactive platform, referred to as FamNet, is available at http://www.gene2function.de/famnet.html. PMID:26754669

Diversifying crop rotations with pulses enhances system productivity

PubMed Central

Gan, Yantai; Hamel, Chantal; O’Donovan, John T.; Cutforth, Herb; Zentner, Robert P.; Campbell, Con A.; Niu, Yining; Poppy, Lee

2015-01-01

Agriculture in rainfed dry areas is often challenged by inadequate water and nutrient supplies. Summerfallowing has been used to conserve rainwater and promote the release of nitrogen via the N mineralization of soil organic matter. However, summerfallowing leaves land without any crops planted for one entire growing season, creating lost production opportunity. Additionally, summerfallowing has serious environmental consequences. It is unknown whether alternative systems can be developed to retain the beneficial features of summerfallowing with little or no environmental impact. Here, we show that diversifying cropping systems with pulse crops can enhance soil water conservation, improve soil N availability, and increase system productivity. A 3-yr cropping sequence study, repeated for five cycles in Saskatchewan from 2005 to 2011, shows that both pulse- and summerfallow-based systems enhances soil N availability, but the pulse system employs biological fixation of atmospheric N2, whereas the summerfallow-system relies on ‘mining’ soil N with depleting soil organic matter. In a 3-yr cropping cycle, the pulse system increased total grain production by 35.5%, improved protein yield by 50.9%, and enhanced fertilizer-N use efficiency by 33.0% over the summerfallow system. Diversifying cropping systems with pulses can serve as an effective alternative to summerfallowing in rainfed dry areas. PMID:26424172

Sexual species are separated by larger genetic gaps than asexual species in rotifers.

PubMed

Tang, Cuong Q; Obertegger, Ulrike; Fontaneto, Diego; Barraclough, Timothy G

2014-10-01

Why organisms diversify into discrete species instead of showing a continuum of genotypic and phenotypic forms is an important yet rarely studied question in speciation biology. Does species discreteness come from adaptation to fill discrete niches or from interspecific gaps generated by reproductive isolation? We investigate the importance of reproductive isolation by comparing genetic discreteness, in terms of intra- and interspecific variation, between facultatively sexual monogonont rotifers and obligately asexual bdelloid rotifers. We calculated the age (phylogenetic distance) and average pairwise genetic distance (raw distance) within and among evolutionarily significant units of diversity in six bdelloid clades and seven monogonont clades sampled for 4211 individuals in total. We find that monogonont species are more discrete than bdelloid species with respect to divergence between species but exhibit similar levels of intraspecific variation (species cohesiveness). This pattern arises because bdelloids have diversified into discrete genetic clusters at a faster net rate than monogononts. Although sampling biases or differences in ecology that are independent of sexuality might also affect these patterns, the results are consistent with the hypothesis that bdelloids diversified at a faster rate into less discrete species because their diversification does not depend on the evolution of reproductive isolation. © 2014 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Working conditions and leisure-time physical activity among waged workers in South Korea: A cross-sectional study.

PubMed

Kim, Chungah; Cho, Youngtae

2015-01-01

Although waged workers' working conditions have notably diversified in South Korea, there is little research addressing this issue. This study explores the relationship between working conditions and engagement in leisure-time physical activities (LTPA) among waged workers in South Korea. Data from 19- to 64-year-old waged workers (men=2,562, women=1,627) from the 11th wave of the Korean Income and Labor Panel Study were included in this study. Multiple logistic regression analyses were conducted to assess the association between LTPA and working conditions by gender. More than 75% of employed persons did not participate in any type of LTPA. For male workers, those in manual, precarious, overtime, and non-shift positions were less likely to engage in LTPA, while for female workers, only manual and overtime work positions were significant factors influencing a low level of LTPA. Some negative work-related factors were associated with low LTPA, especially for male workers. Further studies should be conducted to clarify the pathways and barriers precluding engagement in LTPA due to work-related factors.

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing.

PubMed

Yi, Guoqiang; Qu, Lujiang; Liu, Jianfeng; Yan, Yiyuan; Xu, Guiyun; Yang, Ning

2014-11-07

Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we performed a genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing. A total of 8,840 CNV regions (CNVRs) covering 98.2 Mb and representing 9.4% of the chicken genome were identified, ranging in size from 1.1 to 268.8 kb with an average of 11.1 kb. Sequencing-based predictions were confirmed at a high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson's correlation coefficients between sequencing and aCGH results ranged from 0.435 to 0.755, and qPCR experiments revealed a positive validation rate of 91.71% and a false negative rate of 22.43%. In total, 2,214 (25.0%) predicted CNVRs span 2,216 (36.4%) RefSeq genes associated with specific biological functions. Besides two previously reported copy number variable genes EDN3 and PRLR, we also found some promising genes with potential in phenotypic variation. Two genes, FZD6 and LIMS1, related to disease susceptibility/resistance are covered by CNVRs. The highly duplicated SOCS2 may lead to higher bone mineral density. Entire or partial duplication of some genes like POPDC3 may have great economic importance in poultry breeding. Our results based on extensive genetic diversity provide a more refined chicken CNV map and genome-wide gene copy number estimates, and warrant future CNV association studies for important traits in chickens.

Phylogeny, divergence times, and historical biogeography of the angiosperm family Saxifragaceae.

PubMed

Deng, Jia-bin; Drew, Bryan T; Mavrodiev, Evgeny V; Gitzendanner, Matthew A; Soltis, Pamela S; Soltis, Douglas E

2015-02-01

Saxifragaceae (Saxifragales) contain approximately 640 species and 33 genera, about half of which are monotypic. Due to factors such as morphological stasis, convergent morphological evolution, and disjunct distributions, relationships within Saxifragaceae have historically been troublesome. The family occurs primarily in mountainous regions of the Northern Hemisphere, with the highest generic and species diversity in western North America, but disjunct taxa are known from southern South America. Here, we integrate broad gene (56 loci) and taxon (223 species) sampling strategies, both the most comprehensive to date within Saxifragaceae, with fossil calibrations and geographical distribution data to address relationships, divergence times, and historical biogeography among major lineages of Saxifragaceae. Two previously recognized main clades, the heucheroids (eight groups+Saniculiphyllum) and saxifragoids (Saxifraga s.s.), were re-affirmed by our phylogenetic analyses. Relationships among the eight heucheroid groups, as well as the phylogenetic position of Saniculiphyllum within the heucheroids, were resolved with mostly high support. Divergence time estimates indicate that Saxifragaceae began to diversify ca. 38.37 million years ago (Mya; 95% HPD=30.99-46.11Mya) in the Mid-Late Eocene, and that the two major lineages, the heucheroids and saxifragoids, began to diversify approximately 30.04Mya (95% HPD=23.87-37.15Mya) and 30.85 Mya (95% HPD=23.47-39.33Mya), respectively. We reconstructed ancestral geographic areas using statistical dispersal-vicariance (S-DIVA). These analyses indicate several radiations within Saxifragaceae: one in eastern Asia and multiple radiations in western North America. Our results also demonstrate that large amounts of sequence data coupled with broad taxon sampling can help resolve clade relationships that have thus far seemed intractable. Copyright © 2014 Elsevier Inc. All rights reserved.

High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences

PubMed Central

Vergin, Kevin L; Beszteri, Bánk; Monier, Adam; Cameron Thrash, J; Temperton, Ben; Treusch, Alexander H; Kilpert, Fabian; Worden, Alexandra Z; Giovannoni, Stephen J

2013-01-01

Advances in next-generation sequencing technologies are providing longer nucleotide sequence reads that contain more information about phylogenetic relationships. We sought to use this information to understand the evolution and ecology of bacterioplankton at our long-term study site in the Western Sargasso Sea. A bioinformatics pipeline called PhyloAssigner was developed to align pyrosequencing reads to a reference multiple sequence alignment of 16S ribosomal RNA (rRNA) genes and assign them phylogenetic positions in a reference tree using a maximum likelihood algorithm. Here, we used this pipeline to investigate the ecologically important SAR11 clade of Alphaproteobacteria. A combined set of 2.7 million pyrosequencing reads from the 16S rRNA V1–V2 regions, representing 9 years at the Bermuda Atlantic Time-series Study (BATS) site, was quality checked and parsed into a comprehensive bacterial tree, yielding 929 036 Alphaproteobacteria reads. Phylogenetic structure within the SAR11 clade was linked to seasonally recurring spatiotemporal patterns. This analysis resolved four new SAR11 ecotypes in addition to five others that had been described previously at BATS. The data support a conclusion reached previously that the SAR11 clade diversified by subdivision of niche space in the ocean water column, but the new data reveal a more complex pattern in which deep branches of the clade diversified repeatedly across depth strata and seasonal regimes. The new data also revealed the presence of an unrecognized clade of Alphaproteobacteria, here named SMA-1 (Sargasso Mesopelagic Alphaproteobacteria, group 1), in the upper mesopelagic zone. The high-resolution phylogenetic analyses performed herein highlight significant, previously unknown, patterns of evolutionary diversification, within perhaps the most widely distributed heterotrophic marine bacterial clade, and strongly links to ecosystem regimes. PMID:23466704

High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences.

PubMed

Vergin, Kevin L; Beszteri, Bánk; Monier, Adam; Thrash, J Cameron; Temperton, Ben; Treusch, Alexander H; Kilpert, Fabian; Worden, Alexandra Z; Giovannoni, Stephen J

2013-07-01

Advances in next-generation sequencing technologies are providing longer nucleotide sequence reads that contain more information about phylogenetic relationships. We sought to use this information to understand the evolution and ecology of bacterioplankton at our long-term study site in the Western Sargasso Sea. A bioinformatics pipeline called PhyloAssigner was developed to align pyrosequencing reads to a reference multiple sequence alignment of 16S ribosomal RNA (rRNA) genes and assign them phylogenetic positions in a reference tree using a maximum likelihood algorithm. Here, we used this pipeline to investigate the ecologically important SAR11 clade of Alphaproteobacteria. A combined set of 2.7 million pyrosequencing reads from the 16S rRNA V1-V2 regions, representing 9 years at the Bermuda Atlantic Time-series Study (BATS) site, was quality checked and parsed into a comprehensive bacterial tree, yielding 929 036 Alphaproteobacteria reads. Phylogenetic structure within the SAR11 clade was linked to seasonally recurring spatiotemporal patterns. This analysis resolved four new SAR11 ecotypes in addition to five others that had been described previously at BATS. The data support a conclusion reached previously that the SAR11 clade diversified by subdivision of niche space in the ocean water column, but the new data reveal a more complex pattern in which deep branches of the clade diversified repeatedly across depth strata and seasonal regimes. The new data also revealed the presence of an unrecognized clade of Alphaproteobacteria, here named SMA-1 (Sargasso Mesopelagic Alphaproteobacteria, group 1), in the upper mesopelagic zone. The high-resolution phylogenetic analyses performed herein highlight significant, previously unknown, patterns of evolutionary diversification, within perhaps the most widely distributed heterotrophic marine bacterial clade, and strongly links to ecosystem regimes.

Total-Evidence Dating under the Fossilized Birth–Death Process

PubMed Central

Zhang, Chi; Stadler, Tanja; Klopfstein, Seraina; Heath, Tracy A.; Ronquist, Fredrik

2016-01-01

Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth–death (FBD) process, which has been used to model speciation, extinction, and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of data sets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants, and bees). Previous total-evidence dating analyses of this data set were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push toward more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed. PMID:26493827

Total-Evidence Dating under the Fossilized Birth-Death Process.

PubMed

Zhang, Chi; Stadler, Tanja; Klopfstein, Seraina; Heath, Tracy A; Ronquist, Fredrik

2016-03-01

Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth-death (FBD) process, which has been used to model speciation, extinction, and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of data sets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants, and bees). Previous total-evidence dating analyses of this data set were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push toward more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed. ©The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Impact of Organic Amendments on Global Warming Potential of Diversified Tropical Rice Rotation Systems

NASA Astrophysics Data System (ADS)

Janz, B.; Weller, S.; Kraus, D.; Wassmann, R.; Butterbach-Bahl, K.; Ralf, K.

2017-12-01

Paddy rice cultivation is increasingly challenged by irrigation water scarcity, which is forcing farmers to change traditional rice cultivation from flooded double-rice systems to the introduction of well-aerated upland crops during dry season. Emissions of methane (CH4) are expected to decrease, while there is a risk of increasing emissions of nitrous oxide (N2O) and decreasing soil organic carbon (SOC) stocks through volatilization in the form of carbon dioxide (CO2). We present a unique dataset of long-term continuous greenhouse gas emission measurements (CH4 and N2O) in the Philippines to assess global warming potentials (GWP) of diversified rice crop rotations including different field management practices such as straw residue application and legume intercropping. Since 2012, more than four years of CH4 and N2O emissions in double-rice cropping (R-R) and paddy rice rotations diversified with either maize (R-M) or aerobic rice (R-A) during dry season have been collected. Introduction of upland crops reduced irrigation water use and CH4 emissions by 66-81% and 95-99%, respectively. Although dry season N2O emissions increased twice- to threefold in the diversified systems, the strong reduction of CH4 led to a significantly lower annual GWP (CH4 + N2O) as compared to the traditional R-R system. Diversified crop management practices were first implemented during land-preparation for dry season 2015 where i) 6 t/ha rice straw was returned to the field and ii) mungbean was grown as a cover-crop between dry and wet season in addition to rice straw application. The input of organic material (straw and mungbean) led to higher substrate availability for methanogens during the following season. Therefore, GWP was 9-39% higher following straw incorporation than the control treatment. This increase was mainly driven by additional CH4 emissions. Even more, mungbean intercropping further increased GWPs, whereby the increment was highest in R-R rotation (88%) and lowest in R-M rotation (55%), with annual emissions of 11.8 and 5.6 t CO2 eq. ha-1, respectively. Nevertheless, regarding a future expansion of lowland-upland rotations due to water scarcity in SE Asia it can be expected that input of crop residues can counteract the SOC loss that is likely associated with the shift to more aerated soil conditions under upland crops.

Leadership and adolescent girls: a qualitative study of leadership development.

PubMed

Hoyt, Michael A; Kennedy, Cara L

2008-12-01

This research investigated youth leadership experiences of adolescent girls who participated in a comprehensive feminist-based leadership program. This qualitative study utilized a grounded theory approach to understand changes that occurred in 10 female adolescent participants. The words of the participants revealed that initially they viewed leadership in traditional terms and were hesitant to identify themselves as leaders or to see themselves included within their concepts of leadership. Following the program their view of leadership expanded and diversified in a manner that allowed for inclusion of themselves within it. They spoke with greater strength and confidence and felt better positioned and inspired to act as leaders. Participants identified having examples of women leaders, adopting multiple concepts of leadership, and participating in an environment of mutual respect and trust as factors that contributed to their expanded conceptualization.

Creating diversified response profiles from a single quenchometric sensor element by using phase-resolved luminescence.

PubMed

Tehan, Elizabeth C; Bukowski, Rachel M; Chodavarapu, Vamsy P; Titus, Albert H; Cartwright, Alexander N; Bright, Frank V

2015-01-05

We report a new strategy for generating a continuum of response profiles from a single luminescence-based sensor element by using phase-resolved detection. This strategy yields reliable responses that depend in a predictable manner on changes in the luminescent reporter lifetime in the presence of the target analyte, the excitation modulation frequency, and the detector (lock-in amplifier) phase angle. In the traditional steady-state mode, the sensor that we evaluate exhibits a linear, positive going response to changes in the target analyte concentration. Under phase-resolved conditions the analyte-dependent response profiles: (i) can become highly non-linear; (ii) yield negative going responses; (iii) can be biphasic; and (iv) can exhibit super sensitivity (e.g., sensitivities up to 300 fold greater in comparison to steady-state conditions).

Positive and negative feedback regulatory loops of thiol-oxidative stress response mediated by an unstable isoform of sigmaR in actinomycetes.

PubMed

Kim, Min-Sik; Hahn, Mi-Young; Cho, Yoobok; Cho, Sang-Nae; Roe, Jung-Hye

2009-09-01

Alternate sigma factors provide an effective way of diversifying bacterial gene expression in response to environmental changes. In Streptomyces coelicolor where more than 65 sigma factors are predicted, sigma(R) is the major regulator for response to thiol-oxidative stresses. sigma(R) becomes available when its bound anti-sigma factor RsrA is oxidized at sensitive cysteine thiols to form disulphide bonds. sigma(R) regulon includes genes for itself and multiple thiol-reducing systems, which constitute positive and negative feedback loops respectively. We found that the positive amplification loop involves an isoform of sigma(R) (sigma(R')) with an N-terminal extension of 55 amino acids, produced from an upstream start codon. A major difference between constitutive sigma(R) and inducible sigma(R') is that the latter is markedly unstable (t(1/2) approximately 10 min) compared with the former (> 70 min). The rapid turnover of sigma(R') is partly due to induced ClpP1/P2 proteases from the sigma(R) regulon. This represents a novel way of elaborating positive and negative feedback loops in a control circuit. Similar phenomenon may occur in other actinomycetes that harbour multiple start codons in the sigR homologous gene. We observed that sigH gene, the sigR orthologue in Mycobacterium smegmatis, produces an unstable larger isoform of sigma(H) upon induction by thiol-oxidative stress.

Barriers in Access to the Treatment for People with Gambling Disorders. Are They Different from Those Experienced by People with Alcohol and/or Drug Dependence?

