structurally diverse set: Topics by Science.gov

Sample records for structurally diverse set

The diversity effect in diagnostic reasoning.

PubMed

Rebitschek, Felix G; Krems, Josef F; Jahn, Georg

2016-07-01

Diagnostic reasoning draws on knowledge about effects and their potential causes. The causal-diversity effect in diagnostic reasoning normatively depends on the distribution of effects in causal structures, and thus, a psychological diversity effect could indicate whether causally structured knowledge is used in evaluating the probability of a diagnosis, if the effect were to covary with manipulations of causal structures. In four experiments, participants dealt with a quasi-medical scenario presenting symptom sets (effects) that consistently suggested a specified diagnosis (cause). The probability that the diagnosis was correct had to be rated for two opposed symptom sets that differed with regard to the symptoms' positions (proximal or diverse) in the causal structure that was initially acquired. The causal structure linking the diagnosis to the symptoms and the base rate of the diagnosis were manipulated to explore whether the diagnosis was rated as more probable for diverse than for proximal symptoms when alternative causations were more plausible (e.g., because of a lower base rate of the diagnosis in question). The results replicated the causal diversity effect in diagnostic reasoning across these conditions, but no consistent effects of structure and base rate variations were observed. Diversity effects computed in causal Bayesian networks are presented, illustrating the consequences of the structure manipulations and corroborating that a diversity effect across the different experimental manipulations is normatively justified. The observed diversity effects presumably resulted from shortcut reasoning about the possibilities of alternative causation.
10 CFR 960.3-2-1 - Site screening for potentially acceptable sites.

Code of Federal Regulations, 2011 CFR

2011-01-01

... that contain rock formations of suitable depth, thickness, and lateral extent and have structural... require diversity of geohydrologic settings and rock types and consideration of regionality, as specified... provisions for diversity of geohydrologic settings, diversity of rock types, and regionality (§§ 960.3-1-1...
Genetic diversity and population structure of cowpea (Vigna unguiculata L. Walp)

USDA-ARS?s Scientific Manuscript database

The genetic diversity of cowpea was analyzed and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from USDA GRIN cowpea collection, originally collected from 56 countries worldwide. Genotyping by sequencing was used to discover single nucleotide polymorphism...
Bias-Free Chemically Diverse Test Sets from Machine Learning.

PubMed

Swann, Ellen T; Fernandez, Michael; Coote, Michelle L; Barnard, Amanda S

2017-08-14

Current benchmarking methods in quantum chemistry rely on databases that are built using a chemist's intuition. It is not fully understood how diverse or representative these databases truly are. Multivariate statistical techniques like archetypal analysis and K-means clustering have previously been used to summarize large sets of nanoparticles however molecules are more diverse and not as easily characterized by descriptors. In this work, we compare three sets of descriptors based on the one-, two-, and three-dimensional structure of a molecule. Using data from the NIST Computational Chemistry Comparison and Benchmark Database and machine learning techniques, we demonstrate the functional relationship between these structural descriptors and the electronic energy of molecules. Archetypes and prototypes found with topological or Coulomb matrix descriptors can be used to identify smaller, statistically significant test sets that better capture the diversity of chemical space. We apply this same method to find a diverse subset of organic molecules to demonstrate how the methods can easily be reapplied to individual research projects. Finally, we use our bias-free test sets to assess the performance of density functional theory and quantum Monte Carlo methods.
The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets.

PubMed

Trepalin, Sergey; Osadchiy, Nikolay

2005-01-01

Chemical structure provides exhaustive description of a compound, but it is often proprietary and thus an impediment in the exchange of information. For example, structure disclosure is often needed for the selection of most similar or dissimilar compounds. Authors propose a centroidal algorithm based on structural fragments (screens) that can be efficiently used for the similarity and diversity selections without disclosing structures from the reference set. For an increased security purposes, authors recommend that such set contains at least some tens of structures. Analysis of reverse engineering feasibility showed that the problem difficulty grows with decrease of the screen's radius. The algorithm is illustrated with concrete calculations on known steroidal, quinoline, and quinazoline drugs. We also investigate a problem of scaffold identification in combinatorial library dataset. The results show that relatively small screens of radius equal to 2 bond lengths perform well in the similarity sorting, while radius 4 screens yield better results in diversity sorting. The software implementation of the algorithm taking SDF file with a reference set generates screens of various radii which are subsequently used for the similarity and diversity sorting of external SDFs. Since the reverse engineering of the reference set molecules from their screens has the same difficulty as the RSA asymmetric encryption algorithm, generated screens can be stored openly without further encryption. This approach ensures an end user transfers only a set of structural fragments and no other data. Like other algorithms of encryption, the centroid algorithm cannot give 100% guarantee of protecting a chemical structure from dataset, but probability of initial structure identification is very small-order of 10(-40) in typical cases.
The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets

NASA Astrophysics Data System (ADS)

Trepalin, Sergey; Osadchiy, Nikolay

2005-09-01

Chemical structure provides exhaustive description of a compound, but it is often proprietary and thus an impediment in the exchange of information. For example, structure disclosure is often needed for the selection of most similar or dissimilar compounds. Authors propose a centroidal algorithm based on structural fragments (screens) that can be efficiently used for the similarity and diversity selections without disclosing structures from the reference set. For an increased security purposes, authors recommend that such set contains at least some tens of structures. Analysis of reverse engineering feasibility showed that the problem difficulty grows with decrease of the screen's radius. The algorithm is illustrated with concrete calculations on known steroidal, quinoline, and quinazoline drugs. We also investigate a problem of scaffold identification in combinatorial library dataset. The results show that relatively small screens of radius equal to 2 bond lengths perform well in the similarity sorting, while radius 4 screens yield better results in diversity sorting. The software implementation of the algorithm taking SDF file with a reference set generates screens of various radii which are subsequently used for the similarity and diversity sorting of external SDFs. Since the reverse engineering of the reference set molecules from their screens has the same difficulty as the RSA asymmetric encryption algorithm, generated screens can be stored openly without further encryption. This approach ensures an end user transfers only a set of structural fragments and no other data. Like other algorithms of encryption, the centroid algorithm cannot give 100% guarantee of protecting a chemical structure from dataset, but probability of initial structure identification is very small-order of 10-40 in typical cases.
Challenges in adapting existing clinical natural language processing systems to multiple, diverse health care settings.

PubMed

Carrell, David S; Schoen, Robert E; Leffler, Daniel A; Morris, Michele; Rose, Sherri; Baer, Andrew; Crockett, Seth D; Gourevitch, Rebecca A; Dean, Katie M; Mehrotra, Ateev

2017-09-01

Widespread application of clinical natural language processing (NLP) systems requires taking existing NLP systems and adapting them to diverse and heterogeneous settings. We describe the challenges faced and lessons learned in adapting an existing NLP system for measuring colonoscopy quality. Colonoscopy and pathology reports from 4 settings during 2013-2015, varying by geographic location, practice type, compensation structure, and electronic health record. Though successful, adaptation required considerably more time and effort than anticipated. Typical NLP challenges in assembling corpora, diverse report structures, and idiosyncratic linguistic content were greatly magnified. Strategies for addressing adaptation challenges include assessing site-specific diversity, setting realistic timelines, leveraging local electronic health record expertise, and undertaking extensive iterative development. More research is needed on how to make it easier to adapt NLP systems to new clinical settings. A key challenge in widespread application of NLP is adapting existing systems to new clinical settings. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com
A program for automatically predicting supramolecular aggregates and its application to urea and porphin [A programme for the automated geometry prediction of supra-molecular aggregates and its application to the examples of urea and porphin

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

Sachse, Torsten; Martinez, Todd J.; Dietzek, Benjamin

Not only the molecular structure but also the presence or absence of aggregates determines many properties of organic materials. Theoretical investigation of such aggregates requires the prediction of a suitable set of diverse structures. Here, we present the open–source program EnergyScan for the unbiased prediction of geometrically diverse sets of small aggregates. Its bottom–up approach is complementary to existing ones by performing a detailed scan of an aggregate's potential energy surface, from which diverse local energy minima are selected. We crossvalidate this approach by predicting both literature–known and heretofore unreported geometries of the urea dimer. We also predict a diversemore » set of dimers of the less intensely studied case of porphin, which we investigate further using quantum chemistry. For several dimers, we find strong deviations from a reference absorption spectrum, which we explain using computed transition densities. Furthermore, this proof of principle clearly shows that EnergyScan successfully predicts aggregates exhibiting large structural and spectral diversity.« less
A program for automatically predicting supramolecular aggregates and its application to urea and porphin [A programme for the automated geometry prediction of supra-molecular aggregates and its application to the examples of urea and porphin

DOE PAGES

Sachse, Torsten; Martinez, Todd J.; Dietzek, Benjamin; ...

2018-01-03

Not only the molecular structure but also the presence or absence of aggregates determines many properties of organic materials. Theoretical investigation of such aggregates requires the prediction of a suitable set of diverse structures. Here, we present the open–source program EnergyScan for the unbiased prediction of geometrically diverse sets of small aggregates. Its bottom–up approach is complementary to existing ones by performing a detailed scan of an aggregate's potential energy surface, from which diverse local energy minima are selected. We crossvalidate this approach by predicting both literature–known and heretofore unreported geometries of the urea dimer. We also predict a diversemore » set of dimers of the less intensely studied case of porphin, which we investigate further using quantum chemistry. For several dimers, we find strong deviations from a reference absorption spectrum, which we explain using computed transition densities. Furthermore, this proof of principle clearly shows that EnergyScan successfully predicts aggregates exhibiting large structural and spectral diversity.« less
Fluidized muds: a novel setting for the generation of biosphere diversity through geologic time.

PubMed

Aller, J Y; Aller, R C; Kemp, P F; Chistoserdov, A Y; Madrid, V M

2010-06-01

Reworked and fluidized fine-grained deposits in energetic settings are a major modern-day feature of river deltas and estuaries. Similar environments were probably settings for microbial evolution on the early Earth. These sedimentary systems act as efficient biogeochemical reactors with high bacterial phylogenetic diversity and functional redundancy. They are temporally rather than spatially structured, with repeated cycling of redox conditions and successive stages of microbial metabolic processes. Intense reworking of the fluidized bed entrains bacteria from varied habitats providing new, diverse genetic materials to contribute to horizontal gene transfer events and the creation of new bacterial ecotypes. These vast mud environments may act as exporters and promoters of biosphere diversity and novel adaptations, potentially on a globally important scale.
Diverse, high-quality test set for the validation of protein-ligand docking performance.

PubMed

Hartshorn, Michael J; Verdonk, Marcel L; Chessari, Gianni; Brewerton, Suzanne C; Mooij, Wijnand T M; Mortenson, Paul N; Murray, Christopher W

2007-02-22

A procedure for analyzing and classifying publicly available crystal structures has been developed. It has been used to identify high-resolution protein-ligand complexes that can be assessed by reconstructing the electron density for the ligand using the deposited structure factors. The complexes have been clustered according to the protein sequences, and clusters have been discarded if they do not represent proteins thought to be of direct interest to the pharmaceutical or agrochemical industry. Rules have been used to exclude complexes containing non-drug-like ligands. One complex from each cluster has been selected where a structure of sufficient quality was available. The final Astex diverse set contains 85 diverse, relevant protein-ligand complexes, which have been prepared in a format suitable for docking and are to be made freely available to the entire research community (http://www.ccdc.cam.ac.uk). The performance of the docking program GOLD against the new set is assessed using a variety of protocols. Relatively unbiased protocols give success rates of approximately 80% for redocking into native structures, but it is possible to get success rates of over 90% with some protocols.
Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers.

PubMed

Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2015-01-01

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding.
Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism

PubMed Central

2009-01-01

The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds. PMID:19284689
Genome-wide characterization of genetic diversity and population structure in Secale

PubMed Central

2014-01-01

Background Numerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties. Results Average genetic similarity (GS) coefficients and average polymorphic information content (PIC) values varied among chromosomes. Comparison of chromosome specific average GS within and between germplasm sub-groups indicated regions of chromosomes 1R and 4R as being targeted by selection in current breeding programs. Bayesian clustering, principal coordinate analysis and Neighbor Joining clustering demonstrated that source and improvement status contributed significantly to the structure observed in the analyzed set of Secale germplasm. We revealed a relatively limited diversity in improved rye accessions, both historical and contemporary, as well as lack of correlation between clustering of improved accessions and geographic origin, suggesting common genetic background of rye accessions from diverse geographic regions and extensive germplasm exchange. Moreover, contemporary varieties were distinct from the remaining accessions. Conclusions Our results point to an influence of reproduction methods on the observed diversity patterns and indicate potential of ex situ collections for broadening the genetic diversity in rye breeding programs. Obtained data show that DArT markers provide a realistic picture of the genetic diversity and population structure present in the collection of 379 rye accessions and are an effective platform for rye germplasm characterization and association mapping studies. PMID:25085433
The diversity issue revisited: international students in clinical environment.

PubMed

Pitkäjärvi, Marianne; Eriksson, Elina; Pitkälä, Kaisu

2012-01-01

Background. Globalization within higher education leads to an increase in cultural and linguistic diversity in student populations. The purpose of this study was to explore culturally diverse health care students' experiences in clinical environment in Finland, and to compare them with those of native Finnish students' participating in the same program. Method. A cross-sectional survey was performed at 10 polytechnic faculties of health care in Finland. 283 respondents (148 international and 95 Finnish students) responded to items concerning clinical rotation. The survey included items grouped as dimensions: (1) welcoming clinical environment, (2) unsupportive clinical environment, (3) approach to cultural diversity, (4) communication, and (5) structural arrangements. Results. International students felt as welcome on their placements as Finnish students. Concerning structural arrangements set up to facilitate preceptorship and approach to cultural diversity in the learning environment, the two groups' opinions were similar. However, international students were more likely than Finnish students to experience their clinical learning environment as unsupportive (P < 0.001). In addition, their experiences of communication with the staff was poorer than that of their Finnish peers' (P = 0.04). Conclusions. Awareness of strategies that enhance understanding, acceptance, and appreciation of cultural and linguistic diversity in any health care setting are needed.
Passive Bistatic Radar and Waveform Diversity

DTIC Science & Technology

2009-11-01

transmission, but these are significantly beyond the detection ranges of interest. The sidelobe structure of the ambiguity function is flat , as would...kHz (corresponding to a monostatic range resolution c/2B = 3000 m). The transmitters are usually sited on tall towers or masts in high locations. The...peak and the sidelobe structure are well-defined, though the peak Passive Bistatic Radar and Waveform Diversity RTO-EN-SET-119(2009) 3 - 5
Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers

PubMed Central

Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2015-01-01

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding. PMID:25901573
The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening.