PubMed

Dąbrowska, Katarzyna; Moskalewicz, Jacek; Wieczorek, Łukasz

2017-06-01

A prevalence of gambling disorders is diversified depending on the region of the world. Almost three quarters of pathological gamblers had never sought a professional treatment as well as an assistance in self-help groups. Reasons why they do not initiate a treatment are complex. The aim of the article is to compare barriers to the treatment for people with gambling disorders found in presented study and barriers to alcohol and drug treatment identified in the available literature. The semi structured interviews were applied and conducted with people with gambling disorders, social workers, therapists employed in the addiction treatment facilities, General Practitioners and psychiatrists. Selection of the respondents was based on purposive sampling. In total, 90 interviews were completed. Respondents identified individual barriers as well as structural ones. Individual barriers include internal resistance and a fear of the treatment. In turn structural barriers apply to the organization of the therapy, infrastructure, personnel, and the therapeutic program. A comparison of barriers experienced by people with gambling disorders and substance use disorders showed that they are largely similar, but people with gambling disorders also experience specific barriers. Empirical studies focused specifically on treatment needs of people experiencing gambling disorders may improve an offer of help for them. More adequate treatment options could contribute to the increasing in the number of people who start the treatment. It can result in improving their quality of life and may have positive impact on public health.

Recent evolution of China's virtual water trade: analysis of selected crops and considerations for policy

NASA Astrophysics Data System (ADS)

Shi, J.; Liu, J.; Pinter, L.

2013-09-01

China has dramatically increased its virtual water import unconsciously for recent years. Many studies have focused on the quantity of traded virtual water but very few go into analysing geographic distribution and the properties of China's virtual water trade network. This paper provides a calculation and analysis of the crop-related virtual water trade network of China based on 27 major primary crops between 1986 and 2009. The results show that China is a net importer of virtual water from water-abundant areas of North and South America, and a net virtual water exporter to water-stressed areas of Asia, Africa, and Europe. Virtual water import is far larger than virtual water export and in both import and export a small number of trade partners control the supply chain. Grain crops are the major contributors to virtual water trade, and among grain crops soybeans, mostly imported from the US, Brazil and Argentina are the most significant. As crop yield and crop water productivity in North and South America are generally higher than those in Asia and Africa, the effect of China's crop-related virtual water trade positively contributes to optimizing crop water use efficiency at the global scale. In order to mitigate water scarcity and secure the food supply, virtual water should be actively incorporated into national water management strategies. From the national perspective, China should reduce the export and increase the import of water-intensive crops. But the sources of virtual water import need to be further diversified to reduce supply chain risks and increase resilience.

A Retrospective Study on Genetic Heterogeneity within Treponema Strains: Subpopulations Are Genetically Distinct in a Limited Number of Positions.

PubMed

Čejková, Darina; Strouhal, Michal; Norris, Steven J; Weinstock, George M; Šmajs, David

2015-01-01

Pathogenic uncultivable treponemes comprise human and animal pathogens including agents of syphilis, yaws, bejel, pinta, and venereal spirochetosis in rabbits and hares. A set of 10 treponemal genome sequences including those of 4 Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14), 4 T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), 1 T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPLC) were examined with respect to the presence of nucleotide intrastrain heterogeneous sites. The number of identified intrastrain heterogeneous sites in individual genomes ranged between 0 and 7. Altogether, 23 intrastrain heterogeneous sites (in 17 genes) were found in 5 out of 10 investigated treponemal genomes including TPA strains Nichols (n = 5), DAL-1 (n = 4), and SS14 (n = 7), TPE strain Samoa D (n = 1), and TEN strain Bosnia A (n = 5). Although only one heterogeneous site was identified among 4 tested TPE strains, 16 such sites were identified among 4 TPA strains. Heterogeneous sites were mostly strain-specific and were identified in four tpr genes (tprC, GI, I, K), in genes involved in bacterial motility and chemotaxis (fliI, cheC-fliY), in genes involved in cell structure (murC), translation (prfA), general and DNA metabolism (putative SAM dependent methyltransferase, topA), and in seven hypothetical genes. Heterogeneous sites likely represent both the selection of adaptive changes during infection of the host as well as an ongoing diversifying evolutionary process.

Resistance patterns of diversified phylogroups of Escherichia coli associated with mothers having history of preterm births in Pakistan.

PubMed

Rana, Fiza; Siddiqui, Sidra; Khan, Ayesha; Siddiqui, Fariha; Noreen, Zobia; Bokhari, Sadia; Bokhari, Habib

2017-01-01

Urinary tract infections (UTIs) are caused by extraintestinal pathogenic Escherichia coli (ExPEC), and are one of the key predictors of preterm births. In the light of this fact, present study was conducted to determine the predominant Escherichia coli (E. coli) phylotypes and their associated antibiotic susceptibility patterns, isolated from pregnant mothers with the history of preterm births. Forty seven E. coli strains were isolated out of a total of 80 urine samples of pregnant women. The isolates were phylotyped and further screened for the presence of Clonal group A. Moreover, Antimicrobial susceptibility testing and screening for Extended Spectrum Beta Lactamase (ESBL) producing strains were also performed. Among the 47 isolates, phylogroup B2 was found to be highly prevalent (45%), followed by group D (23%), B1 (10.64%), A (6.38%), E (6.38%), cryptic clade I (4.25%) and F (2.13%). Two isolates belonged to CgA and 41 (87.23%) isolates were found to be multidrug-resistant. Out of nine antibiotics tested in the study, the isolates displayed high resistance to Ampicillin (82.6%), Sulphamethoxazole (65.22%), Nalidixic acid (60.87%), Sulphamethoxazole-Trimethoprim, Doxycycline and Erythromycin (56.52% each). In total, 8 (17.02%) of the isolates were found to be ESBL positive. The prevalence of infections caused by virulent and highly drug resistant E. coli isolates constitute a risk of developing preterm birth complications in pregnant women and requires the selection of appropriate antibiotics for the treatment of infections caused during pregnancy.

Origin and radiation of the earliest vascular land plants.

PubMed

Steemans, Philippe; Hérissé, Alain Le; Melvin, John; Miller, Merrell A; Paris, Florentin; Verniers, Jacques; Wellman, Charles H

2009-04-17

Colonization of the land by plants most likely occurred in a stepwise fashion starting in the Mid-Ordovician. The earliest flora of bryophyte-like plants appears to have been cosmopolitan and dominated the planet, relatively unchanged, for some 30 million years. It is represented by fossilized dispersed cryptospores and fragmentary plant remains. In the Early Silurian, cryptospore abundance and diversity diminished abruptly as trilete spores appeared, became abundant, and underwent rapid diversification. This change coincides approximately with the appearance of vascular plant megafossils and probably represents the origin and adaptive radiation of vascular plants. We have obtained a diverse trilete spore occurrence from the Late Ordovician that suggests that vascular plants originated and diversified earlier than previously hypothesized, in Gondwana, before migrating elsewhere and secondarily diversifying.

The Impacts of Different Expansion Modes on Performance of Small Solar Energy Firms: Perspectives of Absorptive Capacity

PubMed Central

Chen, Hsing Hung; Shen, Tao; Xu, Xin-long; Ma, Chao

2013-01-01

The characteristics of firm's expansion by differentiated products and diversified products are quite different. However, the study employing absorptive capacity to examine the impacts of different modes of expansion on performance of small solar energy firms has never been discussed before. Then, a conceptual model to analyze the tension between strategies and corporate performance is proposed to filling the vacancy. After practical investigation, the results show that stronger organizational institutions help small solar energy firms expanded by differentiated products increase consistency between strategies and corporate performance; oppositely, stronger working attitudes with weak management controls help small solar energy firms expanded by diversified products reduce variance between strategies and corporate performance. PMID:24453837

Pollination Reservoirs in Lowbush Blueberry (Ericales: Ericaceae).

PubMed

Venturini, E M; Drummond, F A; Hoshide, A K; Dibble, A C; Stack, L B

2017-04-01

Pollinator-dependent agriculture heavily relies upon a single pollinator-the honey bee. To diversify pollination strategies, growers are turning to alternatives. Densely planted reservoirs of pollen- and nectar-rich flowers (pollination reservoirs, hereafter "PRs") may improve pollination services provided by wild bees. Our focal agroecosystem, lowbush blueberry (Vaccinium angustifolium Aiton), exists in a simple landscape uniquely positioned to benefit from PRs. First, we contrast bee visitation rates and use of three types of PR. We consider the effects of PRs on wild bee diversity and the composition of bumble bee pollen loads. We contrast field-level crop pollination services between PRs and controls four years postestablishment. Last, we calculate the time to pay for PR investment. Social bees preferentially used clover plantings; solitary bees preferentially used wildflower plantings. On average, bumble bee pollen loads in treatment fields contained 37% PR pollen. PRs significantly increased visitation rates to the crop in year 4, and exerted a marginally significant positive influence on fruit set. The annualized costs of PRs were covered by the fourth year using the measured increase in pollination services. Our findings provide evidence of the positive impact of PRs on crop pollination services. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

Rational selection and engineering of exogenous principal sigma factor (σ(HrdB)) to increase teicoplanin production in an industrial strain of Actinoplanes teichomyceticus.

PubMed

Wang, Haiyong; Yang, Liu; Wu, Kuo; Li, Guanghui

2014-01-16

Transcriptional engineering has presented a strong ability of phenotypic improvement in microorganisms. However, it could not be directly applied to Actinoplanes teichomyceticus L-27 because of the paucity of endogenous transcription factors in the strain. In this study, exogenous transcription factors were rationally selected and transcriptional engineering was carried out to increase the productivity of teicoplanin in L-27. It was illuminated that the σ(HrdB) molecules shared strong similarity of amino acid sequences among some genera of actinomycetes. Combining this advantage with the ability of transcriptional engineering, exogenous sigma factor σ(HrdB) molecules were rationally selected and engineered to improve L-27. hrdB genes from Actinoplanes missouriensis 431, Micromonospora aurantiaca ATCC 27029 and Salinispora arenicola CNS-205 were selected based on molecular evolutionary analysis. Random mutagenesis, DNA shuffling and point mutation were subsequently performed to generate diversified mutants. A recombinant was identified through screening program, yielding 5.3 mg/ml of teicoplanin, over 2-fold compared to that of L-27. More significantly, the engineered strain presented a good performance in 500-l pilot scale fermentation, which meant its valuable potential application in industry. Through rational selection and engineering of exogenous transcriptional factor, we have extended the application of transcriptional engineering. To our knowledge, it is the first time to focus on the related issue. In addition, possessing the advantage of efficient metabolic perturbation in transcription level, this strategy could be useful in analyzing metabolic and physiological mechanisms of strains, especially those with the only information on taxonomy.

Multiple-instance ensemble learning for hyperspectral images

NASA Astrophysics Data System (ADS)

Ergul, Ugur; Bilgin, Gokhan

2017-10-01

An ensemble framework for multiple-instance (MI) learning (MIL) is introduced for use in hyperspectral images (HSIs) by inspiring the bagging (bootstrap aggregation) method in ensemble learning. Ensemble-based bagging is performed by a small percentage of training samples, and MI bags are formed by a local windowing process with variable window sizes on selected instances. In addition to bootstrap aggregation, random subspace is another method used to diversify base classifiers. The proposed method is implemented using four MIL classification algorithms. The classifier model learning phase is carried out with MI bags, and the estimation phase is performed over single-test instances. In the experimental part of the study, two different HSIs that have ground-truth information are used, and comparative results are demonstrated with state-of-the-art classification methods. In general, the MI ensemble approach produces more compact results in terms of both diversity and error compared to equipollent non-MIL algorithms.

“We Do Science Here”: Underrepresented Students’ Interactions with Faculty in Different College Contexts

PubMed Central

Hurtado, Sylvia; Eagan, M. Kevin; Tran, Minh C.; Newman, Christopher B.; Chang, Mitchell J.; Velasco, Paolo

2011-01-01

Faculty members play a key role in the identification and training of the next generation of scientific talent. In the face of the need to advance and diversify the scientific workforce, we examine whether and how specific institutional contexts shape student interactions with faculty. We conducted a mixed methods study to understand institutional contextual differences in the experiences of aspiring scientists. Data from a qualitative five-campus case study and a quantitative longitudinal study of students from over 117 higher education institutions were analyzed to determine how aspiring scientists interact with faculty and gain access to resources that will help them achieve their educational goals. Findings indicate that important structural differences exist between institutions in shaping students’ interactions with faculty. For example, students at more selective institutions typically have less frequent, less personal interactions with faculty whereas Black students at HBCUs report having more support and frequent interactions with faculty. PMID:23503924

Trial watch: Immune checkpoint blockers for cancer therapy.

PubMed

Vanpouille-Box, Claire; Lhuillier, Claire; Bezu, Lucillia; Aranda, Fernando; Yamazaki, Takahiro; Kepp, Oliver; Fucikova, Jitka; Spisek, Radek; Demaria, Sandra; Formenti, Silvia C; Zitvogel, Laurence; Kroemer, Guido; Galluzzi, Lorenzo

2017-01-01

Immune checkpoint blockers (ICBs) are literally revolutionizing the clinical management of an ever more diversified panel of oncological indications. Although considerable attention persists around the inhibition of cytotoxic T lymphocyte-associated protein 4 (CTLA4) and programmed cell death 1 (PDCD1, best known as PD-1) signaling, several other co-inhibitory T-cell receptors are being evaluated as potential targets for the development of novel ICBs. Moreover, substantial efforts are being devoted to the identification of biomarkers that reliably predict the likelihood of each patient to obtain clinical benefits from ICBs in the absence of severe toxicity. Tailoring the delivery of specific ICBs or combinations thereof to selected patient populations in the context of precision medicine programs constitutes indeed a major objective of the future of ICB-based immunotherapy. Here, we discuss recent preclinical and clinical advances on the development of ICBs for oncological indications.

Recent advances in applications of nanomaterials for sample preparation.

PubMed

Xu, Linnan; Qi, Xiaoyue; Li, Xianjiang; Bai, Yu; Liu, Huwei

2016-01-01

Sample preparation is a key step for qualitative and quantitative analysis of trace analytes in complicated matrix. Along with the rapid development of nanotechnology in material science, numerous nanomaterials have been developed with particularly useful applications in analytical chemistry. Benefitting from their high specific areas, increased surface activities, and unprecedented physical/chemical properties, the potentials of nanomaterials for rapid and efficient sample preparation have been exploited extensively. In this review, recent progress of novel nanomaterials applied in sample preparation has been summarized and discussed. Both nanoparticles and nanoporous materials are evaluated for their unusual performance in sample preparation. Various compositions and functionalizations extended the applications of nanomaterials in sample preparations, and distinct size and shape selectivity was generated from the diversified pore structures of nanoporous materials. Such great variety make nanomaterials a kind of versatile tools in sample preparation for almost all categories of analytes. Copyright © 2015 Elsevier B.V. All rights reserved.

A genomic history of Aboriginal Australia.

PubMed

Malaspinas, Anna-Sapfo; Westaway, Michael C; Muller, Craig; Sousa, Vitor C; Lao, Oscar; Alves, Isabel; Bergström, Anders; Athanasiadis, Georgios; Cheng, Jade Y; Crawford, Jacob E; Heupink, Tim H; Macholdt, Enrico; Peischl, Stephan; Rasmussen, Simon; Schiffels, Stephan; Subramanian, Sankar; Wright, Joanne L; Albrechtsen, Anders; Barbieri, Chiara; Dupanloup, Isabelle; Eriksson, Anders; Margaryan, Ashot; Moltke, Ida; Pugach, Irina; Korneliussen, Thorfinn S; Levkivskyi, Ivan P; Moreno-Mayar, J Víctor; Ni, Shengyu; Racimo, Fernando; Sikora, Martin; Xue, Yali; Aghakhanian, Farhang A; Brucato, Nicolas; Brunak, Søren; Campos, Paula F; Clark, Warren; Ellingvåg, Sturla; Fourmile, Gudjugudju; Gerbault, Pascale; Injie, Darren; Koki, George; Leavesley, Matthew; Logan, Betty; Lynch, Aubrey; Matisoo-Smith, Elizabeth A; McAllister, Peter J; Mentzer, Alexander J; Metspalu, Mait; Migliano, Andrea B; Murgha, Les; Phipps, Maude E; Pomat, William; Reynolds, Doc; Ricaut, Francois-Xavier; Siba, Peter; Thomas, Mark G; Wales, Thomas; Wall, Colleen Ma'run; Oppenheimer, Stephen J; Tyler-Smith, Chris; Durbin, Richard; Dortch, Joe; Manica, Andrea; Schierup, Mikkel H; Foley, Robert A; Lahr, Marta Mirazón; Bowern, Claire; Wall, Jeffrey D; Mailund, Thomas; Stoneking, Mark; Nielsen, Rasmus; Sandhu, Manjinder S; Excoffier, Laurent; Lambert, David M; Willerslev, Eske

2016-10-13

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

Impacted science: impact is not importance.

PubMed

Casadevall, Arturo; Fang, Ferric C

2015-10-13

The journal impact factor (IF) exerts a tremendous influence on the conduct of scientists. The obsession with IF has been compared to a medical condition, sometimes referred to as "IF mania" or "impactitis." Here, we analyze the difference between impact and importance, using examples from the history of science to show that these are not equivalent. If impact does not necessarily equal importance, but scientists are focused on high-impact work, there is a danger that misuse of the IF may adversely affect scientific progress. We suggest five measures to fight this malady: (i) diversify journal club selections, (ii) do not judge science on the publication venue, (iii) reduce the reliance on journal citation metrics for employment and advancement, (iv) discuss the misuse of the IF in ethics courses, and (v) cite the most appropriate sources. If IF mania is indeed a medical condition, the most appropriate course of action may be disimpaction. Copyright © 2015 Casadevall and Fang.

Impacted Science: Impact Is Not Importance

PubMed Central

Fang, Ferric C.

2015-01-01

ABSTRACT The journal impact factor (IF) exerts a tremendous influence on the conduct of scientists. The obsession with IF has been compared to a medical condition, sometimes referred to as “IF mania” or “impactitis.” Here, we analyze the difference between impact and importance, using examples from the history of science to show that these are not equivalent. If impact does not necessarily equal importance, but scientists are focused on high-impact work, there is a danger that misuse of the IF may adversely affect scientific progress. We suggest five measures to fight this malady: (i) diversify journal club selections, (ii) do not judge science on the publication venue, (iii) reduce the reliance on journal citation metrics for employment and advancement, (iv) discuss the misuse of the IF in ethics courses, and (v) cite the most appropriate sources. If IF mania is indeed a medical condition, the most appropriate course of action may be disimpaction. PMID:26463169

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.