PubMed

Xia, Jie; Hsieh, Jui-Hua; Hu, Huabin; Wu, Song; Wang, Xiang Simon

2017-06-26

Structure-based virtual screening (SBVS) has become an indispensable technique for hit identification at the early stage of drug discovery. However, the accuracy of current scoring functions is not high enough to confer success to every target and thus remains to be improved. Previously, we had developed binary pose filters (PFs) using knowledge derived from the protein-ligand interface of a single X-ray structure of a specific target. This novel approach had been validated as an effective way to improve ligand enrichment. Continuing from it, in the present work we attempted to incorporate knowledge collected from diverse protein-ligand interfaces of multiple crystal structures of the same target to build PF ensembles (PFEs). Toward this end, we first constructed a comprehensive data set to meet the requirements of ensemble modeling and validation. This set contains 10 diverse targets, 118 well-prepared X-ray structures of protein-ligand complexes, and large benchmarking actives/decoys sets. Notably, we designed a unique workflow of two-layer classifiers based on the concept of ensemble learning and applied it to the construction of PFEs for all of the targets. Through extensive benchmarking studies, we demonstrated that (1) coupling PFE with Chemgauss4 significantly improves the early enrichment of Chemgauss4 itself and (2) PFEs show greater consistency in boosting early enrichment and larger overall enrichment than our prior PFs. In addition, we analyzed the pairwise topological similarities among cognate ligands used to construct PFEs and found that it is the higher chemical diversity of the cognate ligands that leads to the improved performance of PFEs. Taken together, the results so far prove that the incorporation of knowledge from diverse protein-ligand interfaces by ensemble modeling is able to enhance the screening competence of SBVS scoring functions.
SSR-based genetic diversity and structure of garlic accessions from Brazil.

PubMed

da Cunha, Camila Pinto; Resende, Francisco Vilela; Zucchi, Maria Imaculada; Pinheiro, José Baldin

2014-10-01

Garlic is a spice and a medicinal plant; hence, there is an increasing interest in 'developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.
Natural product-like virtual libraries: recursive atom-based enumeration.

PubMed

Yu, Melvin J

2011-03-28

A new molecular enumerator is described that allows chemically and architecturally diverse sets of natural product-like and drug-like structures to be generated from a core structure as simple as a single carbon atom or as complex as a polycyclic ring system. Integrated with a rudimentary machine-learning algorithm, the enumerator has the ability to assemble biased virtual libraries enriched in compounds predicted to meet target criteria. The ability to dynamically generate relatively small focused libraries in a recursive manner could reduce the computational time and infrastructure necessary to construct and manage extremely large static libraries. Depending on enumeration conditions, natural product-like structures can be produced with a wide range of heterocyclic and alicyclic ring assemblies. Because natural products represent a proven source of validated structures for identifying and designing new drug candidates, mimicking the structural and topological diversity found in nature with a dynamic set of virtual natural product-like compounds may facilitate the creation of new ideas for novel, biologically relevant lead structures in areas of uncharted chemical space.

Rational selection of structurally diverse natural product scaffolds with favorable ADME properties for drug discovery.

PubMed

Samiulla, D S; Vaidyanathan, V V; Arun, P C; Balan, G; Blaze, M; Bondre, S; Chandrasekhar, G; Gadakh, A; Kumar, R; Kharvi, G; Kim, H O; Kumar, S; Malikayil, J A; Moger, M; Mone, M K; Nagarjuna, P; Ogbu, C; Pendhalkar, D; Rao, A V S Raja; Rao, G Venkateshwar; Sarma, V K; Shaik, S; Sharma, G V R; Singh, S; Sreedhar, C; Sonawane, R; Timmanna, U; Hardy, L W

2005-01-01

Natural product analogs are significant sources for therapeutic agents. To capitalize efficiently on the effective features of naturally occurring substances, a natural product-based library production platform has been devised at Aurigene for drug lead discovery. This approach combines the attractive biological and physicochemical properties of natural product scaffolds, provided by eons of natural selection, with the chemical diversity available from parallel synthetic methods. Virtual property analysis, using computational methods described here, guides the selection of a set of natural product scaffolds that are both structurally diverse and likely to have favorable pharmacokinetic properties. The experimental characterization of several in vitro ADME properties of twenty of these scaffolds, and of a small set of designed congeners based upon one scaffold, is also described. These data confirm that most of the scaffolds and the designed library members have properties favorable to their utilization for creating libraries of lead-like molecules.
Application of combinatorial biocatalysis for a unique ring expansion of dihydroxymethylzearalenone.

PubMed

Rich, Joseph O; Budde, Cheryl L; McConeghey, Luke D; Cotterill, Ian C; Mozhaev, Vadim V; Singh, Sheo B; Goetz, Michael A; Zhao, Annie; Michels, Peter C; Khmelnitsky, Yuri L

2009-06-01

Combinatorial biocatalysis was applied to generate a diverse set of dihydroxymethylzearalenone analogs with modified ring structure. In one representative chemoenzymatic reaction sequence, dihydroxymethylzearalenone was first subjected to a unique enzyme-catalyzed oxidative ring opening reaction that creates two new carboxylic groups on the molecule. These groups served as reaction sites for further derivatization involving biocatalytic ring closure reactions with structurally diverse bifunctional reagents, including different diols and diamines. As a result, a library of cyclic bislactones and bislactams was created, with modified ring structures covering chemical space and structure activity relationships unattainable by conventional synthetic means.
Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis

PubMed Central

Whitlock, Raj

2014-01-01

Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These results suggest that adaptive and neutral genetic diversity should not be treated as ecologically equivalent measures of intraspecific variation.Synthesis. This study advances the debate over whether relationships between genetic diversity and ecological structure are either simply positive or negative, by showing how the strength and direction of these relationships changes with different measures of diversity and in different ecological contexts. The results provide a solid foundation for assessing when and where an expanded synthesis between ecology and genetics will be most fruitful. PMID:25210204
An improved method to set significance thresholds for β diversity testing in microbial community comparisons.

PubMed

Gülay, Arda; Smets, Barth F

2015-09-01

Exploring the variation in microbial community diversity between locations (β diversity) is a central topic in microbial ecology. Currently, there is no consensus on how to set the significance threshold for β diversity. Here, we describe and quantify the technical components of β diversity, including those associated with the process of subsampling. These components exist for any proposed β diversity measurement procedure. Further, we introduce a strategy to set significance thresholds for β diversity of any group of microbial samples using rarefaction, invoking the notion of a meta-community. The proposed technique was applied to several in silico generated operational taxonomic unit (OTU) libraries and experimental 16S rRNA pyrosequencing libraries. The latter represented microbial communities from different biological rapid sand filters at a full-scale waterworks. We observe that β diversity, after subsampling, is inflated by intra-sample differences; this inflation is avoided in the proposed method. In addition, microbial community evenness (Gini > 0.08) strongly affects all β diversity estimations due to bias associated with rarefaction. Where published methods to test β significance often fail, the proposed meta-community-based estimator is more successful at rejecting insignificant β diversity values. Applying our approach, we reveal the heterogeneous microbial structure of biological rapid sand filters both within and across filters. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.
Population structure in Japanese rice population

PubMed Central

Yamasaki, Masanori; Ideta, Osamu

2013-01-01

It is essential to elucidate genetic diversity and relationships among even related individuals and populations for plant breeding and genetic analysis. Since Japanese rice breeding has improved agronomic traits such as yield and eating quality, modern Japanese rice cultivars originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in Japanese rice population, we used a total of 706 alleles detected by 134 simple sequence repeat markers in a total of 114 cultivars composed of 94 improved varieties and 20 landraces, which are representative and important for Japanese rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Model-based Bayesian clustering analysis revealed six subgroups and admixture situation in the cultivars, showing good agreement with pedigree information. This method could be superior to phylogenetic method in classifying a related population. The leading Japanese rice cultivar, Koshihikari is unique due to the specific genome constitution. We defined Japanese rice diverse sets that capture the maximum number of alleles for given sample sizes. These sets are useful for a variety of genetic application in Japanese rice cultivars. PMID:23641181
STRUCTURE-ACTIVITY APPROACHES AND DATA EXPLORATION TOOLS FOR PRIORITIZING AND ASSESSING THE TOXICITY OF HAZARDOUS AIR POLLUTANTS

EPA Science Inventory

STRUCTURE-ACTIVITY APPROACHES AND DATA EXPLORATION TOOLS FOR PRIORITIZING AND ASSESSING THE TOXICITY OF HAZARDOUS AIR POLLUTANTS

Hazardous Air Pollutants (HAPs) refers to a set of structurally diverse environmental chemicals, many with limited toxicity data, that have...
Infusing Gender and Diversity Issues into Educational Leadership Programs: Transformational Learning and Resistance

ERIC Educational Resources Information Center

Young, Michelle; Mountford, Meredith; Skrla, Linda

2006-01-01

Purpose: The purpose of this article is to consider the impact of incorporating a set of readings focused on issues of gender, diversity, leadership, and feminist thought into the curriculum of a statewide educational leadership doctoral program. Design/methodology/approach: Based data from open-ended surveys, semi-structured interviews, and…
[Effects of agricultural practices on community structure of arbuscular mycorrhizal fungi in agricultural ecosystem: a review].

PubMed

Sheng, Ping-Ping; Li, Min; Liu, Run-Jin

2011-06-01

Arbuscular mycorrhizal (AM) fungi are rich in diversity in agricultural ecosystem, playing a vital role based on their unique community structure. Host plants and environmental factors have important effects on AM fungal community structure, so do the agricultural practices which deserve to pay attention to. This paper summarized the research advances in the effects of agricultural practices such as irrigation, fertilization, crop rotation, intercropping, tillage, and pesticide application on AM fungal community structure, analyzed the related possible mechanisms, discussed the possible ways in improving AM fungal community structure in agricultural ecosystem, and put forward a set of countermeasures, i.e., improving fertilization system and related integrated techniques, increasing plant diversity in agricultural ecosystem, and inoculating AM fungi, to enhance the AM fungal diversity in agricultural ecosystem. The existing problems in current agricultural practices and further research directions were also proposed.
Analysis of Genetic Diversity and Population Structure of Rice Germplasm from North-Eastern Region of India and Development of a Core Germplasm Set

PubMed Central

Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R. K.; Ahmad, Altaf; Singh, N. K.; Singh, Rakesh

2014-01-01

The North-Eastern region (NER) of India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura, is a hot spot for genetic diversity and the most probable origin of rice. North-east rice collections are known to possess various agronomically important traits like biotic and abiotic stress tolerance, unique grain and cooking quality. The genetic diversity and associated population structure of 6,984 rice accessions, originating from NER, were assessed using 36 genome wide unlinked single nucleotide polymorphism (SNP) markers distributed across the 12 rice chromosomes. All of the 36 SNP loci were polymorphic and bi-allelic, contained five types of base substitutions and together produced nine types of alleles. The polymorphic information content (PIC) ranged from 0.004 for Tripura to 0.375 for Manipur and major allele frequency ranged from 0.50 for Assam to 0.99 for Tripura. Heterozygosity ranged from 0.002 in Nagaland to 0.42 in Mizoram and gene diversity ranged from 0.006 in Arunachal Pradesh to 0.50 in Manipur. The genetic relatedness among the rice accessions was evaluated using an unrooted phylogenetic tree analysis, which grouped all accessions into three major clusters. For determining population structure, populations K = 1 to K = 20 were tested and population K = 3 was present in all the states, with the exception of Meghalaya and Manipur where, K = 5 and K = 4 populations were present, respectively. Principal Coordinate Analysis (PCoA) showed that accessions were distributed according to their population structure. AMOVA analysis showed that, maximum diversity was partitioned at the individual accession level (73% for Nagaland, 58% for Arunachal Pradesh and 57% for Tripura). Using POWERCORE software, a core set of 701 accessions was obtained, which accounted for approximately 10% of the total NE India collections, representing 99.9% of the allelic diversity. The rice core set developed will be a valuable resource for future genomic studies and crop improvement strategies. PMID:25412256
Atomic force microscopy of starch systems.

PubMed

Zhu, Fan

2017-09-22

Atomic force microscopy (AFM) generates information on topography, adhesion, and elasticity of sample surface by touching with a tip. Under suitable experimental settings, AFM can image biopolymers of few nanometers. Starch is a major food and industrial component. AFM has been used to probe the morphology, properties, modifications, and interactions of starches from diverse botanical origins at both micro- and nano-structural levels. The structural information obtained by AFM supports the blocklet structure of the granules, and provides qualitative and quantitative basis for some physicochemical properties of diverse starch systems. It becomes evident that AFM can complement other microscopic techniques to provide novel structural insights for starch systems.
An efficient algorithm for generating diverse microstructure sets and delineating properties closures

DOE PAGES

Johnson, Oliver K.; Kurniawan, Christian

2018-02-03

Properties closures delineate the theoretical objective space for materials design problems, allowing designers to make informed trade-offs between competing constraints and target properties. In this paper, we present a new algorithm called hierarchical simplex sampling (HSS) that approximates properties closures more efficiently and faithfully than traditional optimization based approaches. By construction, HSS generates samples of microstructure statistics that span the corresponding microstructure hull. As a result, we also find that HSS can be coupled with synthetic polycrystal generation software to generate diverse sets of microstructures for subsequent mesoscale simulations. Finally, by more broadly sampling the space of possible microstructures, itmore » is anticipated that such diverse microstructure sets will expand our understanding of the influence of microstructure on macroscale effective properties and inform the construction of higher-fidelity mesoscale structure-property models.« less
An efficient algorithm for generating diverse microstructure sets and delineating properties closures

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

Johnson, Oliver K.; Kurniawan, Christian

Properties closures delineate the theoretical objective space for materials design problems, allowing designers to make informed trade-offs between competing constraints and target properties. In this paper, we present a new algorithm called hierarchical simplex sampling (HSS) that approximates properties closures more efficiently and faithfully than traditional optimization based approaches. By construction, HSS generates samples of microstructure statistics that span the corresponding microstructure hull. As a result, we also find that HSS can be coupled with synthetic polycrystal generation software to generate diverse sets of microstructures for subsequent mesoscale simulations. Finally, by more broadly sampling the space of possible microstructures, itmore » is anticipated that such diverse microstructure sets will expand our understanding of the influence of microstructure on macroscale effective properties and inform the construction of higher-fidelity mesoscale structure-property models.« less
A Component-Based Diffusion Model With Structural Diversity for Social Networks.