Evaluating intra- and inter-individual variation in the human placental transcriptome.

PubMed

Hughes, David A; Kircher, Martin; He, Zhisong; Guo, Song; Fairbrother, Genevieve L; Moreno, Carlos S; Khaitovich, Philipp; Stoneking, Mark

2015-03-19

Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta. We estimate that on average, 33.2%, 58.9%, and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals, and among human groups, respectively. Additionally, when technical and biological traits are included in models of gene expression they each account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling, and metabolism. Many biological traits demonstrate correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection, directional selection, or diversifying selection. We apportion placental gene expression variation into individual, population, and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection.

Parity Now!

ERIC Educational Resources Information Center

Library Journal, 1971

1971-01-01

The preconference on Recruitment of Minorities featured a diversified program with an array of speakers, a panel discussion, concurrent sessions on problem solving, and summaries and critiques from two conference "floaters." (Author)

30 CFR 706.17 - What to report.

Code of Federal Regulations, 2011 CFR

2011-07-01

... report holdings in widely diversified mutual funds, investment clubs or regulated investment companies... ordinary household and living expenses. (c) Employee certification, and if applicable, a listing of...

76 FR 75536 - Procurement List; Proposed Addition

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-02

... listed: Service Service Type/Location: Grounds Maintenance, Beale AFB, CA. NPA: Crossroads Diversified Service, Inc., Sacramento, CA. Contracting Activity: 9th Contracting Squadron, Beale AFB, CA. Patricia...

The genomic substrate for adaptive radiation in African cichlid fish.

PubMed

Brawand, David; Wagner, Catherine E; Li, Yang I; Malinsky, Milan; Keller, Irene; Fan, Shaohua; Simakov, Oleg; Ng, Alvin Y; Lim, Zhi Wei; Bezault, Etienne; Turner-Maier, Jason; Johnson, Jeremy; Alcazar, Rosa; Noh, Hyun Ji; Russell, Pamela; Aken, Bronwen; Alföldi, Jessica; Amemiya, Chris; Azzouzi, Naoual; Baroiller, Jean-François; Barloy-Hubler, Frederique; Berlin, Aaron; Bloomquist, Ryan; Carleton, Karen L; Conte, Matthew A; D'Cotta, Helena; Eshel, Orly; Gaffney, Leslie; Galibert, Francis; Gante, Hugo F; Gnerre, Sante; Greuter, Lucie; Guyon, Richard; Haddad, Natalie S; Haerty, Wilfried; Harris, Rayna M; Hofmann, Hans A; Hourlier, Thibaut; Hulata, Gideon; Jaffe, David B; Lara, Marcia; Lee, Alison P; MacCallum, Iain; Mwaiko, Salome; Nikaido, Masato; Nishihara, Hidenori; Ozouf-Costaz, Catherine; Penman, David J; Przybylski, Dariusz; Rakotomanga, Michaelle; Renn, Suzy C P; Ribeiro, Filipe J; Ron, Micha; Salzburger, Walter; Sanchez-Pulido, Luis; Santos, M Emilia; Searle, Steve; Sharpe, Ted; Swofford, Ross; Tan, Frederick J; Williams, Louise; Young, Sarah; Yin, Shuangye; Okada, Norihiro; Kocher, Thomas D; Miska, Eric A; Lander, Eric S; Venkatesh, Byrappa; Fernald, Russell D; Meyer, Axel; Ponting, Chris P; Streelman, J Todd; Lindblad-Toh, Kerstin; Seehausen, Ole; Di Palma, Federica

2014-09-18

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

Maternal source of variability in the embryo development of an annual killifish.

PubMed

Polačik, M; Smith, C; Reichard, M

2017-04-01

Organisms inhabiting unpredictable environments often evolve diversified reproductive bet-hedging strategies, expressed as production of multiple offspring phenotypes, thereby avoiding complete reproductive failure. To cope with unpredictable rainfall, African annual killifish from temporary savannah pools lay drought-resistant eggs that vary widely in the duration of embryo development. We examined the sources of variability in the duration of individual embryo development, egg production and fertilization rate in Nothobranchius furzeri. Using a quantitative genetics approach (North Carolina type II design), we found support for maternal effects rather than polyandrous mating as the primary source of the variability in the duration of embryo development. The number of previously laid eggs appeared to serve as an internal physiological cue initiating a shift from rapid-to-slow embryo developmental mode. In annual killifish, extensive phenotypic variability in progeny traits is adaptive, as the conditions experienced by parents have limited relevance to the offspring generation. In contrast to genetic control, with high phenotypic expression and heritability, maternal control of traits under natural selection prevents standing genetic diversity from potentially detrimental effects of selection in fluctuating environments. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Spillovers among regional and international stock markets

NASA Astrophysics Data System (ADS)

Huen, Tan Bee; Arsad, Zainudin; Chun, Ooi Po

2014-07-01

Realizing the greater risk by the increase in the level of financial market integration, this study investigates the dynamic of international and regional stock markets co-movement among Asian countries with the world leading market, the US. The data utilized in this study comprises of weekly closing prices for four stock indices, that consists of two developing markets (Malaysia and China) and two developed markets (Japan and the US), and encompasses the period from January 1996 to December 2012. Multivariate Generalized Autoregressive Conditional Heteroscedasticity (MGARCH) model with the BEKK parameterization is employed to investigate the mean and volatility spillover effects among the selected stock indices. The results show significant mean spillover not only from the larger developed markets to smaller developing markets but also from the smaller developing markets to larger developed markets. Volatility spillover between the developed markets is found to be smaller than that between the developing markets. Conditional correlations among the stock markets are found to increase over the sample period. The findings of significant mean and volatility spillovers are considered as bad news for international investors as it reduces the benefit from portfolio diversification but act as useful information for investors to be more aware in diversifying their investment or stock selection.

Chimpanzee quiet hoo variants differ according to context.

PubMed

Crockford, Catherine; Gruber, Thibaud; Zuberbühler, Klaus

2018-05-01

In comparative studies of evolution of communication, the function and use of animal quiet calls have typically been understudied, despite that these signals are presumably under selection like other vocalizations, such as alarm calls. Here, we examine vocalization diversification of chimpanzee quiet 'hoos' produced in three contexts-travel, rest and alert-and potential pressures promoting diversification. Previous playback and observational studies have suggested that the overarching function of chimpanzee hoos is to stay in contact with others, particularly bond partners. We conducted an acoustic analysis of hoos using audio recordings from wild chimpanzees ( Pan troglodytes schweinfurthii ) of Budongo Forest, Uganda. We identified three acoustically distinguishable, context-specific hoo variants. Each call variant requires specific responses from receivers to avoid breaking up the social unit. We propose that callers may achieve coordination by using acoustically distinguishable calls, advertising their own behavioural intentions. We conclude that natural selection has acted towards acoustically diversifying an inconspicuous, quiet vocalization, the chimpanzee hoo. This evolutionary process may have been favoured by the fact that signallers and recipients share the same goal, to maintain social cohesion, particularly among those who regularly cooperate, suggesting that call diversification has been favoured by the demands of cooperative activities.

Chemoselective ligation and antigen vectorization.

PubMed

Gras-Masse, H

2001-01-01

The interest in cocktail-lipopeptide vaccines has now been confirmed by phase I clinical trials: highly diversified B-, T-helper or cytotoxic T-cell epitopes can be combined with a lipophilic vector for the induction of B- and T-cell responses of predetermined specificity. With the goal of producing an improved vaccine that should ideally induce a multispecific response in non-selected populations, increasing the diversity of the immunizing mixture represents one of the most obvious strategies.The selective delivery of antigens to professional antigen-presenting cells represents another promising approach for the improvement of vaccine efficacy. In this context, the mannose-receptor represents an attractive entry point for the targeting to dendritic cells of antigens linked to clustered glycosides or glycomimetics. In all cases, highly complex but fully characterized molecules must be produced. To develop a modular and flexible strategy which could be generally applicable to a large set of peptide antigens, we elected to explore the potentialities of chemoselective ligation methods. The hydrazone bond was found particularly reliable and fully compatible with sulphide ligation. Hydrazone/thioether orthogonal ligation systems could be developed to account for the nature of the antigens and the solubility of the vector systems. Copyright 2001 The International Association for Biologicals.

Correlated evolution of beak morphology and song in the neotropical woodcreeper radiation.

PubMed

Derryberry, Elizabeth Perrault; Seddon, Nathalie; Claramunt, Santiago; Tobias, Joseph Andrew; Baker, Adam; Aleixo, Alexandre; Brumfield, Robb Thomas

2012-09-01

Mating signals may diversify as a byproduct of morphological adaptation to different foraging niches, potentially driving speciation. Although many studies have focused on the direct influence of ecological and sexual selection on signal divergence, the role of indirect mechanisms remains poorly understood. Using phenotypic and molecular datasets, we explored the interplay between morphological and vocal evolution in an avian radiation characterized by dramatic beak variation, the Neotropical woodcreepers (Dendrocolaptinae). We found evidence of a trade-off between the rate of repetition of song syllables and frequency bandwidth: slow paced songs had either narrow or wide frequency bandwidths, and bandwidth decreased as song pace increased. This bounded phenotypic space for song structure supports the hypothesis that passerine birds face a motor constraint during song production. Diversification of acoustic characters within this bounded space was correlated with diversification of beak morphology. In particular, species with larger beaks produced slower songs with narrower frequency bandwidths, suggesting that ecological selection on beak morphology influences the diversification of woodcreeper songs. Because songs in turn mediate mate choice and species recognition in birds, these results indicate a broader role for ecology in avian diversification. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

The genomic substrate for adaptive radiation in African cichlid fish

PubMed Central

Malinsky, Milan; Keller, Irene; Fan, Shaohua; Simakov, Oleg; Ng, Alvin Y.; Lim, Zhi Wei; Bezault, Etienne; Turner-Maier, Jason; Johnson, Jeremy; Alcazar, Rosa; Noh, Hyun Ji; Russell, Pamela; Aken, Bronwen; Alföldi, Jessica; Amemiya, Chris; Azzouzi, Naoual; Baroiller, Jean-François; Barloy-Hubler, Frederique; Berlin, Aaron; Bloomquist, Ryan; Carleton, Karen L.; Conte, Matthew A.; D'Cotta, Helena; Eshel, Orly; Gaffney, Leslie; Galibert, Francis; Gante, Hugo F.; Gnerre, Sante; Greuter, Lucie; Guyon, Richard; Haddad, Natalie S.; Haerty, Wilfried; Harris, Rayna M.; Hofmann, Hans A.; Hourlier, Thibaut; Hulata, Gideon; Jaffe, David B.; Lara, Marcia; Lee, Alison P.; MacCallum, Iain; Mwaiko, Salome; Nikaido, Masato; Nishihara, Hidenori; Ozouf-Costaz, Catherine; Penman, David J.; Przybylski, Dariusz; Rakotomanga, Michaelle; Renn, Suzy C. P.; Ribeiro, Filipe J.; Ron, Micha; Salzburger, Walter; Sanchez-Pulido, Luis; Santos, M. Emilia; Searle, Steve; Sharpe, Ted; Swofford, Ross; Tan, Frederick J.; Williams, Louise; Young, Sarah; Yin, Shuangye; Okada, Norihiro; Kocher, Thomas D.; Miska, Eric A.; Lander, Eric S.; Venkatesh, Byrappa; Fernald, Russell D.; Meyer, Axel; Ponting, Chris P.; Streelman, J. Todd; Lindblad-Toh, Kerstin; Seehausen, Ole; Di Palma, Federica

2015-01-01

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification. PMID:25186727

Diversification through multitrait evolution in a coevolving interaction.

PubMed

Thompson, John N; Schwind, Christopher; Guimarães, Paulo R; Friberg, Magne

2013-07-09

Mutualisms between species are interactions in which reciprocal exploitation results in outcomes that are mutually beneficial. This reciprocal exploitation is evident in the more than a thousand plant species that are pollinated exclusively by insects specialized to lay their eggs in the flowers they pollinate. By pollinating each flower in which she lays eggs, an insect guarantees that her larval offspring have developing seeds on which to feed, whereas the plant gains a specialized pollinator at the cost of some seeds. These mutualisms are often reciprocally obligate, potentially driving not only ongoing coadaptation but also diversification. The lack of known intermediate stages in most of these mutualisms, however, makes it difficult to understand whether these interactions could have begun to diversify even before they became reciprocally obligate. Experimental studies of the incompletely obligate interactions between woodland star (Lithophragma; Saxifragaceae) plants and their pollinating floral parasites in the moth genus Greya (Prodoxidae) show that, as these lineages have diversified, the moths and plants have evolved in ways that maintain effective oviposition and pollination. Experimental assessment of pollination in divergent species and quantitative evaluation of time-lapse photographic sequences of pollination viewed on surgically manipulated flowers show that various combinations of traits are possible for maintaining the mutualism. The results suggest that at least some forms of mutualism can persist and even diversify when the interaction is not reciprocally obligate.

Diversified clinical presentations associated with a novel sal-like 4 gene mutation in a Chinese pedigree with Duane retraction syndrome.

PubMed

Yang, Ming-ming; Ho, Mary; Lau, Henry H W; Tam, Pancy O S; Young, Alvin L; Pang, Chi Pui; Yip, Wilson W K; Chen, LiJia

2013-01-01

To determine the underlying genetic cause of Duane retraction syndrome (DRS) in a non-consanguineous Chinese Han family. Detailed ophthalmic and physical examinations were performed on all members from a pedigree with DRS. All exons and their adjacent splicing junctions of the sal-like 4 (SALL4) gene were amplified with polymerase chain reaction and analyzed with direct sequencing in all the recruited family members and 200 unrelated control subjects. Clinical examination revealed a broad spectrum of phenotypes in the DRS family. Mutation analysis of SALL4 identified a novel heterozygous duplication mutation, c.1919dupT, which was completely cosegregated with the disease in the family and absent in controls. This mutation was predicted to cause a frameshift, introducing a premature stop codon, when translated, resulting in a truncated SALL4 protein, i.e., p.Met640IlefsX25. Bioinformatics analysis showed that the affected region of SALL4 shared a highly conserved sequence across different species. Diversified clinical manifestations were observed in the c.1919dupT carriers of the family. We identified a novel truncating mutation in the SALL4 gene that leads to diversified clinical features of DRS in a Chinese family. This mutation is predicted to result in a truncated SALL4 protein affecting two functional domains and cause disease development due to haploinsufficiency through nonsense-mediated mRNA decay.

The influence of curricular and extracurricular learning activities on students' choice of chiropractic technique

PubMed Central

Sikorski, David M.; KizhakkeVeettil, Anupama; Tobias, Gene S.

2016-01-01

Objective: Surveys for the National Board of Chiropractic Examiners indicate that diversified chiropractic technique is the most commonly used chiropractic manipulation method. The study objective was to investigate the influences of our diversified core technique curriculum, a technique survey course, and extracurricular technique activities on students' future practice technique preferences. Methods: We conducted an anonymous, voluntary survey of 1st, 2nd, and 3rd year chiropractic students at our institution. Surveys were pretested for face validity, and data were analyzed using descriptive and inferential statistics. Results: We had 164 students (78% response rate) participate in the survey. Diversified was the most preferred technique for future practice by students, and more than half who completed the chiropractic technique survey course reported changing their future practice technique choice as a result. The students surveyed agreed that the chiropractic technique curriculum and their experiences with chiropractic practitioners were the two greatest bases for their current practice technique preference, and that their participation in extracurricular technique clubs and seminars was less influential. Conclusions: Students appear to have the same practice technique preferences as practicing chiropractors. The chiropractic technique curriculum and the students' experience with chiropractic practitioners seem to have the greatest influence on their choice of chiropractic technique for future practice. Extracurricular activities, including technique clubs and seminars, although well attended, showed a lesser influence on students' practice technique preferences. PMID:26655282

The influence of curricular and extracurricular learning activities on students' choice of chiropractic technique.

PubMed

Sikorski, David M; KizhakkeVeettil, Anupama; Tobias, Gene S

2016-03-01

Surveys for the National Board of Chiropractic Examiners indicate that diversified chiropractic technique is the most commonly used chiropractic manipulation method. The study objective was to investigate the influences of our diversified core technique curriculum, a technique survey course, and extracurricular technique activities on students' future practice technique preferences. We conducted an anonymous, voluntary survey of 1st, 2nd, and 3rd year chiropractic students at our institution. Surveys were pretested for face validity, and data were analyzed using descriptive and inferential statistics. We had 164 students (78% response rate) participate in the survey. Diversified was the most preferred technique for future practice by students, and more than half who completed the chiropractic technique survey course reported changing their future practice technique choice as a result. The students surveyed agreed that the chiropractic technique curriculum and their experiences with chiropractic practitioners were the two greatest bases for their current practice technique preference, and that their participation in extracurricular technique clubs and seminars was less influential. Students appear to have the same practice technique preferences as practicing chiropractors. The chiropractic technique curriculum and the students' experience with chiropractic practitioners seem to have the greatest influence on their choice of chiropractic technique for future practice. Extracurricular activities, including technique clubs and seminars, although well attended, showed a lesser influence on students' practice technique preferences.

Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms

PubMed Central

Clouse, Ronald M.; Linchangco, Gregorio V.; Kerr, Alexander M.; Reid, Robert W.; Janies, Daniel A.

2015-01-01

Tissue inhibitors of metalloproteinases (TIMPs) help regulate the extracellular matrix (ECM) in animals, mostly by inhibiting matrix metalloproteinases (MMPs). They are important activators of mutable collagenous tissue (MCT), which have been extensively studied in echinoderms, and the four TIMP copies in humans have been studied for their role in cancer. To understand the evolution of TIMPs, we combined 405 TIMPs from an echinoderm transcriptome dataset built from 41 specimens representing all five classes of echinoderms with variants from protostomes and chordates. We used multiple sequence alignment with various stringencies of alignment quality to cull highly divergent sequences and then conducted phylogenetic analyses using both nucleotide and amino acid sequences. Phylogenetic hypotheses consistently recovered TIMPs as diversifying in the ancestral deuterostome and these early lineages continuing to diversify in echinoderms. The four vertebrate TIMPs diversified from a single copy in the ancestral chordate, all other copies being lost. Consistent with greater MCT needs owing to body wall liquefaction, evisceration, autotomy and reproduction by fission, holothuroids had significantly more TIMPs and higher read depths per contig. Ten cysteine residues, an HPQ binding site and several other residues were conserved in at least 70% of all TIMPs. The conservation of binding sites and the placement of echinoderm TIMPs involved in MCT modification suggest that ECM regulation remains the primary function of TIMP genes, although within this role there are a large number of specialized copies. PMID:27017967

Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards.

PubMed

Hagey, Travis J; Uyeda, Josef C; Crandell, Kristen E; Cheney, Jorn A; Autumn, Kellar; Harmon, Luke J

2017-10-01

Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics. Here, we ask whether convergent evolution of pad-bearing lizards has followed similar evolutionary dynamics, or whether independent origins are accompanied by unique constraints and selective pressures over macroevolutionary time. We hypothesized that geckos and anoles each have unique evolutionary tempos and modes. Using performance data from 59 species, we modified Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to account for repeated origins estimated using Bayesian ancestral state reconstructions. We discovered that adhesive performance in geckos evolved in a fashion consistent with Brownian motion with a trend, whereas anoles evolved in bounded performance space consistent with more constrained evolution (an Ornstein-Uhlenbeck model). Our results suggest that convergent phenotypes can have quite distinctive evolutionary patterns, likely as a result of idiosyncratic constraints or ecological opportunities. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Photonic generation of ultra-wideband doublet pulse using a semiconductor-optical-amplifier based polarization-diversified loop.

PubMed

Luo, Bowen; Dong, Jianji; Yu, Yuan; Yang, Ting; Zhang, Xinliang

2012-06-15

We propose and demonstrate a novel scheme of ultra-wideband (UWB) doublet pulse generation using a semiconductor optical amplifier (SOA) based polarization-diversified loop (PDL) without any assistant light. In our scheme, the incoming gaussian pulse is split into two parts by the PDL, and each of them is intensity modulated by the other due to cross-gain modulation (XGM) in the SOA. Then, both parts are recombined with incoherent summation to form a UWB doublet pulse. Bi-polar UWB doublet pulse generation is demonstrated using an inverted gaussian pulse injection. Moreover, pulse amplitude modulation of UWB doublet is also experimentally demonstrated. Our scheme shows some advantages, such as simple implementation without assistant light and single optical carrier operation with good fiber dispersion tolerance.

Development and Deployment of NASA's Budget Execution Dashboard

NASA Technical Reports Server (NTRS)

Putz, Peter

2009-01-01

This paper discusses the successful implementation of a highly visible company-wide management system and its potential to change managerial and accounting policies, processes and practices in support of organizational goals. Applying the conceptual framework of innovation in organizations, this paper describes the development and deployment process of the NASA Budget Execution Dashboard and the first two fiscal years of its use. It discusses the positive organizational changes triggered by the dashboard, like higher visibility of financial goals and variances between plans and actuals, increased involvement of all management levels in tracking and correcting of plan deviations, establishing comparable data standards across a strongly diversified organization, and enhanced communication between line organizations (NASA Centers) and product organizations (Mission Directorates). The paper also discusses the critical success factors experienced in this project: Strong leadership and division of management roles, rapid and responsive technology development, and frequent communication among stakeholders.

Evolving healthcare delivery paradigms and the optimization of 'value' in anesthesiology.

PubMed

Alem, Navid; Kain, Zeev

2017-04-01

Healthcare worldwide is evolving to yield enhanced care provided at a lowered cost. Patient-centric paradigms that hasten surgical recovery and strengthen collaboration amongst medical professionals are gaining impetus. This review will discuss the changing healthcare landscape and outline its implications on anesthesiology practice. Anesthesiologists must be nimble and versatile as they adapt to healthcare redesign. An increased responsibility for patient outcomes should be embraced by extending the breadth and depth of clinical practice throughout the surgical care continuum. The perioperative surgical home and enhanced recovery after surgery provide paradigms to further integrate expanding clinical opportunities and improved patient outcomes. Investment is needed in perioperative medical education and research efforts to best position anesthesiologists for success both now and in the future. Exemplifying opportunities to demonstrate value-added care, the scope of anesthesiology education and clinical practice should diversify to further integrate perioperative care of surgical patients.

On-farm renewables and resilience: a water-energy-food nexus case study

NASA Astrophysics Data System (ADS)

Todman, Lindsay

2017-04-01

On farm renewables diversify farm income sources (or reduce energy costs) and are thus generally considered to increase farm resilience. Whilst they clearly contribute to renewable energy production targets they can also affect water quality either positively (e.g. use of farmyard manure for anaerobic digestion) or negatively (particularly during construction). Here the interactions within the water-energy-food nexus are examined as they relate to on-farm renewables, where possible quantifying the relative magnitude of feedbacks between the three sectors. Particular focus is given to the dynamics of the system in changing climatic conditions. These analyses reveal a complex picture, with trade-offs between the 'resilience' in different parts of the nexus. This highlights the need for dialogue between stakeholders to identify the key functions in each sector that would be susceptible to particular climatic stresses so that these can be prioritised during planning.

Species richness and morphological diversity of passerine birds

PubMed Central

Ricklefs, Robert E.

2012-01-01

The relationship between species richness and the occupation of niche space can provide insight into the processes that shape patterns of biodiversity. For example, if species interactions constrained coexistence, one might expect tendencies toward even spacing within niche space and positive relationships between diversity and total niche volume. I use morphological diversity of passerine birds as a proxy for diet, foraging maneuvers, and foraging substrates and examine the morphological space occupied by regional and local passerine avifaunas. Although independently diversified regional faunas exhibit convergent morphology, species are clustered rather than evenly distributed, the volume of the morphological space is weakly related to number of species per taxonomic family, and morphological volume is unrelated to number of species within both regional avifaunas and local assemblages. These results seemingly contradict patterns expected when species interactions constrain regional or local diversity, and they suggest a larger role for diversification, extinction, and dispersal limitation in shaping species richness. PMID:22908271

The effects of integrating service learning into computer science: an inter-institutional longitudinal study

NASA Astrophysics Data System (ADS)

Payton, Jamie; Barnes, Tiffany; Buch, Kim; Rorrer, Audrey; Zuo, Huifang

2015-07-01

This study is a follow-up to one published in computer science education in 2010 that reported preliminary results showing a positive impact of service learning on student attitudes associated with success and retention in computer science. That paper described how service learning was incorporated into a computer science course in the context of the Students & Technology in Academia, Research, and Service (STARS) Alliance, an NSF-supported broadening participation in computing initiative that aims to diversify the computer science pipeline through innovative pedagogy and inter-institutional partnerships. The current paper describes how the STARS Alliance has expanded to diverse institutions, all using service learning as a vehicle for broadening participation in computing and enhancing attitudes and behaviors associated with student success. Results supported the STARS model of service learning for enhancing computing efficacy and computing commitment and for providing diverse students with many personal and professional development benefits.

Media Representation of Tongxinglian in China: A Case Study of the People's Daily.

PubMed

Huang, Yixiong

2018-01-01

Over the past few decades, the worldwide lesbian and gay movements have diversified and increased their rights claims. The achievement of gay rights claims in society is the result of an interplay among various social factors and forces. Media is one of most influential players in building homosexual images and promoting mutual understanding. Chinese homosexuals were not treated as criminals or mental illness patients anymore in 1997 and 2001, respectively, after decriminalization and depathologization. Thus this article aims to explore how homosexuals were portrayed in the official media of China, particularly the People's Daily, to illustrate the changing perception of homosexuals in China's political and social spheres. It argues that representation of homosexuals in the People's Daily changed gradually from a negative perception to a more positive one with less discrimination and prejudice as shown by the article's quantitative and qualitative results.

Alternative fossil-based transportation fuels

DOT National Transportation Integrated Search

2008-01-01

"Alternative fuels derived from oil sands and from coal liquefaction can cost-effectively diversify fuel supplies, but neither type significantly reduces U.S. carbon-dioxide emissions enough to arrest long-term climate change".

Somatic diversification of chicken immunoglobulin light chains by point mutations.

PubMed

Parvari, R; Ziv, E; Lantner, F; Heller, D; Schechter, I

1990-04-01

The light-chain locus of chicken has 1 functional V lambda 1 gene, 1 J gene, and 25 pseudo-V lambda-genes (where V = variable and J = joining). A major problem is which somatic mechanisms expand this extremely limited germ-line information to generate many different antibodies. Weill's group [Reynaud, C. A., Anquez, V., Grimal, H. & Weill, J. C. (1987) Cell 48, 379-388] has shown that the pseudo-V lambda-genes diversify the rearranged V lambda 1 by gene conversion. Here we demonstrate that chicken light chains are further diversified by somatic point mutations and by V lambda 1-J flexible joining. Somatic point mutations were identified in the J and 3' noncoding DNA of rearranged light-chain genes of chicken. These regions were analyzed because point mutations in V lambda 1 are obscured by gene conversion; the J and 3' noncoding DNA are presented in one copy per haploid genome and are not subject to gene conversion. In rodents point mutations occur as frequently in the V-J coding regions as in the adjacent flanking DNA. Therefore, we conclude that somatic point mutations diversify the V lambda 1 of chicken. The frequency (0-1%) and distribution of the mutations (decreasing in number with increased distance from the V lambda 1 segment) in chicken were as observed in rodents. Sequence variability at the V lambda 1-J junctions could be attributed to imprecise joining of the V lambda 1 and J genes. The modification by gene conversion of rearranged V lambda 1 genes in the bursa was similar in chicken aged 3 months (9.5%) or 3 weeks (9.1%)--i.e., gene conversion that generates the preimmune repertoire in the bursa seems to level off around 3 weeks of age. This preimmune repertoire can be further diversified by somatic point mutations that presumably lead to the formation of antibodies with increased affinity. A segment with structural features of a matrix association region [(A + T)-rich and four topoisomerase II binding sites] was identified in the middle of the J-C lambda intron (where C = constant).

Study on diversified cultivation orientation and pattern of optoelectronic major undergraduates

NASA Astrophysics Data System (ADS)

Liu, Zhiying

2017-08-01

To improve the research quality preparation for graduate study and looking for job competition ability of undergraduates students, the education orientation objective need to be explicit. Universities need develop undergraduates' cultivation plan according to students' classification. Based on analysis of students export characteristic, there will be corresponding cultivation plan. Keep tracking study during the cultivation plan implantation process, the Curriculum system and related manage documents are revised corresponding to exist problems. There are mainly three kinds of undergraduates' career direction plan for opto-electronic major undergraduates. In addition to the vast majority university graduates opting for direct employment, nearly one third of university students choose to take part in the postgraduate entrance exams and other further education abroad, and also one-tenth choose their own businesses, university chooses are diversified. The exports are further studying as graduates, working and study abroad. Because national defense students are also recruited, the cultivation plan will be diversified to four types. For students, who go to work directly after graduation, the "Excellence engineers plan" is implemented to enhance their practice ability. For students, who will study further as graduate student, the scientific innovation research ability cultivation is paid more attention to make good foundation for their subsequent development. For students, who want to study abroad after graduation, the bilingual teaching method is introduced, and the English environment is built. We asked foreign professionals to give lectures for students. The knowledge range is extending, and the exchange and cooperation chance is provided at the same time. And the cultivation plan is revised during docking with Universities abroad. For national defense students, combat training and other defense theory courses are added to make them familiar with force knowledge. And with national defense students' excellence engineer plan, more army practice chance is provided. The students can integrate into army life much faster. The advantages of national defense students are much more highlighted. The graduates can serve motherland better than before. It is shown from the practice process that the revised cultivation plan is suitable for diversified undergraduates. And the education result is improved in a large amount consequently.

13 CFR 313.5 - Technical assistance.

Code of Federal Regulations, 2010 CFR

2010-01-01

... technical assistance to: (1) Diversify and strengthen the economy in the Impacted Community; (2) Identify...; and (3) Develop or update a Strategic Plan in accordance with § 313.6 to address economic adjustment...

Thermophoretic motion behavior of submicron particles in boundary-layer-separation flow around a droplet.

PubMed

Wang, Ao; Song, Qiang; Ji, Bingqiang; Yao, Qiang

2015-12-01

As a key mechanism of submicron particle capture in wet deposition and wet scrubbing processes, thermophoresis is influenced by the flow and temperature fields. Three-dimensional direct numerical simulations were conducted to quantify the characteristics of the flow and temperature fields around a droplet at three droplet Reynolds numbers (Re) that correspond to three typical boundary-layer-separation flows (steady axisymmetric, steady plane-symmetric, and unsteady plane-symmetric flows). The thermophoretic motion of submicron particles was simulated in these cases. Numerical results show that the motion of submicron particles around the droplet and the deposition distribution exhibit different characteristics under three typical flow forms. The motion patterns of particles are dependent on their initial positions in the upstream and flow forms. The patterns of particle motion and deposition are diversified as Re increases. The particle motion pattern, initial position of captured particles, and capture efficiency change periodically, especially during periodic vortex shedding. The key effects of flow forms on particle motion are the shape and stability of the wake behind the droplet. The drag force of fluid and the thermophoretic force in the wake contribute jointly to the deposition of submicron particles after the boundary-layer separation around a droplet.

Generation, estimation, utilization, availability and compatibility aspects of geodetic and meteorological data

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

Luetzow, H.B.v.

1983-08-01

Following an introduction, the paper discusses in section 2 the collection or generation of final geodetic data from conventional surveys, satellite observations, satellite altimetry, the Global Positioning System, and moving base gravity gradiometers. Section 3 covers data utilization and accuracy aspects including gravity programmed inertial positioning and subterraneous mass detection. Section 4 addresses the usefulness and limitation of the collocation method of physical geodesy. Section 5 is concerned with the computation of classical climatological data. In section 6, meteorological data assimilation is considered. Section 7 deals with correlated aspects of initial data generation with emphasis on initial wind field determination,more » parameterized and classical hydrostatic prediction models, non-hydrostatic prediction, computational networks, and computer capacity. The paper concludes that geodetic and meteorological data are expected to become increasingly more diversified and voluminous both regionally and globally, that its general availability will be more or less restricted for some time to come, that its quality and quantity are subject to change, and that meteorological data generation, accuracy and density have to be considered in conjunction with advanced as well as cost-effective numerical weather prediction models and associated computational efforts.« less

Hospital diversification strategy.

PubMed

Eastaugh, Steven R

2014-01-01

To determine the impact of health system restructuring on the levels of hospital diversification and operating ratio this article analyzed 94 teaching hospitals and 94 community hospitals during the period 2008-2013. The 47 teaching hospitals are matched with 47 other teaching hospitals experiencing the same financial market position in 2008, but with different levels of preference for risk and diversification in their strategic plan. Covariates in the analysis included levels of hospital competition and the degree of local government planning (for example, highly regulated in New York, in contrast to Texas). Moreover, 47 nonteaching community hospitals are matched with 47 other community hospitals in 2008, having varying manager preferences for service-line diversification and risk. Diversification and operating ratio are modeled in a two-stage least squares (TSLS) framework as jointly dependent. Institutional diversification is found to yield better financial position, and the better operating profits provide the firm the wherewithal to diversify. Some services are in a growth phase, like bariatric weight-loss surgery and sleep disorder clinics. Hospital managers' preferences for risk/return potential were considered. An institution life cycle hypothesis is advanced to explain hospital behavior: boom and bust, diversification, and divestiture, occasionally leading to closure or merger.

Diversification and enrichment of clinical biomaterials inspired by Darwinian evolution.

PubMed

Green, D W; Watson, G S; Watson, J A; Lee, D-J; Lee, J-M; Jung, H-S

2016-09-15

Regenerative medicine and biomaterials design are driven by biomimicry. There is the essential requirement to emulate human cell, tissue, organ and physiological complexity to ensure long-lasting clinical success. Biomimicry projects for biomaterials innovation can be re-invigorated with evolutionary insights and perspectives, since Darwinian evolution is the original dynamic process for biological organisation and complexity. Many existing human inspired regenerative biomaterials (defined as a nature generated, nature derived and nature mimicking structure, produced within a biological system, which can deputise for, or replace human tissues for which it closely matches) are without important elements of biological complexity such as, hierarchy and autonomous actions. It is possible to engineer these essential elements into clinical biomaterials via bioinspired implementation of concepts, processes and mechanisms played out during Darwinian evolution; mechanisms such as, directed, computational, accelerated evolutions and artificial selection contrived in the laboratory. These dynamos for innovation can be used during biomaterials fabrication, but also to choose optimal designs in the regeneration process. Further evolutionary information can help at the design stage; gleaned from the historical evolution of material adaptations compared across phylogenies to changes in their environment and habitats. Taken together, harnessing evolutionary mechanisms and evolutionary pathways, leading to ideal adaptations, will eventually provide a new class of Darwinian and evolutionary biomaterials. This will provide bioengineers with a more diversified and more efficient innovation tool for biomaterial design, synthesis and function than currently achieved with synthetic materials chemistry programmes and rational based materials design approach, which require reasoned logic. It will also inject further creativity, diversity and richness into the biomedical technologies that we make. All of which are based on biological principles. Such evolution-inspired biomaterials have the potential to generate innovative solutions, which match with existing bioengineering problems, in vital areas of clinical materials translation that include tissue engineering, gene delivery, drug delivery, immunity modulation, and scar-less wound healing. Evolution by natural selection is a powerful generator of innovations in molecular, materials and structures. Man has influenced evolution for thousands of years, to create new breeds of farm animals and crop plants, but now molecular and materials can be molded in the same way. Biological molecules and simple structures can be evolved, literally in the laboratory. Furthermore, they are re-designed via lessons learnt from evolutionary history. Through a 3-step process to (1) create variants in material building blocks, (2) screen the variants with beneficial traits/properties and (3) select and support their self-assembly into usable materials, improvements in design and performance can emerge. By introducing biological molecules and small organisms into this process, it is possible to make increasingly diversified, sophisticated and clinically relevant materials for multiple roles in biomedicine. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection.