PubMed

Qing Bao; Cheung, William K; Yu Zhang; Jiming Liu

2017-04-01

Diffusion on social networks refers to the process where opinions are spread via the connected nodes. Given a set of observed information cascades, one can infer the underlying diffusion process for social network analysis. The independent cascade model (IC model) is a widely adopted diffusion model where a node is assumed to be activated independently by any one of its neighbors. In reality, how a node will be activated also depends on how its neighbors are connected and activated. For instance, the opinions from the neighbors of the same social group are often similar and thus redundant. In this paper, we extend the IC model by considering that: 1) the information coming from the connected neighbors are similar and 2) the underlying redundancy can be modeled using a dynamic structural diversity measure of the neighbors. Our proposed model assumes each node to be activated independently by different communities (or components) of its parent nodes, each weighted by its effective size. An expectation maximization algorithm is derived to infer the model parameters. We compare the performance of the proposed model with the basic IC model and its variants using both synthetic data sets and a real-world data set containing news stories and Web blogs. Our empirical results show that incorporating the community structure of neighbors and the structural diversity measure into the diffusion model significantly improves the accuracy of the model, at the expense of only a reasonable increase in run-time.
Stand Structure and Substrate Diversity as Two Major Drivers for Bryophyte Distribution in a Temperate Montane Ecosystem

PubMed Central

Chen, Yun; Niu, Shuai; Li, Peikun; Jia, Hongru; Wang, Hailiang; Ye, Yongzhong; Yuan, Zhiliang

2017-01-01

Elucidating the major drivers of bryophyte distribution is the first step to protecting bryophyte diversity. Topography, forest, substrates (ground, tree trunks, roots, rocks, and rotten wood), and spatial factor, which factors are the major drivers of bryophyte distribution? In this study, 53 plots were set in 400 m2 along the elevation gradient in Xiaoqinling, China. All bryophytes in the plots were collected and identified. Regression analysis was used to examine the relationship between bryophyte and substrate diversity. We compared the patterns of overall bryophyte diversity and diversity of bryophytes found on the ground, tree, and rock along elevational gradients. Canonical correspondence analysis was applied to relate species composition to selected environmental variables. The importance of topography, forest, substrates, and spatial factors was determined by variance partitioning. A total of 1378 bryophyte specimens were collected, and 240 species were identified. Bryophyte diversity was closely related to substrate diversity. The overall bryophyte diversity significantly increased with elevation; however, the response varied among ground, tree, and rock bryophytes. Tree diversity and herb layer were considered important environmental factors in determining bryophyte distribution. Species abundance was best explained by stand structure (17%), and species diversity was best explained by stand structure (35%) and substrate (40%). Results directly indicated that substrate diversity can improve bryophyte species diversity. The effects of micro-habitat formed by stand structure and substrate diversity were higher than those of spatial processes and topography factors on bryophyte distribution. This study proved that the determinant factors influencing bryophyte diversity reflect the trends in recent forest management, providing a real opportunity to improve forest biodiversity conservation. PMID:28603535
Stand Structure and Substrate Diversity as Two Major Drivers for Bryophyte Distribution in a Temperate Montane Ecosystem.

PubMed

Chen, Yun; Niu, Shuai; Li, Peikun; Jia, Hongru; Wang, Hailiang; Ye, Yongzhong; Yuan, Zhiliang

2017-01-01

Elucidating the major drivers of bryophyte distribution is the first step to protecting bryophyte diversity. Topography, forest, substrates (ground, tree trunks, roots, rocks, and rotten wood), and spatial factor, which factors are the major drivers of bryophyte distribution? In this study, 53 plots were set in 400 m 2 along the elevation gradient in Xiaoqinling, China. All bryophytes in the plots were collected and identified. Regression analysis was used to examine the relationship between bryophyte and substrate diversity. We compared the patterns of overall bryophyte diversity and diversity of bryophytes found on the ground, tree, and rock along elevational gradients. Canonical correspondence analysis was applied to relate species composition to selected environmental variables. The importance of topography, forest, substrates, and spatial factors was determined by variance partitioning. A total of 1378 bryophyte specimens were collected, and 240 species were identified. Bryophyte diversity was closely related to substrate diversity. The overall bryophyte diversity significantly increased with elevation; however, the response varied among ground, tree, and rock bryophytes. Tree diversity and herb layer were considered important environmental factors in determining bryophyte distribution. Species abundance was best explained by stand structure (17%), and species diversity was best explained by stand structure (35%) and substrate (40%). Results directly indicated that substrate diversity can improve bryophyte species diversity. The effects of micro-habitat formed by stand structure and substrate diversity were higher than those of spatial processes and topography factors on bryophyte distribution. This study proved that the determinant factors influencing bryophyte diversity reflect the trends in recent forest management, providing a real opportunity to improve forest biodiversity conservation.
An Innovative Supply Chain Management Programme Structure: Broadening the SCM Skill Set

ERIC Educational Resources Information Center

Okongwu, Uche

2007-01-01

This paper proposes a matrix structure for training Supply Chain Management (SCM) professionals. It is an innovative programme structure that combines two approaches: cross-border and inter-organisational. It enables the students to comprehend complex and specific business environments and to understand the diverse nature of SCM systems in both…
Leader Delegation and Trust in Global Software Teams

ERIC Educational Resources Information Center

Zhang, Suling

2008-01-01

Virtual teams are an important work structure in global software development. The distributed team structure enables access to a diverse set of expertise which is often not available in one location, to a cheaper labor force, and to a potentially accelerated development process that uses a twenty-four hour work structure. Many software teams…
The organisational structure of urban environmental stewardship

Treesearch

Dana R. Fisher; Lindsay Campbell; Erika S. Svendsen

2012-01-01

How is the organisational structure of urban environmental stewardship groups related to the diverse ways that civic stewardship is taking place in urban settings? The findings of the limited number of studies that have explored the organisational structure of civic environmentalism are combined with the research on civic stewardship to answer this question. By...
From genes to ecosystems: Measuring evolutionary diversity and community structure with Forest Inventory and Analysis (FIA) data

Treesearch

Kevin M. Potter

2009-01-01

Forest genetic sustainability is an important component of forest health because genetic diversity and evolutionary processes allow for the adaptation of species and for the maintenance of ecosystem functionality and resilience. Phylogenetic community analyses, a set of new statistical methods for describing the evolutionary relationships among species, offer an...
Five African American Male Superintendents and Their Leadership in Diverse School Districts in Texas

ERIC Educational Resources Information Center

Smothers, Aneil Chrisfor

2012-01-01

The focus of this research is in the area of African American male superintendents and their leadership in diverse settings. The research approach adopted in this dissertation used semi-structured interviews with five African American male superintendents that consisted of three main issues: (1) personal; (2) leadership quality/effectiveness and…

Exploration of Novel Chemical Space: Synthesis and in vitro Evaluation of N-Functionalized Tertiary Sulfonimidamides.