PubMed

Kjærner-Semb, Erik; Ayllon, Fernando; Furmanek, Tomasz; Wennevik, Vidar; Dahle, Geir; Niemelä, Eero; Ozerov, Mikhail; Vähä, Juha-Pekka; Glover, Kevin A; Rubin, Carl J; Wargelius, Anna; Edvardsen, Rolf B

2016-08-11

Populations of Atlantic salmon display highly significant genetic differences with unresolved molecular basis. These differences may result from separate postglacial colonization patterns, diversifying natural selection and adaptation, or a combination. Adaptation could be influenced or even facilitated by the recent whole genome duplication in the salmonid lineage which resulted in a partly tetraploid species with duplicated genes and regions. In order to elucidate the genes and genomic regions underlying the genetic differences, we conducted a genome wide association study using whole genome resequencing data from eight populations from Northern and Southern Norway. From a total of ~4.5 million sequencing-derived SNPs, more than 10 % showed significant differentiation between populations from these two regions and ten selective sweeps on chromosomes 5, 10, 11, 13-15, 21, 24 and 25 were identified. These comprised 59 genes, of which 15 had one or more differentiated missense mutation. Our analysis showed that most sweeps have paralogous regions in the partially tetraploid genome, each lacking the high number of significant SNPs found in the sweeps. The most significant sweep was found on Chr 25 and carried several missense mutations in the antiviral mx genes, suggesting that these populations have experienced differing viral pressures. Interestingly the second most significant sweep, found on Chr 5, contains two genes involved in the NF-KB pathway (nkap and nkrf), which is also a known pathogen target that controls a large number of processes in animals. Our results show that natural selection acting on immune related genes has contributed to genetic divergence between salmon populations in Norway. The differences between populations may have been facilitated by the plasticity of the salmon genome. The observed signatures of selection in duplicated genomic regions suggest that the recently duplicated genome has provided raw material for evolutionary adaptation.

Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes.

PubMed

Pritchard, Victoria L; Mäkinen, Hannu; Vähä, Juha-Pekka; Erkinaro, Jaakko; Orell, Panu; Primmer, Craig R

2018-06-01

Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study, we used a dense SNP array to identify candidate loci potentially underlying fine-scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene-environment association and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at subdrainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis and immune defence. These included the large-effect age-at-maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations and that is also a candidate for local selection over the global range of Atlantic salmon. This region colocalized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and covaries with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research. © 2018 John Wiley & Sons Ltd.

Rational selection and engineering of exogenous principal sigma factor (σHrdB) to increase teicoplanin production in an industrial strain of Actinoplanes teichomyceticus

PubMed Central

2014-01-01

Background Transcriptional engineering has presented a strong ability of phenotypic improvement in microorganisms. However, it could not be directly applied to Actinoplanes teichomyceticus L-27 because of the paucity of endogenous transcription factors in the strain. In this study, exogenous transcription factors were rationally selected and transcriptional engineering was carried out to increase the productivity of teicoplanin in L-27. Results It was illuminated that the σHrdB molecules shared strong similarity of amino acid sequences among some genera of actinomycetes. Combining this advantage with the ability of transcriptional engineering, exogenous sigma factor σHrdB molecules were rationally selected and engineered to improve L-27. hrdB genes from Actinoplanes missouriensis 431, Micromonospora aurantiaca ATCC 27029 and Salinispora arenicola CNS-205 were selected based on molecular evolutionary analysis. Random mutagenesis, DNA shuffling and point mutation were subsequently performed to generate diversified mutants. A recombinant was identified through screening program, yielding 5.3 mg/ml of teicoplanin, over 2-fold compared to that of L-27. More significantly, the engineered strain presented a good performance in 500-l pilot scale fermentation, which meant its valuable potential application in industry. Conclusions Through rational selection and engineering of exogenous transcriptional factor, we have extended the application of transcriptional engineering. To our knowledge, it is the first time to focus on the related issue. In addition, possessing the advantage of efficient metabolic perturbation in transcription level, this strategy could be useful in analyzing metabolic and physiological mechanisms of strains, especially those with the only information on taxonomy. PMID:24428890

Glacial history affected phenotypic differentiation in the alpine plant, Campanula thyrsoides.

PubMed

Scheepens, J F; Frei, Eva S; Stöcklin, Jürg

2013-01-01

Numerous widespread Alpine plant species show molecular differentiation among populations from distinct regions. This has been explained as the result of genetic drift during glacial survival in isolated refugia along the border of the European Alps. Since genetic drift may affect molecular markers and phenotypic traits alike, we asked whether phenotypic differentiation mirrors molecular patterns among Alpine plant populations from different regions. Phenotypic traits can be under selection, so we additionally investigated whether part of the phenotypic differentiation can be explained by past selection and/or current adaptation. Using the monocarpic Campanula thyrsoides as our study species, a common garden experiment with plants from 21 populations from four phylogeographic groups located in regions across the Alps and the Jura Mountains was performed to test for differentiation in morphological and phenological traits. Past selection was investigated by comparing phenotypic differentiation among and within regions with molecular differentiation among and within regions. The common garden results indicated regional differentiation among populations for all investigated phenotypic traits, particularly in phenology. Delayed flowering in plants from the South-eastern Alps suggested adaptation to long sub-mediterranean summers and contrasted with earlier flowering of plants experiencing shorter growing seasons in regions with higher elevation to the West. Comparisons between molecular and phenotypic differentiation revealed diversifying selection among regions in height and biomass, which is consistent with adaptation to environmental conditions in glacial refugia. Within regions, past selection acted against strong diversification for most phenotypic traits, causing restricted postglacial adaptation. Evidence consistent with post-glacial adaptation was also given by negative correlation coefficients between several phenotypic traits and elevation of the population's origin. In conclusion, our study suggests that, irrespective of adaptation of plants to their current environment, glacial history can have a strong and long-lasting influence on the phenotypic evolution of Alpine plants.

Selection and Trans-Species Polymorphism of Major Histocompatibility Complex Class II Genes in the Order Crocodylia

PubMed Central

Jaratlerdsiri, Weerachai; Isberg, Sally R.; Higgins, Damien P.; Miles, Lee G.; Gongora, Jaime

2014-01-01

Major Histocompatibility Complex (MHC) class II genes encode for molecules that aid in the presentation of antigens to helper T cells. MHC characterisation within and between major vertebrate taxa has shed light on the evolutionary mechanisms shaping the diversity within this genomic region, though little characterisation has been performed within the Order Crocodylia. Here we investigate the extent and effect of selective pressures and trans-species polymorphism on MHC class II α and β evolution among 20 extant species of Crocodylia. Selection detection analyses showed that diversifying selection influenced MHC class II β diversity, whilst diversity within MHC class II α is the result of strong purifying selection. Comparison of translated sequences between species revealed the presence of twelve trans-species polymorphisms, some of which appear to be specific to the genera Crocodylus and Caiman. Phylogenetic reconstruction clustered MHC class II α sequences into two major clades representing the families Crocodilidae and Alligatoridae. However, no further subdivision within these clades was evident and, based on the observation that most MHC class II α sequences shared the same trans-species polymorphisms, it is possible that they correspond to the same gene lineage across species. In contrast, phylogenetic analyses of MHC class II β sequences showed a mixture of subclades containing sequences from Crocodilidae and/or Alligatoridae, illustrating orthologous relationships among those genes. Interestingly, two of the subclades containing sequences from both Crocodilidae and Alligatoridae shared specific trans-species polymorphisms, suggesting that they may belong to ancient lineages pre-dating the divergence of these two families from the common ancestor 85–90 million years ago. The results presented herein provide an immunogenetic resource that may be used to further assess MHC diversity and functionality in Crocodylia. PMID:24503938

Point of View: Diversity in STEM: Doctor, Heal Thyself

ERIC Educational Resources Information Center

Nilsson, Melanie R.

2017-01-01

This column shares reflections or thoughtful opinions on issues of broad interest to the community. This month's issue calls on STEM professionals to take three simple steps toward diversifying the STEM workforce.

18 CFR 1300.107 - Financial interest exemptions.

Code of Federal Regulations, 2011 CFR

2011-04-01

...; (c) Shares or investments in a well-diversified money market or mutual fund; (d) Vested interests in a pension fund arising out of former employment and to which no further contributions are being made...

Diversifying Food Systems in the Pursuit of Sustainable Food Production and Healthy Diets.

PubMed

Dwivedi, Sangam L; Lammerts van Bueren, Edith T; Ceccarelli, Salvatore; Grando, Stefania; Upadhyaya, Hari D; Ortiz, Rodomiro

2017-10-01

Increasing demand for nutritious, safe, and healthy food because of a growing population, and the pledge to maintain biodiversity and other resources, pose a major challenge to agriculture that is already threatened by a changing climate. Diverse and healthy diets, largely based on plant-derived food, may reduce diet-related illnesses. Investments in plant sciences will be necessary to design diverse cropping systems balancing productivity, sustainability, and nutritional quality. Cultivar diversity and nutritional quality are crucial. We call for better cooperation between food and medical scientists, food sector industries, breeders, and farmers to develop diversified and nutritious cultivars that reduce soil degradation and dependence on external inputs, such as fertilizers and pesticides, and to increase adaptation to climate change and resistance to emerging pests. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

MIX and match: mobile T6SS MIX-effectors enhance bacterial fitness

PubMed Central

Salomon, Dor

2016-01-01

ABSTRACT Protein secretion systems that mediate interbacterial competition secret a wide repertoire of antibacterial toxins. A major player in these competitions is the newly discovered bacterial type VI secretion system (T6SS). We recently found that a subset of polymorphic MIX-effectors, which are a widespread class of effectors secreted by T6SSs, are horizontally shared between marine bacteria and are used to diversify their T6SS effector repertoires, thus enhancing their environmental fitness. In this commentary, I expand on the ideas that were introduced in the previous report, and further speculate on the possible mobility of other MIX-effectors. In addition, I discuss the possible role of horizontal gene transfer in the dissemination of MIX-effectors through bacterial genomes, as well as its possible role in diversifying the T6SS effector repertoire. PMID:27066305

The Origin and Diversification of Birds.

PubMed

Brusatte, Stephen L; O'Connor, Jingmai K; Jarvis, Erich D

2015-10-05

Birds are one of the most recognizable and diverse groups of modern vertebrates. Over the past two decades, a wealth of new fossil discoveries and phylogenetic and macroevolutionary studies has transformed our understanding of how birds originated and became so successful. Birds evolved from theropod dinosaurs during the Jurassic (around 165-150 million years ago) and their classic small, lightweight, feathered, and winged body plan was pieced together gradually over tens of millions of years of evolution rather than in one burst of innovation. Early birds diversified throughout the Jurassic and Cretaceous, becoming capable fliers with supercharged growth rates, but were decimated at the end-Cretaceous extinction alongside their close dinosaurian relatives. After the mass extinction, modern birds (members of the avian crown group) explosively diversified, culminating in more than 10,000 species distributed worldwide today. Copyright © 2015 Elsevier Ltd. All rights reserved.

Intensification through diversified resource use: the human ecology of a successful agricultural industry in Indonesian Borneo

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

Vondal, P.J.

1987-03-01

The success of an agricultural industry in commercial duck egg production in the swamplands of South Kalimantan (Borneo) is examined through the utilization of a human ecology framework. Seasonality of resource availability and human population growth are identified as two major constraints to production faced by farmers. Population increases in the urban sectors of southeastern Borneo also present economic opportunities for farmers because of the growing demand for poultry products. Farmers have responded by developing an intensification strategy in egg production based on the use of diversified resources for duck feed. The long-term consequences of these and other innovations inmore » duck farming are discussed; and diversity-stability theory is examined for its applicability to this case of agricultural development and for rural development theory and practice.« less

EVOLUTION. Fruit flies diversify their offspring in response to parasite infection.

PubMed

Singh, Nadia D; Criscoe, Dallas R; Skolfield, Shelly; Kohl, Kathryn P; Keebaugh, Erin S; Schlenke, Todd A

2015-08-14

The evolution of sexual reproduction is often explained by Red Queen dynamics: Organisms must continually evolve to maintain fitness relative to interacting organisms, such as parasites. Recombination accompanies sexual reproduction and helps diversify an organism's offspring, so that parasites cannot exploit static host genotypes. Here we show that Drosophila melanogaster plastically increases the production of recombinant offspring after infection. The response is consistent across genetic backgrounds, developmental stages, and parasite types but is not induced after sterile wounding. Furthermore, the response appears to be driven by transmission distortion rather than increased recombination. Our study extends the Red Queen model to include the increased production of recombinant offspring and uncovers a remarkable ability of hosts to actively distort their recombination fraction in rapid response to environmental cues. Copyright © 2015, American Association for the Advancement of Science.

Transgenes sustain epigeal insect biodiversity in diversified vegetable farm systems.

PubMed

Leslie, T W; Hoheisel, G A; Biddinger, D J; Rohr, J R; Fleischer, S J

2007-02-01

Many ecological studies have focused on the effects of transgenes in field crops, but few have considered multiple transgenes in diversified vegetable systems. We compared the epigeal, or soil surface-dwelling, communities of Coleoptera and Formicidae between transgenic and isoline vegetable systems consisting of sweet corn, potato, and acorn squash, with transgenic cultivars expressing Cry1(A)b, Cry3, or viral coat proteins. Vegetables were grown in replicated split plots over 2 yr with integrated pest management (IPM) standards defining insecticide use patterns. More than 77.6% of 11,925 insects from 1,512 pitfall traps were identified to species, and activity density was used to compare dominance distribution, species richness, and community composition. Measures of epigeal biodiversity were always equal in transgenic vegetables, which required fewer insecticide applications than their near isolines. There were no differences in species richness between transgenic and isoline treatments at the farm system and individual crop level. Dominance distributions were also similar between transgenic and isoline farming systems. Crop type, and not genotype, had a significant influence on Carabidae and Staphylinidae community composition in the first year, but there were no treatment effects in the second year, possibly because of homogenizing effects of crop rotations. Communities were more influenced by crop type, and possibly crop rotation, than by genotype. The heterogeneity of crops and rotations in diversified vegetable farms seems to aid in preserving epigeal biodiversity, which may be supplemented by reductions in insecticide use associated with transgenic cultivars.

Design and implementation of a telecare information platform.

PubMed

Li, Shing-Han; Wang, Ching-Yao; Lu, Wen-Hui; Lin, Yuan-Yuan; Yen, David C

2012-06-01

For the aging population and for people with dominant chronic diseases, countries all over the world are promoting an "Aging in Place" program with its primary focus on the implementation of telecare. In 2009, Taiwan held a "Health Care Value-Added Platinum Program" with the goal of promoting the development of "Telecare" services by integrating medical treatment, healthcare, information communication, medical equipment and materials and by linking related cross-discipline professions to enable people to familiarize themselves with preventive healthcare services offered in their household and community environments. In addition, this program can be utilized to effectively provide diversified healthcare service benefitting society as a whole. This study aims to promote a diversified telecare service network in Taiwan's household and community environments, establish telecare information platforms, build an internal network of various healthcare service modes, standardize externally interfacing telecare information networks, effectively utilize related healthcare service resources, and complete reasonable service resource links forming an up-to-date health information exchange network. To this end, the telecare information platform based on service oriented architecture (SOA) is designed to promote an open telecare information interface and sharing environment to assist in such tasks as developing healthcare information exchange services, integrating service resources among various different healthcare service modes, accessing externally complex community affairs information, supporting remote physiological information transmissions, and providing diversified remote innovative services. Information system architecture and system monitoring indices of various types of healthcare service modes are used for system integrations for future development and/or expansions.

DNA barcoding of Rhodiola (crassulaceae): a case study on a group of recently diversified medicinal plants from the Qinghai-Tibetan Plateau.

PubMed

Zhang, Jian-Qiang; Meng, Shi-Yong; Wen, Jun; Rao, Guang-Yuan

2015-01-01

DNA barcoding, the identification of species using one or a few short standardized DNA sequences, is an important complement to traditional taxonomy. However, there are particular challenges for barcoding plants, especially for species with complex evolutionary histories. We herein evaluated the utility of five candidate sequences - rbcL, matK, trnH-psbA, trnL-F and the internal transcribed spacer (ITS) - for barcoding Rhodiola species, a group of high-altitude plants frequently used as adaptogens, hemostatics and tonics in traditional Tibetan medicine. Rhodiola was suggested to have diversified rapidly recently. The genus is thus a good model for testing DNA barcoding strategies for recently diversified medicinal plants. This study analyzed 189 accessions, representing 47 of the 55 recognized Rhodiola species in the Flora of China treatment. Based on intraspecific and interspecific divergence and degree of monophyly statistics, ITS was the best single-locus barcode, resolving 66% of the Rhodiola species. The core combination rbcL+matK resolved only 40.4% of them. Unsurprisingly, the combined use of all five loci provided the highest discrimination power, resolving 80.9% of the species. However, this is weaker than the discrimination power generally reported in barcoding studies of other plant taxa. The observed complications may be due to the recent diversification, incomplete lineage sorting and reticulate evolution of the genus. These processes are common features of numerous plant groups in the high-altitude regions of the Qinghai-Tibetan Plateau.

Learning to rank diversified results for biomedical information retrieval from multiple features.

PubMed

Wu, Jiajin; Huang, Jimmy; Ye, Zheng

2014-01-01

Different from traditional information retrieval (IR), promoting diversity in IR takes consideration of relationship between documents in order to promote novelty and reduce redundancy thus to provide diversified results to satisfy various user intents. Diversity IR in biomedical domain is especially important as biologists sometimes want diversified results pertinent to their query. A combined learning-to-rank (LTR) framework is learned through a general ranking model (gLTR) and a diversity-biased model. The former is learned from general ranking features by a conventional learning-to-rank approach; the latter is constructed with diversity-indicating features added, which are extracted based on the retrieved passages' topics detected using Wikipedia and ranking order produced by the general learning-to-rank model; final ranking results are given by combination of both models. Compared with baselines BM25 and DirKL on 2006 and 2007 collections, the gLTR has 0.2292 (+16.23% and +44.1% improvement over BM25 and DirKL respectively) and 0.1873 (+15.78% and +39.0% improvement over BM25 and DirKL respectively) in terms of aspect level of mean average precision (Aspect MAP). The LTR method outperforms gLTR on 2006 and 2007 collections with 4.7% and 2.4% improvement in terms of Aspect MAP. The learning-to-rank method is an efficient way for biomedical information retrieval and the diversity-biased features are beneficial for promoting diversity in ranking results.

Selection of full-length IgGs by tandem display on filamentous phage particles and Escherichia coli fluorescence-activated cell sorting screening.

PubMed

Mazor, Yariv; Van Blarcom, Thomas; Carroll, Sean; Georgiou, George

2010-05-01

Phage display of antibody libraries is a powerful tool for antibody discovery and evolution. Recombinant antibodies have been displayed on phage particles as scFvs or Fabs, and more recently as bivalent F(ab')(2). We recently developed a technology (E-clonal) for screening of combinatorial IgG libraries using bacterial periplasmic display and selection by fluorescence-activated cell sorting (FACS) [Mazor Y et al. (2007) Nat Biotechnol 25, 563-565]. Although, as a single-cell analysis technique, FACS is very powerful, especially for the isolation of high-affinity binders, even with state of the art instrumentation the screening of libraries with diversity > 10(8) is technically challenging. We report here a system that takes advantage of display of full-length IgGs on filamentous phage particles as a prescreening step to reduce library size and enable subsequent rounds of FACS screening in Escherichia coli. For the establishment of an IgG phage display system, we utilized phagemid-encoded IgG with the fUSE5-ZZ phage as a helper phage. These phage particles display the Fc-binding ZZ protein on all copies of the phage p3 coat protein, and are exploited as both helper phages and anchoring surfaces for the soluble IgG. We demonstrate that tandem phage selection followed by FACS allows the selection of a highly diversified profile of binders from antibody libraries without undersampling, and at the same time capitalizes on the advantages of FACS for real-time monitoring and optimization of the screening process.

Influences of a yoga intervention on the postural skills of the Italian short track speed skating team

PubMed Central

Brunelle, Jean-François; Blais-Coutu, Sébastien; Gouadec, Kenan; Bédard, Éric; Fait, Philippe

2015-01-01

Introduction In preparation for a short track speed skating season, eight men and seven women were given yoga sessions during an 8-week high volume training cycle. The sessions were planned according to the postural aspects specific to short track speed skating technical requirements. Three specific goals were selected for the intervention: 1) to observe whether the practice of yoga as postural training could improve the efficiency and the athlete’s repertoire along the muscular synergies solicited in the short track speed skating specific technique; 2) to enhance and diversify the motor time-on-task of athletes without changing the prescription of other training stimulus; and 3) to lower the risk of injury during periods with high volumes of training. Methods A total of 36 sessions of yoga were given. Three postural tests were administered before and after the intervention with 14 angles analyzed. Non-parametric Wilcoxon test was used to compare angles’ variations. Results The 36 yoga sessions totalized 986 minutes of motor time-on-task, registering a proportion of 30% of the global motor time-on-task of the training cycle. Improvements were found in eleven of the 14 angles measured when comparing pre- and post-postural tests (P-value from 0.01 to 0.005). During the 8 weeks, excepting traumatic injuries due to short track speed skating accidents, no skaters suffered injuries linked to the high volume of training. Following the intervention, coaches noticed, following their on-ice feedbacks, an adjustment in the efficiency of the skating technique, in particular regarding hip dissociation. Conclusion These results suggest that yoga could be inserted into out-of-season training cycles, even in a high volume training cycle. Planned with the decision training tools, it allows athletes to diversify their motor time-on-task by integrating a new functional range of generic movements with the solicitation of neuromuscular synergies related to the specificity of their sport. PMID:25709511

Are efforts to attract graduate applicants to UK medical schools effective in increasing the participation of under-represented socioeconomic groups? A national cohort study.

PubMed

Kumwenda, Ben; Cleland, Jennifer; Greatrix, Rachel; MacKenzie, Rhoda Katharine; Prescott, Gordon

2018-02-14

Attracting graduates was recommended as a means of diversifying the UK medical student population. Graduates now make up nearly a quarter of the total medical student population. Research to date has focused on comparing the sociodemographic characteristics of applicants to and/or students on traditional and graduate entry programmes (GEMs), yet GEMs account for only 40% of the graduate medical student population. Thus, we aimed to compare the sociodemographic characteristic and outcomes of graduates and non-graduate applicants across a range of programmes. This was an observational study of 117 214 applicants to medicine who took the UK Clinical Aptitude Test (UKCAT) from 2006 to 2014 and who applied to medical school through Universities and Colleges Admissions Service (UCAS). We included applicant demographics, UKCAT total score and offers in our analysis. Applicants were assigned as graduates or non-graduates on the basis of their highest qualification. Multiple logistic regression was used to predict the odds of receiving an offer, after adjusting for confounders. Irrespective of graduate or non-graduate status, most applicants were from the highest socioeconomic groups and were from a white ethnic background. Receiving an offer was related to gender and ethnicity in both graduates and non-graduates. After adjusting for UKCAT score, the OR of an offer for graduates versus non-graduates was approximately 0.5 (OR=0.48, 95% CI 0.46 to 0.49). Our findings indicate that the aim of diversifying the medical student population on socioeconomic grounds by attracting graduates has been only marginally successful. Graduate applicants from widening access backgrounds are less likely than others to be offered a place at medical school. Different approaches must be considered if medicine is to attract and select more socially diverse applicants. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Are efforts to attract graduate applicants to UK medical schools effective in increasing the participation of under-represented socioeconomic groups? A national cohort study

PubMed Central

Cleland, Jennifer; Greatrix, Rachel; Prescott, Gordon

2018-01-01

Introduction Attracting graduates was recommended as a means of diversifying the UK medical student population. Graduates now make up nearly a quarter of the total medical student population. Research to date has focused on comparing the sociodemographic characteristics of applicants to and/or students on traditional and graduate entry programmes (GEMs), yet GEMs account for only 40% of the graduate medical student population. Thus, we aimed to compare the sociodemographic characteristic and outcomes of graduates and non-graduate applicants across a range of programmes. Methods This was an observational study of 117 214 applicants to medicine who took the UK Clinical Aptitude Test (UKCAT) from 2006 to 2014 and who applied to medical school through Universities and Colleges Admissions Service (UCAS). We included applicant demographics, UKCAT total score and offers in our analysis. Applicants were assigned as graduates or non-graduates on the basis of their highest qualification. Multiple logistic regression was used to predict the odds of receiving an offer, after adjusting for confounders. Results Irrespective of graduate or non-graduate status, most applicants were from the highest socioeconomic groups and were from a white ethnic background. Receiving an offer was related to gender and ethnicity in both graduates and non-graduates. After adjusting for UKCAT score, the OR of an offer for graduates versus non-graduates was approximately 0.5 (OR=0.48, 95% CI 0.46 to 0.49). Discussion Our findings indicate that the aim of diversifying the medical student population on socioeconomic grounds by attracting graduates has been only marginally successful. Graduate applicants from widening access backgrounds are less likely than others to be offered a place at medical school. Different approaches must be considered if medicine is to attract and select more socially diverse applicants. PMID:29444782

A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation

PubMed Central

2011-01-01

Background One member of the W family of human endogenous retroviruses (HERV) appears to have been functionally adopted by the human host. Nevertheless, a highly diversified and regulated transcription from a range of HERV-W elements has been observed in human tissues and cells. Aberrant expression of members of this family has also been associated with human disease such as multiple sclerosis (MS) and schizophrenia. It is not known whether this broad expression of HERV-W elements represents transcriptional leakage or specific transcription initiated from the retroviral promoter in the long terminal repeat (LTR) region. Therefore, potential influences of genomic context, structure and orientation on the expression levels of individual HERV-W elements in normal human tissues were systematically investigated. Results Whereas intronic HERV-W elements with a pseudogene structure exhibited a strong anti-sense orientation bias, intronic elements with a proviral structure and solo LTRs did not. Although a highly variable expression across tissues and elements was observed, systematic effects of context, structure and orientation were also observed. Elements located in intronic regions appeared to be expressed at higher levels than elements located in intergenic regions. Intronic elements with proviral structures were expressed at higher levels than those elements bearing hallmarks of processed pseudogenes or solo LTRs. Relative to their corresponding genes, intronic elements integrated on the sense strand appeared to be transcribed at higher levels than those integrated on the anti-sense strand. Moreover, the expression of proviral elements appeared to be independent from that of their corresponding genes. Conclusions Intronic HERV-W provirus integrations on the sense strand appear to have elicited a weaker negative selection than pseudogene integrations of transcripts from such elements. Our current findings suggest that the previously observed diversified and tissue-specific expression of elements in the HERV-W family is the result of both directed transcription (involving both the LTR and internal sequence) and leaky transcription of HERV-W elements in normal human tissues. PMID:21226900

How immediate and significant is the outcome of training on diversified diets, hygiene and food safety? An effort to mitigate child undernutrition in rural Malawi.

PubMed

Seetha, Anitha; Tsusaka, Takuji W; Munthali, Timalizge W; Musukwa, Maggie; Mwangwela, Agnes; Kalumikiza, Zione; Manani, Tinna; Kachulu, Lizzie; Kumwenda, Nelson; Musoke, Mike; Okori, Patrick

2018-04-01

The present study examined the impacts of training on nutrition, hygiene and food safety designed by the Nutrition Working Group, Child Survival Collaborations and Resources Group (CORE). Adapted from the 21d Positive Deviance/Hearth model, mothers were trained on the subjects of appropriate complementary feeding, water, sanitation and hygiene (WASH) practices, and aflatoxin contamination in food. To assess the impacts on child undernutrition, a randomised controlled trial was implemented on a sample of 179 mothers and their children (<2 years old) in two districts of Malawi, namely Mzimba and Balaka. Settings A 21d intensive learning-by-doing process using the positive deviance approach. Malawian children and mothers. Difference-in-difference panel regression analysis revealed that the impacts of the comprehensive training were positive and statistically significant on the Z-scores for wasting and underweight, where the effects increased constantly over time within the 21d time frame. As for stunting, the coefficients were not statistically significant during the 21d programme, although the level of significance started increasing in 2 weeks, indicating that stunting should also be alleviated in a slightly longer time horizon. The study clearly suggests that comprehensive training immediately guides mothers into improved dietary and hygiene practices, and that improved practices take immediate and progressive effects in ameliorating children's undernutrition.

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes.

PubMed

Studer, Romain A; Penel, Simon; Duret, Laurent; Robinson-Rechavi, Marc

2008-09-01

A stringent branch-site codon model was used to detect positive selection in vertebrate evolution. We show that the test is robust to the large evolutionary distances involved. Positive selection was detected in 77% of 884 genes studied. Most positive selection concerns a few sites on a single branch of the phylogenetic tree: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome duplication or the two rounds at the origin of vertebrates. Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.

Case-based reasoning using electronic health records efficiently identifies eligible patients for clinical trials

PubMed Central

Miotto, Riccardo

2015-01-01

Objective To develop a cost-effective, case-based reasoning framework for clinical research eligibility screening by only reusing the electronic health records (EHRs) of minimal enrolled participants to represent the target patient for each trial under consideration. Materials and Methods The EHR data—specifically diagnosis, medications, laboratory results, and clinical notes—of known clinical trial participants were aggregated to profile the “target patient” for a trial, which was used to discover new eligible patients for that trial. The EHR data of unseen patients were matched to this “target patient” to determine their relevance to the trial; the higher the relevance, the more likely the patient was eligible. Relevance scores were a weighted linear combination of cosine similarities computed over individual EHR data types. For evaluation, we identified 262 participants of 13 diversified clinical trials conducted at Columbia University as our gold standard. We ran a 2-fold cross validation with half of the participants used for training and the other half used for testing along with other 30 000 patients selected at random from our clinical database. We performed binary classification and ranking experiments. Results The overall area under the ROC curve for classification was 0.95, enabling the highlight of eligible patients with good precision. Ranking showed satisfactory results especially at the top of the recommended list, with each trial having at least one eligible patient in the top five positions. Conclusions This relevance-based method can potentially be used to identify eligible patients for clinical trials by processing patient EHR data alone without parsing free-text eligibility criteria, and shows promise of efficient “case-based reasoning” modeled only on minimal trial participants. PMID:25769682

Immune genes and divergent antimicrobial peptides in flies of the subgenus Drosophila.

PubMed

Hanson, Mark A; Hamilton, Phineas T; Perlman, Steve J

2016-10-24

Drosophila is an important model for studying the evolution of animal immunity, due to the powerful genetic tools developed for D. melanogaster. However, Drosophila is an incredibly speciose lineage with a wide range of ecologies, natural histories, and diverse natural enemies. Surprisingly little functional work has been done on immune systems of species other than D. melanogaster. In this study, we examine the evolution of immune genes in the speciose subgenus Drosophila, which diverged from the subgenus Sophophora (that includes D. melanogaster) approximately 25-40 Mya. We focus on D. neotestacea, a woodland species used to study interactions between insects and parasitic nematodes, and combine recent transcriptomic data with infection experiments to elucidate aspects of host immunity. We found that the vast majority of genes involved in the D. melanogaster immune response are conserved in D. neotestacea, with a few interesting exceptions, particularly in antimicrobial peptides (AMPs); until recently, AMPs were not thought to evolve rapidly in Drosophila. Unexpectedly, we found a distinct diptericin in subgenus Drosophila flies that appears to have evolved under diversifying (positive) selection. We also describe the presence of the AMP drosocin, which was previously thought to be restricted to the subgenus Sophophora, in the subgenus Drosophila. We challenged two subgenus Drosophila species, D. neotestacea and D. virilis with bacterial and fungal pathogens and quantified AMP expression. While diptericin in D. virilis was induced by exposure to gram-negative bacteria, it was not induced in D. neotestacea, showing that conservation of immune genes does not necessarily imply conservation of the realized immune response. Our study lends support to the idea that invertebrate AMPs evolve rapidly, and that Drosophila harbor a diverse repertoire of AMPs with potentially important functional consequences.

Crop Fertilization Impacts Epidemics and Optimal Latent Period of Biotrophic Fungal Pathogens.

PubMed

Précigout, Pierre-Antoine; Claessen, David; Robert, Corinne

2017-10-01

Crop pathogens are known to rapidly adapt to agricultural practices. Although cultivar resistance breakdown and resistance to pesticides have been broadly studied, little is known about the adaptation of crop pathogens to fertilization regimes and no epidemiological model has addressed that question. However, this is a critical issue for developing sustainable low-input agriculture. In this article, we use a model of life history evolution of biotrophic wheat fungal pathogens in order to understand how they could adapt to changes in fertilization practices. We focus on a single pathogen life history trait, the latent period, which directly determines the amount of resources allocated to growth and reproduction along with the speed of canopy colonization. We implemented three fertilization scenarios, corresponding to major effects of increased nitrogen fertilization on crops: (i) increase in nutrient concentration in leaves, (ii) increase of leaf lifespan, and (iii) increase of leaf number (tillering) and size that leads to a bigger canopy size. For every scenario, we used two different fitness measures to identify putative evolutionary responses of latent period to changes in fertilization level. We observed that annual spore production increases with fertilization, because it results in more resources available to the pathogens. Thus, diminishing the use of fertilizers could reduce biotrophic fungal epidemics. We found a positive relationship between the optimal latent period and fertilization when maximizing total spore production over an entire season. In contrast, we found a negative relationship between the optimal latent period and fertilization when maximizing the within-season exponential growth rate of the pathogen. These contrasting results were consistent over the three tested fertilization scenarios. They suggest that between-strain diversity in the latent period, as has been observed in the field, may be due to diversifying selection in different cultural environments.

The molecular basis of targeting protein kinases in cancer therapeutics.

PubMed

Tsai, Chung-Jung; Nussinov, Ruth

2013-08-01

In this paper, we provide an overview of targeted anticancer therapies with small molecule kinase inhibitors. First, we discuss why a single constitutively active kinase emanating from a variety of aberrant genetic alterations is capable of transforming a normal cell, leading it to acquire the hallmarks of a cancer cell. To draw attention to the fact that kinase inhibition in targeted cancer therapeutics differs from conventional cytotoxic chemotherapy, we exploit a conceptual framework explaining why suppressed kinase activity will selectively kill only the so-called oncogene 'addicted' cancer cell, while sparing the healthy cell. Second, we introduce the protein kinase superfamily in light of its common active conformation with precisely positioned structural elements, and the diversified auto-inhibitory conformations among the kinase families. Understanding the detailed activation mechanism of individual kinases is essential to relate the observed oncogenic alterations to the elevated constitutively active state, to identify the mechanism of consequent drug resistance, and to guide the development of the next-generation inhibitors. To clarify the vital importance of structural guidelines in studies of oncogenesis, we explain how somatic mutations in EGFR result in kinase constitutive activation. Third, in addition to the common theme of secondary (acquired) mutations that prevent drug binding from blocking a signaling pathway which is hijacked by the aberrant activated kinase, we discuss scenarios of drug resistance and relapse by compensating lesions that bypass the inactivated pathway in a vertical or horizontal fashion. Collectively, these suggest that the future challenge of cancer therapy with small molecule kinase inhibitors will rely on the discovery of distinct combinations of optimized drugs to target individual subtypes of different cancers. Copyright © 2013 Elsevier Ltd. All rights reserved.