PubMed

Izzo, Flavia; Schäfer, Martina; Lienau, Philip; Ganzer, Ursula; Stockman, Robert; Lücking, Ulrich

2018-05-04

An unprecedented set of structurally diverse sulfonimidamides (47 compounds) has been prepared by various N-functionalization reactions of tertiary =NH sulfonimidamide 2 aa. These N-functionalization reactions of model compound 2 aa include arylation, alkylation, trifluoromethylation, cyanation, sulfonylation, alkoxycarbonylation (carbamate formation) and aminocarbonylation (urea formation). Small molecule X-ray analyses of selected N-functionalized products are reported. To gain further insight into the properties of sulfonimidamides relevant to medicinal chemistry, a variety of structurally diverse reaction products were tested in selected in vitro assays. The described N-functionalization reactions provide a short and efficient approach to structurally diverse sulfonimidamides which have been the subject of recent, growing interest in the life sciences. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Increasingly diverse brain dynamics in the developmental arc: using Pareto-optimization to infer a mechanism

NASA Astrophysics Data System (ADS)

Tang, Evelyn; Giusti, Chad; Baum, Graham; Gu, Shi; Pollock, Eli; Kahn, Ari; Roalf, David; Moore, Tyler; Ruparel, Kosha; Gur, Ruben; Gur, Raquel; Satterthwaite, Theodore; Bassett, Danielle

Motivated by a recent demonstration that the network architecture of white matter supports emerging control of diverse neural dynamics as children mature into adults, we seek to investigate structural mechanisms that support these changes. Beginning from a network representation of diffusion imaging data, we simulate network evolution with a set of simple growth rules built on principles of network control. Notably, the optimal evolutionary trajectory displays a striking correspondence to the progression of child to adult brain, suggesting that network control is a driver of development. More generally, and in comparison to the complete set of available models, we demonstrate that all brain networks from child to adult are structured in a manner highly optimized for the control of diverse neural dynamics. Within this near-optimality, we observe differences in the predicted control mechanisms of the child and adult brains, suggesting that the white matter architecture in children has a greater potential to increasingly support brain state transitions, potentially underlying cognitive switching.
CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON THE INTERNET: MOVING TOWARDS A FLAT WORLD

EPA Science Inventory

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives th...
Genetic diversity of lake whitefish in lakes Michigan and Huron: sampling, standardization, and research priorities

USGS Publications Warehouse

Stott, Wendylee; VanDeHey, Justin A.; Sloss, Brian L.

2010-01-01

We combined data from two laboratories to increase the spatial extent of a genetic data set for lake whitefish Coregonus clupeaformis from lakes Huron and Michigan and saw that genetic diversity was greatest between lakes, but that there was also structuring within lakes. Low diversity among stocks may be a reflection of relatively recent colonization of the Great Lakes, but other factors such as recent population fluctuation and localized stresses such as lamprey predation or heavy exploitation may also have a homogenizing effect. Our data suggested that there is asymmetrical movement of lake whitefish between Lake Huron and Lake Michigan; more genotypes associated with Lake Michigan were observed in Lake Huron. Adding additional collections to the calibrated set will allow further examination of diversity in other Great Lakes, answer questions regarding movement among lakes, and estimate contributions of stocks to commercial yields. As the picture of genetic diversity and population structure of lake whitefish in the Great Lakes region emerges, we need to develop methods to combine data types to help identify important areas for biodiversity and thus conservation. Adding genetic data to existing models will increase the precision of predictions of the impacts of new stresses and changes in existing pressures on an ecologically and commercially important species.
Genomic diversity and macroecology of the crop wild relatives of domesticated pea.

PubMed

Smýkal, Petr; Hradilová, Iveta; Trněný, Oldřich; Brus, Jan; Rathore, Abhishek; Bariotakis, Michael; Das, Roma Rani; Bhattacharyya, Debjyoti; Richards, Christopher; Coyne, Clarice J; Pirintsos, Stergios

2017-12-12

There is growing interest in the conservation and utilization of crop wild relatives (CWR) in international food security policy and research. Legumes play an important role in human health, sustainable food production, global food security, and the resilience of current agricultural systems. Pea belongs to the ancient set of cultivated plants of the Near East domestication center and remains an important crop today. Based on genome-wide analysis, P. fulvum was identified as a well-supported species, while the diversity of wild P. sativum subsp. elatius was structured into 5 partly geographically positioned clusters. We explored the spatial and environmental patterns of two progenitor species of domesticated pea in the Mediterranean Basin and in the Fertile Crescent in relation to the past and current climate. This study revealed that isolation by distance does not explain the genetic structure of P. sativum subsp. elatius in its westward expansion from its center of origin. The genetic diversity of wild pea may be driven by Miocene-Pliocene events, while the phylogenetic diversity centers may reflect Pleisto-Holocene climatic changes. These findings help set research and discussion priorities and provide geographical and ecological information for germplasm-collecting missions, as well as for the preservation of extant diversity in ex-situ collections.
Animal social networks as substrate for cultural behavioural diversity.

PubMed

Whitehead, Hal; Lusseau, David

2012-02-07

We used individual-based stochastic models to examine how social structure influences the diversity of socially learned behaviour within a non-human population. For continuous behavioural variables we modelled three forms of dyadic social learning, averaging the behavioural value of the two individuals, random transfer of information from one individual to the other, and directional transfer from the individual with highest behavioural value to the other. Learning had potential error. We also examined the transfer of categorical behaviour between individuals with random directionality and two forms of error, the adoption of a randomly chosen existing behavioural category or the innovation of a new type of behaviour. In populations without social structuring the diversity of culturally transmitted behaviour increased with learning error and population size. When the populations were structured socially either by making individuals members of permanent social units or by giving them overlapping ranges, behavioural diversity increased with network modularity under all scenarios, although the proportional increase varied considerably between continuous and categorical behaviour, with transmission mechanism, and population size. Although functions of the form e(c)¹(m)⁻(c)² + (c)³(Log(N)) predicted the mean increase in diversity with modularity (m) and population size (N), behavioural diversity could be highly unpredictable both between simulations with the same set of parameters, and within runs. Errors in social learning and social structuring generally promote behavioural diversity. Consequently, social learning may be considered to produce culture in populations whose social structure is sufficiently modular. Copyright © 2011 Elsevier Ltd. All rights reserved.
Genomic Prediction of Gene Bank Wheat Landraces.

PubMed

Crossa, José; Jarquín, Diego; Franco, Jorge; Pérez-Rodríguez, Paulino; Burgueño, Juan; Saint-Pierre, Carolina; Vikram, Prashant; Sansaloni, Carolina; Petroli, Cesar; Akdemir, Deniz; Sneller, Clay; Reynolds, Matthew; Tattaris, Maria; Payne, Thomas; Guzman, Carlos; Peña, Roberto J; Wenzl, Peter; Singh, Sukhwinder

2016-07-07

This study examines genomic prediction within 8416 Mexican landrace accessions and 2403 Iranian landrace accessions stored in gene banks. The Mexican and Iranian collections were evaluated in separate field trials, including an optimum environment for several traits, and in two separate environments (drought, D and heat, H) for the highly heritable traits, days to heading (DTH), and days to maturity (DTM). Analyses accounting and not accounting for population structure were performed. Genomic prediction models include genotype × environment interaction (G × E). Two alternative prediction strategies were studied: (1) random cross-validation of the data in 20% training (TRN) and 80% testing (TST) (TRN20-TST80) sets, and (2) two types of core sets, "diversity" and "prediction", including 10% and 20%, respectively, of the total collections. Accounting for population structure decreased prediction accuracy by 15-20% as compared to prediction accuracy obtained when not accounting for population structure. Accounting for population structure gave prediction accuracies for traits evaluated in one environment for TRN20-TST80 that ranged from 0.407 to 0.677 for Mexican landraces, and from 0.166 to 0.662 for Iranian landraces. Prediction accuracy of the 20% diversity core set was similar to accuracies obtained for TRN20-TST80, ranging from 0.412 to 0.654 for Mexican landraces, and from 0.182 to 0.647 for Iranian landraces. The predictive core set gave similar prediction accuracy as the diversity core set for Mexican collections, but slightly lower for Iranian collections. Prediction accuracy when incorporating G × E for DTH and DTM for Mexican landraces for TRN20-TST80 was around 0.60, which is greater than without the G × E term. For Iranian landraces, accuracies were 0.55 for the G × E model with TRN20-TST80. Results show promising prediction accuracies for potential use in germplasm enhancement and rapid introgression of exotic germplasm into elite materials. Copyright © 2016 Crossa et al.
Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing.

PubMed

Shi, Ainong; Qin, Jun; Mou, Beiquan; Correll, James; Weng, Yuejin; Brenner, David; Feng, Chunda; Motes, Dennis; Yang, Wei; Dong, Lingdi; Bhattarai, Gehendra; Ravelombola, Waltram

2017-01-01

Spinach (Spinacia oleracea L., 2n = 2x = 12) is an economically important vegetable crop worldwide and one of the healthiest vegetables due to its high concentrations of nutrients and minerals. The objective of this research was to conduct genetic diversity and population structure analysis of a collection of world-wide spinach genotypes using single nucleotide polymorphisms (SNPs) markers. Genotyping by sequencing (GBS) was used to discover SNPs in spinach genotypes. Three sets of spinach genotypes were used: 1) 268 USDA GRIN spinach germplasm accessions originally collected from 30 countries; 2) 45 commercial spinach F1 hybrids from three countries; and 3) 30 US Arkansas spinach cultivars/breeding lines. The results from this study indicated that there was genetic diversity among the 343 spinach genotypes tested. Furthermore, the genetic background in improved commercial F1 hybrids and in Arkansas cultivars/lines had a different structured populations from the USDA germplasm. In addition, the genetic diversity and population structures were associated with geographic origin and germplasm from the US Arkansas breeding program had a unique genetic background. These data could provide genetic diversity information and the molecular markers for selecting parents in spinach breeding programs.
Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing

PubMed Central

Qin, Jun; Mou, Beiquan; Correll, James; Weng, Yuejin; Brenner, David; Feng, Chunda; Motes, Dennis; Yang, Wei; Dong, Lingdi; Bhattarai, Gehendra; Ravelombola, Waltram

2017-01-01

Spinach (Spinacia oleracea L., 2n = 2x = 12) is an economically important vegetable crop worldwide and one of the healthiest vegetables due to its high concentrations of nutrients and minerals. The objective of this research was to conduct genetic diversity and population structure analysis of a collection of world-wide spinach genotypes using single nucleotide polymorphisms (SNPs) markers. Genotyping by sequencing (GBS) was used to discover SNPs in spinach genotypes. Three sets of spinach genotypes were used: 1) 268 USDA GRIN spinach germplasm accessions originally collected from 30 countries; 2) 45 commercial spinach F1 hybrids from three countries; and 3) 30 US Arkansas spinach cultivars/breeding lines. The results from this study indicated that there was genetic diversity among the 343 spinach genotypes tested. Furthermore, the genetic background in improved commercial F1 hybrids and in Arkansas cultivars/lines had a different structured populations from the USDA germplasm. In addition, the genetic diversity and population structures were associated with geographic origin and germplasm from the US Arkansas breeding program had a unique genetic background. These data could provide genetic diversity information and the molecular markers for selecting parents in spinach breeding programs. PMID:29190770
spads 1.0: a toolbox to perform spatial analyses on DNA sequence data sets.

PubMed

Dellicour, Simon; Mardulyn, Patrick

2014-05-01

SPADS 1.0 (for 'Spatial and Population Analysis of DNA Sequences') is a population genetic toolbox for characterizing genetic variability within and among populations from DNA sequences. In view of the drastic increase in genetic information available through sequencing methods, spads was specifically designed to deal with multilocus data sets of DNA sequences. It computes several summary statistics from populations or groups of populations, performs input file conversions for other population genetic programs and implements locus-by-locus and multilocus versions of two clustering algorithms to study the genetic structure of populations. The toolbox also includes two MATLAB and r functions, GDISPAL and GDIVPAL, to display differentiation and diversity patterns across landscapes. These functions aim to generate interpolating surfaces based on multilocus distance and diversity indices. In the case of multiple loci, such surfaces can represent a useful alternative to multiple pie charts maps traditionally used in phylogeography to represent the spatial distribution of genetic diversity. These coloured surfaces can also be used to compare different data sets or different diversity and/or distance measures estimated on the same data set. © 2013 John Wiley & Sons Ltd.
Genetic Diversity and Population Structure in a Legacy Collection of Spring Barley Landraces Adapted to a Wide Range of Climates

PubMed Central

Walther, Alexander; Özkan, Hakan; Graner, Andreas; Kilian, Benjamin

2014-01-01

Global environmental change and increasing human population emphasize the urgent need for higher yielding and better adapted crop plants. One strategy to achieve this aim is to exploit the wealth of so called landraces of crop species, representing diverse traditional domesticated populations of locally adapted genotypes. In this study, we investigated a comprehensive set of 1485 spring barley landraces (Lrc1485) adapted to a wide range of climates, which were selected from one of the largest genebanks worldwide. The landraces originated from 5° to 62.5° N and 16° to 71° E. The whole collection was genotyped using 42 SSR markers to assess the genetic diversity and population structure. With an average allelic richness of 5.74 and 372 alleles, Lrc1485 harbours considerably more genetic diversity than the most polymorphic current GWAS panel for barley. Ten major clusters defined most of the population structure based on geographical origin, row type of the ear and caryopsis type – and were assigned to specific climate zones. The legacy core reference set Lrc648 established in this study will provide a long-lasting resource and a very valuable tool for the scientific community. Lrc648 is best suited for multi-environmental field testing to identify candidate genes underlying quantitative traits but also for allele mining approaches. PMID:25541702
Synthesis of structurally diverse major groove DNA interstrand crosslinks using three different aldehyde precursors

PubMed Central

Mukherjee, Shivam; Guainazzi, Angelo; Schärer, Orlando D.

2014-01-01

DNA interstrand crosslinks (ICLs) are extremely cytotoxic lesions that block essential cellular processes, such as replication and transcription. Crosslinking agents are widely used in cancer chemotherapy and form an array of structurally diverse ICLs. Despite the clinical success of these agents, resistance of tumors to crosslinking agents, for example, through repair of these lesions by the cellular machinery remains a problem. We have previously reported the synthesis of site-specific ICLs mimicking those formed by nitrogen mustards to facilitate the studies of cellular responses to ICL formation. Here we extend these efforts and report the synthesis of structurally diverse major groove ICLs that induce severe, little or no distortion in the DNA. Our approach employs the incorporation of aldehyde precursors of different lengths into complementary strands and ICL formation using a double reductive amination with a variety of amines. Our studies provide insight into the structure and reactivity parameters of ICL formation by double reductive amination and yield a set of diverse ICLs that will be invaluable for exploring structure–activity relationships in ICL repair. PMID:24782532
Workplace diversity: a leadership challenge. Managing diversity is a social, financial, and moral imperative.