Expression of Momordica charantia MAP30 and its antitumor effect on bladder cancer cells.

PubMed

Hlin, Hao; Zhi-Guo, Zhang; Cong-Hui, Han; Yan, Zhao; Qing, Liang; Bo, Jiang; Hou-Guang, He; Jun-Jie, Zhang; Pei-Ying, Zhang

2016-06-01

Momordica charantia (MC) is an edible medicinal plant that is known for its diversified biological functions. Momordica Antiviral Protein 30kD (MAP30) is a type I single chain ribosome-inactivating protein (RIP) isolated from the mature fruit and seeds of MC. Since MAP30 content in MC is limited, the study aim was to generate the recombinant MAP30 protein using prokaryotic expression system and determine its apoptotic/growth inhibitory effects on bladder cancer 5637 cells. MAP30 gene was amplified by PCR from MC genomic DNA and identified by sequencing. The target gene was inserted into pET-28a (+) vector and transformed into E. coli BL21 (DE3) cells. Positive clones were selected by PCR. Recombinant protein was efficiently expressed under induction with 1.0 mM Isopropylthio-β-D-galactoside (IPTG) at 30° C for 4 hours. Cytotoxicity studies were performed using MTT assay by treating 5637 bladder cancer cells with 100 µg/mL, 200 µg/mL, and 400 µg/mL concentrations of MAP30 for 24 hours and 48 hours, respectively. Flow cytometry was used to measure the apoptosis of MAP30-treatedcells in time course experiments. Full-length MAP30 gene was successfully expressed in Escherichia coli (E. coli) BL21 strain and MAP30 recombinant protein inhibited the growth of bladder cancer 5637 cells at 200 µg/mL and 400 µg/mL concentrations by inducing apoptosis of target cells in a dose- and time-dependent manner. It was, therefore, concluded that the MAP30 recombinant protein displayed potent antitumor activity in vitro.

Not “Pulling up the Ladder”: Women Who Organize Conference Symposia Provide Greater Opportunities for Women to Speak at Conservation Conferences

PubMed Central

Sardelis, Stephanie; Drew, Joshua A.

2016-01-01

The scientific community faces numerous challenges in achieving gender equality among its participants. One method of highlighting the contributions made by female scientists is through their selection as featured speakers in symposia held at the conferences of professional societies. Because they are specially invited, symposia speakers obtain a prestigious platform from which to display their scientific research, which can elevate the recognition of female scientists. We investigated the number of female symposium speakers in two professional societies (the Society of Conservation Biology (SCB) from 1999 to 2015, and the American Society of Ichthyologists and Herpetologists (ASIH) from 2005 to 2015), in relation to the number of female symposium organizers. Overall, we found that 36.4% of symposia organizers and 31.7% of symposia speakers were women at the Society of Conservation Biology conferences, while 19.1% of organizers and 28% of speakers were women at the American Society of Ichthyologists and Herpetologists conferences. For each additional female organizer at the SCB and ASIH conferences, there was an average increase of 95% and 70% female speakers, respectively. As such, we found a significant positive relationship between the number of women organizing a symposium and the number of women speaking in that symposium. We did not, however, find a significant increase in the number of women speakers or organizers per symposium over time at either conference, suggesting a need for revitalized efforts to diversify our scientific societies. To further those ends, we suggest facilitating gender equality in professional societies by removing barriers to participation, including assisting with travel, making conferences child-friendly, and developing thorough, mandatory Codes of Conduct for all conferences. PMID:27467580

A New Morphological Phylogeny of the Ophiuroidea (Echinodermata) Accords with Molecular Evidence and Renders Microfossils Accessible for Cladistics

PubMed Central

Thuy, Ben; Stöhr, Sabine

2016-01-01

Ophiuroid systematics is currently in a state of upheaval, with recent molecular estimates fundamentally clashing with traditional, morphology-based classifications. Here, we attempt a long overdue recast of a morphological phylogeny estimate of the Ophiuroidea taking into account latest insights on microstructural features of the arm skeleton. Our final estimate is based on a total of 45 ingroup taxa, including 41 recent species covering the full range of extant ophiuroid higher taxon diversity and 4 fossil species known from exceptionally preserved material, and the Lower Carboniferous Aganaster gregarius as the outgroup. A total of 130 characters were scored directly on specimens. The tree resulting from the Bayesian inference analysis of the full data matrix is reasonably well resolved and well supported, and refutes all previous classifications, with most traditional families discredited as poly- or paraphyletic. In contrast, our tree agrees remarkably well with the latest molecular estimate, thus paving the way towards an integrated new classification of the Ophiuroidea. Among the characters which were qualitatively found to accord best with our tree topology, we selected a list of potential synapomorphies for future formal clade definitions. Furthermore, an analysis with 13 of the ingroup taxa reduced to the lateral arm plate characters produced a tree which was essentially similar to the full dataset tree. This suggests that dissociated lateral arm plates can be analysed in combination with fully known taxa and thus effectively unlocks the extensive record of fossil lateral arm plates for phylogenetic estimates. Finally, the age and position within our tree implies that the ophiuroid crown-group had started to diversify by the Early Triassic. PMID:27227685

Critical Materials Institute

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

King, Alex

2013-01-09

Ames Laboratory Director Alex King talks about the goals of the Critical Materials Institute in diversifying the supply of critical materials, developing substitute materials, developing tools and techniques for recycling critical materials, and forecasting materials needs to avoid future shortages.

Identity Preserved Grain: Logistical Overview

DOT National Transportation Integrated Search

2000-01-01

This study was designed to be a resource for producers, shippers, and exporters seeking to diversify their markets through IP shipments. Included are examples of markets for IP grains, trends for containerized movements of grain, and general logistic...

75 FR 56099 - Announcement of the Board of Trustees for the National Environmental Education Foundation

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-15

... open and effective partnership among Federal, State, and local government, business, industry, academic... diversified media company that owned newspapers, local television stations, database centers and print and...

Critical Materials Institute

ScienceCinema

King, Alex

2017-12-22

Ames Laboratory Director Alex King talks about the goals of the Critical Materials Institute in diversifying the supply of critical materials, developing substitute materials, developing tools and techniques for recycling critical materials, and forecasting materials needs to avoid future shortages.

Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses.

PubMed

Rutter, William B; Salcedo, Andres; Akhunova, Alina; He, Fei; Wang, Shichen; Liang, Hanquan; Bowden, Robert L; Akhunov, Eduard

2017-04-12

Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt). The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub-network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors. Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen's ability to infect the host.

NEWS - SUSTAINABILITY SCIENCE

EPA Science Inventory

A series of papers contributed by a diversified collection of researchers endeavor to depict sustainability science as an incomplete but necessary global endeavor. Their concern rests on the perceived inability of science and technology to solely lead the development of sustain...

Theme: In-Agriculture Curriculum.

ERIC Educational Resources Information Center

Elliot, Jack, Ed.; And Others

1991-01-01

Seven theme articles review the history and philosophy of vocational agriculture, its relationship to the national goals for education, the place of sustainable agriculture and supervised experience in the curriculum, diversifying the curriculum, and fisheries education programs in Alaska. (SK)

Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica.

PubMed

Yang, J; Liu, G; Zhao, N; Chen, S; Liu, D; Ma, W; Hu, Z; Zhang, M

2016-05-01

The genus Brassica has many species that are important for oil, vegetable and other food products. Three mitochondrial genome types (mitotype) originated from its common ancestor. In this paper, a B. nigra mitochondrial main circle genome with 232,407 bp was generated through de novo assembly. Synteny analysis showed that the mitochondrial genomes of B. rapa and B. oleracea had a better syntenic relationship than B. nigra. Principal components analysis and development of a phylogenetic tree indicated maternal ancestors of three allotetraploid species in Us triangle of Brassica. Diversified mitotypes were found in allotetraploid B. napus, in which napus-type B. napus was derived from B. oleracea, while polima-type B. napus was inherited from B. rapa. In addition, the mitochondrial genome of napus-type B. napus was closer to botrytis-type than capitata-type B. oleracea. The sub-stoichiometric shifting of several mitochondrial genes suggested that mitochondrial genome rearrangement underwent evolutionary selection during domestication and/or plant breeding. Our findings clarify the role of diploid species in the maternal origin of allotetraploid species in Brassica and suggest the possibility of breeding selection of the mitochondrial genome. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

Project analysis procedures for an OPEC country: case study of Qatar's Northwest Dome Gas Project

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

Ali, A.B.; Khalifah, H.

1986-01-01

The discovery of oil in most OPEC countries in the 1940s changed the economies of these countries from a state of capital shortage and stagnation to a state of capital surplus and economic growth. This growth, however, is lopsided. Oil production and export dominate the gross domestic products (GDPs) of those economies. Concern arising during the 1970s about overdependence on crude oil export as the main source of national income has resulted in the initiation of various industrial development programs in OPEC states aiming to diversify their economies. This study was conducted with two primary objectives: (1) to identify andmore » understand the features of selected OPEC countries' development problems, strategies and plans, focusing on the role of oil and gas resources and opportunities for diversification, and (2) to suggest an appropriate development strategy, with project evaluation implications, for capital-abundant, labor-scarce OPEC countries in the Gulf region such as Qatar. This proposed approach is designed to evaluate the project from its contribution to the national income, people's welfare, the expansion of the economy's absorptive capacity, and relief of the economy's dependence on nonrenewable resources. The Northwest Dome Gas Project in Qatar was selected as an illustrative case study for this approach.« less

Engineered antibody CH2 domains binding to nucleolin: Isolation, characterization and improvement of aggregation.

PubMed

Li, Dezhi; Gong, Rui; Zheng, Jun; Chen, Xihai; Dimitrov, Dimiter S; Zhao, Qi

2017-04-01

Smaller recombinant antibody fragments are now emerging as alternatives of conventional antibodies. Especially, immunoglobulin (Ig) constant CH2 domain and engineered CH2 with improved stability are promising as scaffolds for selection of specific binders to various antigens. We constructed a yeast display library based on an engineered human IgG1 CH2 scaffold with diversified loop regions. A group of CH2 binders were isolated from this yeast display library by panning against nucleolin, which is a tumor-associated antigen involved in cell proliferation, tumor cell growth and angiogenesis. Out of 20 mutants, we selected 3 clones exhibiting relatively high affinities to nucleolin on yeasts. However, recombinant CH2 mutants aggregated when they were expressed. To find the mechanism of the aggregation, we employed computational prediction approaches through structural homology models of CH2 binders. The analysis of potential aggregation prone regions (APRs) and solvent accessible surface areas (ASAs) indicated two hydrophobic residues, Val 264 and Leu 309 , in the β-sheet, in which replacement of both charged residues led to significant decrease of the protein aggregation. The newly identified CH2 binders could be improved to use as candidate therapeutics or research reagents in the future. Copyright © 2017 Elsevier Inc. All rights reserved.

Self-assembled titanium calcium oxide nanopatterns as versatile reactive nanomasks for dry etching lithographic transfer with high selectivity.

PubMed

Faustini, Marco; Drisko, Glenna L; Letailleur, Alban A; Montiel, Rafael Salas; Boissière, Cédric; Cattoni, Andrea; Haghiri-Gosnet, Anne Marie; Lerondel, Gilles; Grosso, David

2013-02-07

We report the simple preparation of ultra-thin self-assembled nanoperforated titanium calcium oxide films and their use as reactive nanomasks for selective dry etching of silicon. This novel reactive nanomask is composed of TiO(2) in which up to 50% of Ti was replaced by Ca (Ca(x)Ti(1-x)O(2-x)). The system was prepared by evaporation induced self-assembly of dip-coated solution of CaCl(2), TiCl(4) and poly(butadiene-block-ethylene oxide) followed by 5 min of thermal treatment at 500 °C in air. The mask exhibits enhanced selectivity by forming a CaF(2) protective layer in the presence of a chemically reactive fluorinated plasma. In particular it is demonstrated that ordered nano-arrays of dense Si pillars, or deep cylindrical wells, with high aspect ratio i.e. lateral dimensions as small as 20 nm and height up to 200 nm, can be formed. Both wells and pillars were formed by tuning the morphology and the homogeneity of the deposited mask. The mask preparation is extremely fast and simple, low-cost and easily scalable. Its combination with reactive ion etching constitutes one of the first examples of what can be achieved when sol-gel chemistry is coupled with top-down technologies. The resulting Si nanopatterns and nanostructures are of high interest for applications in many fields of nanotechnology including electronics and optics. This work extends and diversifies the toolbox of nanofabrication methods.

Diversification, evolution and sub-functionalization of 70kDa heat-shock proteins in two sister species of antarctic krill: differences in thermal habitats, responses and implications under climate change.

PubMed

Cascella, Kévin; Jollivet, Didier; Papot, Claire; Léger, Nelly; Corre, Erwan; Ravaux, Juliette; Clark, Melody S; Toullec, Jean-Yves

2015-01-01

A comparative thermal tolerance study was undertaken on two sister species of Euphausiids (Antarctic krills) Euphausia superba and Euphausia crystallorophias. Both are essential components of the Southern Ocean ecosystem, but occupy distinct environmental geographical locations with slightly different temperature regimes. They therefore provide a useful model system for the investigation of adaptations to thermal tolerance. Initial CTmax studies showed that E. superba was slightly more thermotolerant than E. crystallorophias. Five Hsp70 mRNAs were characterized from the RNAseq data of both species and subsequent expression kinetics studies revealed notable differences in induction of each of the 5 orthologues between the two species, with E. crystallorophias reacting more rapidly than E. superba. Furthermore, analyses conducted to estimate the evolutionary rates and selection strengths acting on each gene tended to support the hypothesis that diversifying selection has contributed to the diversification of this gene family, and led to the selective relaxation on the inducible C form with its possible loss of function in the two krill species. The sensitivity of the epipelagic species E. crystallorophias to temperature variations and/or its adaptation to cold is enhanced when compared with its sister species, E. superba. These results indicate that ice krill could be the first of the two species to be impacted by the warming of coastal waters of the Austral ocean in the coming years due to climate change.

Design and experimentation of an empirical multistructure framework for accurate, sharp and reliable hydrological ensembles

NASA Astrophysics Data System (ADS)

Seiller, G.; Anctil, F.; Roy, R.

2017-09-01

This paper outlines the design and experimentation of an Empirical Multistructure Framework (EMF) for lumped conceptual hydrological modeling. This concept is inspired from modular frameworks, empirical model development, and multimodel applications, and encompasses the overproduce and select paradigm. The EMF concept aims to reduce subjectivity in conceptual hydrological modeling practice and includes model selection in the optimisation steps, reducing initial assumptions on the prior perception of the dominant rainfall-runoff transformation processes. EMF generates thousands of new modeling options from, for now, twelve parent models that share their functional components and parameters. Optimisation resorts to ensemble calibration, ranking and selection of individual child time series based on optimal bias and reliability trade-offs, as well as accuracy and sharpness improvement of the ensemble. Results on 37 snow-dominated Canadian catchments and 20 climatically-diversified American catchments reveal the excellent potential of the EMF in generating new individual model alternatives, with high respective performance values, that may be pooled efficiently into ensembles of seven to sixty constitutive members, with low bias and high accuracy, sharpness, and reliability. A group of 1446 new models is highlighted to offer good potential on other catchments or applications, based on their individual and collective interests. An analysis of the preferred functional components reveals the importance of the production and total flow elements. Overall, results from this research confirm the added value of ensemble and flexible approaches for hydrological applications, especially in uncertain contexts, and open up new modeling possibilities.

Manipulation for plasmid elimination by transforming synthetic competitors diversifies lactococcus lactis starters applicable to food products.

PubMed

Kobayashi, Miho; Nomura, Masaru; Kimoto, Hiromi

2007-11-01

This study was designed selectively to eliminate a theta-plasmid from Lactococcus lactis strains by transforming synthetic competitors. A shuttle vector for Escherichia coli and L. lactis, pDB1, was constructed by ligating a partial replicon of pDR1-1B, which is a 7.3 kb theta-plasmid in L. lactis DRC1, with an erythromycin resistance gene into pBluescript II KS(+). This versatile vector was used to construct competitors to common lactococcal theta-plasmids. pDB1 contains the 5' half of the replication origin and the 3' region of repB of pDR1-1B, but lacks the 1.1-kb region normally found between these two segments. A set of primers, Pv3 and Pv4, was designed to amplify the 1.1-kb middle parts of the general theta-replicons of lactococcal plasmids. When the PCR products were cloned into the Nru I and Xho I sites of pDB1, synthetic replicons were constructed and replication activity was restored. A number of theta-plasmids in L. lactis ssp. lactis and cremoris were eliminated selectively by transforming the synthetic competitors. These competitors were easily eliminated by subculture for a short time in the absence of selection. The resulting variants contained no exogenous DNA and are suitable for food products, since part of the phenotype was altered without altering other plasmids indispensable for fermentation.

Rapid postglacial diversification and long-term stasis within the songbird genus Junco: phylogeographic and phylogenomic evidence.

PubMed

Friis, Guillermo; Aleixandre, Pau; Rodríguez-Estrella, Ricardo; Navarro-Sigüenza, Adolfo G; Milá, Borja

2016-12-01

Natural systems composed of closely related taxa that vary in the degree of phenotypic divergence and geographic isolation provide an opportunity to investigate the rate of phenotypic diversification and the relative roles of selection and drift in driving lineage formation. The genus Junco (Aves: Emberizidae) of North America includes parapatric northern forms that are markedly divergent in plumage pattern and colour, in contrast to geographically isolated southern populations in remote areas that show moderate phenotypic divergence. Here, we quantify patterns of phenotypic divergence in morphology and plumage colour and use mitochondrial DNA genes, a nuclear intron, and genomewide SNPs to reconstruct the demographic and evolutionary history of the genus to infer relative rates of evolutionary divergence among lineages. We found that geographically isolated populations have evolved independently for hundreds of thousands of years despite little differentiation in phenotype, in sharp contrast to phenotypically diverse northern forms, which have diversified within the last few thousand years as a result of the rapid postglacial recolonization of North America. SNP data resolved young northern lineages into reciprocally monophyletic lineages, indicating low rates of gene flow even among closely related parapatric forms, and suggesting a role for strong genetic drift or multifarious selection acting on multiple loci in driving lineage divergence. Juncos represent a compelling example of speciation in action, where the combined effects of historical and selective factors have produced one of the fastest cases of speciation known in vertebrates. © 2016 John Wiley & Sons Ltd.

Single locus typing of MHC class I and class II B loci in a population of red jungle fowl.

PubMed

Worley, K; Gillingham, M; Jensen, P; Kennedy, L J; Pizzari, T; Kaufman, J; Richardson, D S

2008-05-01

In species with duplicated major histocompatibility complex (MHC) genes, estimates of genetic variation often rely on multilocus measures of diversity. It is possible that such measures might not always detect more detailed patterns of selection at individual loci. Here, we describe a method that allows us to investigate classical MHC diversity in red jungle fowl (Gallus gallus), the wild ancestor of the domestic chicken, using a single locus approach. This is possible due to the well-characterised gene organisation of the 'minimal essential' MHC (BF/BL region) of the domestic chicken, which comprises two differentially expressed duplicated class I (BF) and two class II B (BLB) genes. Using a combination of reference strand-mediated conformation analysis, cloning and sequencing, we identify nine BF and ten BLB alleles in a captive population of jungle fowl. We show that six BF and five BLB alleles are from the more highly expressed locus of each gene, BF2 and BLB2, respectively. An excess of non-synonymous substitutions across the jungle fowl BF/BL region suggests that diversifying selection has acted on this population. Importantly, single locus screening reveals that the strength of selection is greatest on the highly expressed BF2 locus. This is the first time that a population of red jungle fowl has been typed at the MHC region, laying the basis for further research into the underlying processes acting to maintain MHC diversity in this and other species.

Characterization of Function of the GlgA2 Glycogen/Starch Synthase in Cyanobacterium sp. Clg1 Highlights Convergent Evolution of Glycogen Metabolism into Starch Granule Aggregation1

PubMed Central

Kadouche, Derifa; Arias, Maria Cecilia

2016-01-01

At variance with the starch-accumulating plants and most of the glycogen-accumulating cyanobacteria, Cyanobacterium sp. CLg1 synthesizes both glycogen and starch. We now report the selection of a starchless mutant of this cyanobacterium that retains wild-type amounts of glycogen. Unlike other mutants of this type found in plants and cyanobacteria, this mutant proved to be selectively defective for one of the two types of glycogen/starch synthase: GlgA2. This enzyme is phylogenetically related to the previously reported SSIII/SSIV starch synthase that is thought to be involved in starch granule seeding in plants. This suggests that, in addition to the selective polysaccharide debranching demonstrated to be responsible for starch rather than glycogen synthesis, the nature and properties of the elongation enzyme define a novel determinant of starch versus glycogen accumulation. We show that the phylogenies of GlgA2 and of 16S ribosomal RNA display significant congruence. This suggests that this enzyme evolved together with cyanobacteria when they diversified over 2 billion years ago. However, cyanobacteria can be ruled out as direct progenitors of the SSIII/SSIV ancestral gene found in Archaeplastida. Hence, both cyanobacteria and plants recruited similar enzymes independently to perform analogous tasks, further emphasizing the importance of convergent evolution in the appearance of starch from a preexisting glycogen metabolism network. PMID:27208262

Characterization of Function of the GlgA2 Glycogen/Starch Synthase in Cyanobacterium sp. Clg1 Highlights Convergent Evolution of Glycogen Metabolism into Starch Granule Aggregation.

PubMed

Kadouche, Derifa; Ducatez, Mathieu; Cenci, Ugo; Tirtiaux, Catherine; Suzuki, Eiji; Nakamura, Yasunori; Putaux, Jean-Luc; Terrasson, Amandine Durand; Diaz-Troya, Sandra; Florencio, Francisco Javier; Arias, Maria Cecilia; Striebeck, Alexander; Palcic, Monica; Ball, Steven G; Colleoni, Christophe

2016-07-01

At variance with the starch-accumulating plants and most of the glycogen-accumulating cyanobacteria, Cyanobacterium sp. CLg1 synthesizes both glycogen and starch. We now report the selection of a starchless mutant of this cyanobacterium that retains wild-type amounts of glycogen. Unlike other mutants of this type found in plants and cyanobacteria, this mutant proved to be selectively defective for one of the two types of glycogen/starch synthase: GlgA2. This enzyme is phylogenetically related to the previously reported SSIII/SSIV starch synthase that is thought to be involved in starch granule seeding in plants. This suggests that, in addition to the selective polysaccharide debranching demonstrated to be responsible for starch rather than glycogen synthesis, the nature and properties of the elongation enzyme define a novel determinant of starch versus glycogen accumulation. We show that the phylogenies of GlgA2 and of 16S ribosomal RNA display significant congruence. This suggests that this enzyme evolved together with cyanobacteria when they diversified over 2 billion years ago. However, cyanobacteria can be ruled out as direct progenitors of the SSIII/SSIV ancestral gene found in Archaeplastida. Hence, both cyanobacteria and plants recruited similar enzymes independently to perform analogous tasks, further emphasizing the importance of convergent evolution in the appearance of starch from a preexisting glycogen metabolism network. © 2016 American Society of Plant Biologists. All Rights Reserved.

Spread of risk across financial markets: better to invest in the peripheries

NASA Astrophysics Data System (ADS)

Pozzi, F.; Di Matteo, T.; Aste, T.

2013-04-01

Risk is not uniformly spread across financial markets and this fact can be exploited to reduce investment risk contributing to improve global financial stability. We discuss how, by extracting the dependency structure of financial equities, a network approach can be used to build a well-diversified portfolio that effectively reduces investment risk. We find that investments in stocks that occupy peripheral, poorly connected regions in financial filtered networks, namely Minimum Spanning Trees and Planar Maximally Filtered Graphs, are most successful in diversifying, improving the ratio between returns' average and standard deviation, reducing the likelihood of negative returns, while keeping profits in line with the general market average even for small baskets of stocks. On the contrary, investments in subsets of central, highly connected stocks are characterized by greater risk and worse performance. This methodology has the added advantage of visualizing portfolio choices directly over the graphic layout of the network.

Spread of risk across financial markets: better to invest in the peripheries

PubMed Central

Pozzi, F.; Di Matteo, T.; Aste, T.

2013-01-01

Risk is not uniformly spread across financial markets and this fact can be exploited to reduce investment risk contributing to improve global financial stability. We discuss how, by extracting the dependency structure of financial equities, a network approach can be used to build a well-diversified portfolio that effectively reduces investment risk. We find that investments in stocks that occupy peripheral, poorly connected regions in financial filtered networks, namely Minimum Spanning Trees and Planar Maximally Filtered Graphs, are most successful in diversifying, improving the ratio between returns' average and standard deviation, reducing the likelihood of negative returns, while keeping profits in line with the general market average even for small baskets of stocks. On the contrary, investments in subsets of central, highly connected stocks are characterized by greater risk and worse performance. This methodology has the added advantage of visualizing portfolio choices directly over the graphic layout of the network. PMID:23588852

(Quickly) Testing the Tester via Path Coverage

NASA Technical Reports Server (NTRS)

Groce, Alex

2009-01-01

The configuration complexity and code size of an automated testing framework may grow to a point that the tester itself becomes a significant software artifact, prone to poor configuration and implementation errors. Unfortunately, testing the tester by using old versions of the software under test (SUT) may be impractical or impossible: test framework changes may have been motivated by interface changes in the tested system, or fault detection may become too expensive in terms of computing time to justify running until errors are detected on older versions of the software. We propose the use of path coverage measures as a "quick and dirty" method for detecting many faults in complex test frameworks. We also note the possibility of using techniques developed to diversify state-space searches in model checking to diversify test focus, and an associated classification of tester changes into focus-changing and non-focus-changing modifications.

Competition both drives and impedes diversification in a model adaptive radiation

PubMed Central

Bailey, Susan F.; Dettman, Jeremy R.; Rainey, Paul B.; Kassen, Rees

2013-01-01

Competitors are known to be important in governing the outcome of evolutionary diversification during an adaptive radiation, but the precise mechanisms by which they exert their effects remain elusive. Using the model adaptive radiation of Pseudomonas fluorescens, we show experimentally that the effect of competition on diversification of a focal lineage depends on both the strength of competition and the ability of the competitors to diversify. We provide evidence that the extent of diversification in the absence of interspecific competitors depends on the strength of resource competition. We also show that the presence of competitors can actually increase diversity by increasing interspecific resource competition. Competitors that themselves are able to diversify prevent diversification of the focal lineage by removing otherwise available ecological opportunities. These results suggest that the progress of an adaptive radiation depends ultimately on the strength of resource competition, an effect that can be exaggerated or impeded by the presence of competitors. PMID:23843392

The University Entrance Exam that Diversified and the Problem

NASA Astrophysics Data System (ADS)

Kondo, Osamu

The percentage of students who go on to universities or junior colleges is over fifty percent which is more than half of high school students. However the nation's birthrate is in decline and the total number of university-age children shows a declining tendency. Hence we cannot expect an increase in the number of applicants in the future. On the other hand, the number of universities has been increasing year by year. The competition among universities to survive is very fierce. The diversification of entrance examination is a symbol of this competition. By diversifying entrance exams, universities aimed at the quality of excellent students in the beginning. However, they have changed their direction to pursue the quantity of students. As of Today the entrance examination is losing its original starting function which means most or all applicants can enter universities. It is time all of the universities return to its starting line.

A Method for WD40 Repeat Detection and Secondary Structure Prediction

PubMed Central

Wang, Yang; Jiang, Fan; Zhuo, Zhu; Wu, Xian-Hui; Wu, Yun-Dong

2013-01-01

WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar β-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction. PMID:23776530

Integrating internal and external bioanalytical support to deliver a diversified pharmaceutical portfolio.

PubMed

Summerfield, Scott G; Evans, Christopher; Spooner, Neil; Dunn, John A; Szapacs, Matthew E; Yang, Eric

2014-05-01

The portfolios of pharmaceutical companies have diversified substantially over recent years in recognition that monotherapies and/or small molecules are less suitable for modulating many complex disease etiologies. Furthermore, there has been increased pressure on drug-development budgets over this same period. This has placed new challenges in the path of bioanalytical scientists, both within the industry and with contract research organizations (CROs). Large pharmaceutical, biotechnology and small-medium healthcare enterprises have had to make important decisions on what internal capabilities they wish to retain and where CROs offers a significant strategic benefit to their business model. Our journey has involved asking where we believe an internal bioanalytical facility offers the greatest benefit to progressing drug candidates through the drug-development cycle and where externalization can help free up internal resources, adding flexibility to our organization in order to deal with the inevitable peaks and troughs in workload.

Teamwork Seminar Practice to Foster Diversified Thinking and Leadership Among Students

NASA Astrophysics Data System (ADS)

Maruyama, Naoki; Yoshida, Kazumi; Yamao, Hidenori

A new course entitled “Mechanical Engineering Seminar” has begun in the Department of Mechanical Engineering, Mie University. This course consists of three parts, a teamwork seminar, a creative design seminar and a comprehensive achievement examination. Its aim is to foster a broad social and international outlook, ethical thinking, autonomy, partnership, leadership, presentation ability, originality, overall creativity in students, and to help them become aware of their real ability. The teaching method used in this seminar is based on problem-based learning (PBL) , and pro-active student participation is required. The purpose of this paper is to report the features, teaching method and educational effectiveness of the teamwork seminar, which seeks to educate students with a broad, diversified outlook. The results of a student questionnaire show that these new fields of study stimulate students' will to learn, and they express general satisfaction with the seminar.

Diversify your sources of capital through debt offerings

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

Burkhardt, D.A.; Soucy, S.T.

1993-09-01

Despite the trend toward diversification in many areas of the utility industry, most utility executives have yet to realize that many of the benefits derived from diversifying equity ownership can also be gained through a similar approach to their debt securities. Although institutional investors have long been regarded as the exclusive market for utility debt securities, individuals are an increasingly important component of this market. The factors that motivate individuals to purchase utility debt securities are the same as those that influence purchases of utility stocks: safety and dependable income. The benefits of retail ownership of utility debt securities domore » not, however, accrue exclusively to the investor. Utility companies that actively market debt offerings to individual investors also can expect to enjoy a number of tangible benefits. Nowhere are these benefits more obvious than in the area of tax-exempt utility securities.« less

Evolution of trees and mycorrhizal fungi intensifies silicate mineral weathering.

PubMed

Quirk, Joe; Beerling, David J; Banwart, Steve A; Kakonyi, Gabriella; Romero-Gonzalez, Maria E; Leake, Jonathan R

2012-12-23

Forested ecosystems diversified more than 350 Ma to become major engines of continental silicate weathering, regulating the Earth's atmospheric carbon dioxide concentration by driving calcium export into ocean carbonates. Our field experiments with mature trees demonstrate intensification of this weathering engine as tree lineages diversified in concert with their symbiotic mycorrhizal fungi. Preferential hyphal colonization of the calcium silicate-bearing rock, basalt, progressively increased with advancement from arbuscular mycorrhizal (AM) to later, independently evolved ectomycorrhizal (EM) fungi, and from gymnosperm to angiosperm hosts with both fungal groups. This led to 'trenching' of silicate mineral surfaces by AM and EM fungi, with EM gymnosperms and angiosperms releasing calcium from basalt at twice the rate of AM gymnosperms. Our findings indicate mycorrhiza-driven weathering may have originated hundreds of millions of years earlier than previously recognized and subsequently intensified with the evolution of trees and mycorrhizas to affect the Earth's long-term CO(2) and climate history.

Comparison of lead and cadmium contents in cruciferous vegetables grown under diversified ecological conditions: Cracow region of Poland.

PubMed

Kapusta-Duch, Joanna; Leszczyńska, Teresa; Florkiewicz, Adam; Filipiak-Florkiewicz, Agnieszka

2011-01-01

The aim of the present study was to compare lead and cadmium contents in cruciferous vegetables grown under diversified ecological conditions for three consecutive years, independently of the climatic and agrotechnical conditions. The research was conducted in the Cracow region of Poland and tests vegetables near the Steelworks, from ecological farms, and from local markets. The heavy metal contents were determined using the validated Atomic Absorption Spectrometry method, including electrothermal atomization, with an ET-AAS graphite cuvette (Varian AA240Z, made by Varian). Cruciferous vegetables cultivated in the areas surrounding the steelworks were characterized by alarmingly high lead content versus ecological and commercially available vegetables, while the contents of this metal in vegetables from the two latter locations did not differ. It cannot be definitively stated that the origin of vegetables influenced their cadmium content.

Somatic hypermutation of T cell receptor α chain contributes to selection in nurse shark thymus.

PubMed

Ott, Jeannine A; Castro, Caitlin D; Deiss, Thaddeus C; Ohta, Yuko; Flajnik, Martin F; Criscitiello, Michael F

2018-04-17

Since the discovery of the T cell receptor (TcR), immunologists have assigned somatic hypermutation (SHM) as a mechanism employed solely by B cells to diversify their antigen receptors. Remarkably, we found SHM acting in the thymus on α chain locus of shark TcR. SHM in developing shark T cells likely is catalyzed by activation-induced cytidine deaminase (AID) and results in both point and tandem mutations that accumulate non-conservative amino acid replacements within complementarity-determining regions (CDRs). Mutation frequency at TcRα was as high as that seen at B cell receptor loci (BcR) in sharks and mammals, and the mechanism of SHM shares unique characteristics first detected at shark BcR loci. Additionally, fluorescence in situ hybridization showed the strongest AID expression in thymic corticomedullary junction and medulla. We suggest that TcRα utilizes SHM to broaden diversification of the primary αβ T cell repertoire in sharks, the first reported use in vertebrates. © 2018, Ott et al.

Somatic hypermutation of T cell receptor α chain contributes to selection in nurse shark thymus

PubMed Central

Ott, Jeannine A; Castro, Caitlin D; Deiss, Thaddeus C; Ohta, Yuko; Flajnik, Martin F

2018-01-01

Since the discovery of the T cell receptor (TcR), immunologists have assigned somatic hypermutation (SHM) as a mechanism employed solely by B cells to diversify their antigen receptors. Remarkably, we found SHM acting in the thymus on α chain locus of shark TcR. SHM in developing shark T cells likely is catalyzed by activation-induced cytidine deaminase (AID) and results in both point and tandem mutations that accumulate non-conservative amino acid replacements within complementarity-determining regions (CDRs). Mutation frequency at TcRα was as high as that seen at B cell receptor loci (BcR) in sharks and mammals, and the mechanism of SHM shares unique characteristics first detected at shark BcR loci. Additionally, fluorescence in situ hybridization showed the strongest AID expression in thymic corticomedullary junction and medulla. We suggest that TcRα utilizes SHM to broaden diversification of the primary αβ T cell repertoire in sharks, the first reported use in vertebrates. PMID:29664399