PubMed

Lappetito, J

1994-03-01

Fostering workplace diversity is about building an organizational culture that embraces personal differences and encourages heterogeneous persons to work together toward a common end. Setting in motion the transition to a more inclusive and productive workplace is an uncommon challenge and the primary responsibility of leaders, especially in Catholic healthcare. The origins of diversity can be found in creation itself. Not only are we united as a people of God and as members of the body of Christ, we are bound together through our shared humanity. Three values are especially relevant to promoting diversity in the workplace: respect for human dignity, the common good, and distributive justice as participation in the common good. Economic incentives strengthen the theological and moral motives for developing a diverse work force. Organizations' financial success will depend ultimately on how well diversity is integrated into the organizational culture. As a process, managing diversity enables healthcare leaders to discover new ways to develop the potential of all employees and at the same time improve performance and production. At the heart of managing diversity lies the reform of internal systems, structures, and processes. Managing diversity also requires the transformation of the organization's culture. Initiatives that are useful for setting a positive future course include conducting a cultural audit, establishing a cultural diversity task force, and putting in place a diversity "champion" who is accountable directly to the chief executive officer.
Surflex-Dock: Docking benchmarks and real-world application

NASA Astrophysics Data System (ADS)

Spitzer, Russell; Jain, Ajay N.

2012-06-01

Benchmarks for molecular docking have historically focused on re-docking the cognate ligand of a well-determined protein-ligand complex to measure geometric pose prediction accuracy, and measurement of virtual screening performance has been focused on increasingly large and diverse sets of target protein structures, cognate ligands, and various types of decoy sets. Here, pose prediction is reported on the Astex Diverse set of 85 protein ligand complexes, and virtual screening performance is reported on the DUD set of 40 protein targets. In both cases, prepared structures of targets and ligands were provided by symposium organizers. The re-prepared data sets yielded results not significantly different than previous reports of Surflex-Dock on the two benchmarks. Minor changes to protein coordinates resulting from complex pre-optimization had large effects on observed performance, highlighting the limitations of cognate ligand re-docking for pose prediction assessment. Docking protocols developed for cross-docking, which address protein flexibility and produce discrete families of predicted poses, produced substantially better performance for pose prediction. Performance on virtual screening performance was shown to benefit by employing and combining multiple screening methods: docking, 2D molecular similarity, and 3D molecular similarity. In addition, use of multiple protein conformations significantly improved screening enrichment.
Cell wall evolution and diversity

PubMed Central

Fangel, Jonatan U.; Ulvskov, Peter; Knox, J. P.; Mikkelsen, Maria D.; Harholt, Jesper; Popper, Zoë A.; Willats, William G.T.

2012-01-01

Plant cell walls display a considerable degree of diversity in their compositions and molecular architectures. In some cases the functional significance of a particular cell wall type appears to be easy to discern: secondary cells walls are often reinforced with lignin that provides durability; the thin cell walls of pollen tubes have particular compositions that enable their tip growth; lupin seed cell walls are characteristically thickened with galactan used as a storage polysaccharide. However, more frequently the evolutionary mechanisms and selection pressures that underpin cell wall diversity and evolution are unclear. For diverse green plants (chlorophytes and streptophytes) the rapidly increasing availability of transcriptome and genome data sets, the development of methods for cell wall analyses which require less material for analysis, and expansion of molecular probe sets, are providing new insights into the diversity and occurrence of cell wall polysaccharides and associated biosynthetic genes. Such research is important for refining our understanding of some of the fundamental processes that enabled plants to colonize land and to subsequently radiate so comprehensively. The study of cell wall structural diversity is also an important aspect of the industrial utilization of global polysaccharide bio-resources. PMID:22783271
Single High Fidelity Geometric Data Sets for LCM - Model Requirements

DTIC Science & Technology

2006-11-01

are extensive single 3D CAD data models incorporating hull structure, propulsion, steering, piping , electrical, HVAC and other systems, which make...single 3D CAD data models incorporating hull structure, propulsion, steering, piping , electrical, HVAC and other systems. During this same period...be sufficiently flexible to accommodate the diverse requirements of various types of structural analyses. Section Properties & Material Data
Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.

PubMed

Eltaher, Shamseldeen; Sallam, Ahmed; Belamkar, Vikas; Emara, Hamdy A; Nower, Ahmed A; Salem, Khaled F M; Poland, Jesse; Baenziger, Peter S

2018-01-01

The availability of information on the genetic diversity and population structure in wheat ( Triticum aestivum L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F 3:6 ) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon's information index ( I ) = 0.494, diversity index ( h ) = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity ( I = 0.348, h = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars.
Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing

PubMed Central

Eltaher, Shamseldeen; Sallam, Ahmed; Belamkar, Vikas; Emara, Hamdy A.; Nower, Ahmed A.; Salem, Khaled F. M.; Poland, Jesse; Baenziger, Peter S.

2018-01-01

The availability of information on the genetic diversity and population structure in wheat (Triticum aestivum L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F3:6) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon’s information index (I) = 0.494, diversity index (h) = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity (I = 0.348, h = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars. PMID:29593779
Benchmarking density functional theory predictions of framework structures and properties in a chemically diverse test set of metal-organic frameworks

DOE PAGES

Nazarian, Dalar; Ganesh, P.; Sholl, David S.

2015-09-30

We compiled a test set of chemically and topologically diverse Metal–Organic Frameworks (MOFs) with high accuracy experimentally derived crystallographic structure data. The test set was used to benchmark the performance of Density Functional Theory (DFT) functionals (M06L, PBE, PW91, PBE-D2, PBE-D3, and vdW-DF2) for predicting lattice parameters, unit cell volume, bonded parameters and pore descriptors. On average PBE-D2, PBE-D3, and vdW-DF2 predict more accurate structures, but all functionals predicted pore diameters within 0.5 Å of the experimental diameter for every MOF in the test set. The test set was also used to assess the variance in performance of DFT functionalsmore » for elastic properties and atomic partial charges. The DFT predicted elastic properties such as minimum shear modulus and Young's modulus can differ by an average of 3 and 9 GPa for rigid MOFs such as those in the test set. Moreover, we calculated the partial charges by vdW-DF2 deviate the most from other functionals while there is no significant difference between the partial charges calculated by M06L, PBE, PW91, PBE-D2 and PBE-D3 for the MOFs in the test set. We find that while there are differences in the magnitude of the properties predicted by the various functionals, these discrepancies are small compared to the accuracy necessary for most practical applications.« less
Increasing the availability and usability of terrestrial ecology data through geospatial Web services and visualization tools (Invited)

NASA Astrophysics Data System (ADS)

Santhana Vannan, S.; Cook, R. B.; Wilson, B. E.; Wei, Y.

2010-12-01

Terrestrial ecology data sets are produced from diverse data sources such as model output, field data collection, laboratory analysis and remote sensing observation. These data sets can be created, distributed, and consumed in diverse ways as well. However, this diversity can hinder the usability of the data, and limit data users’ abilities to validate and reuse data for science and application purposes. Geospatial web services, such as those described in this paper, are an important means of reducing this burden. Terrestrial ecology researchers generally create the data sets in diverse file formats, with file and data structures tailored to the specific needs of their project, possibly as tabular data, geospatial images, or documentation in a report. Data centers may reformat the data to an archive-stable format and distribute the data sets through one or more protocols, such as FTP, email, and WWW. Because of the diverse data preparation, delivery, and usage patterns, users have to invest time and resources to bring the data into the format and structure most useful for their analysis. This time-consuming data preparation process shifts valuable resources from data analysis to data assembly. To address these issues, the ORNL DAAC, a NASA-sponsored terrestrial ecology data center, has utilized geospatial Web service technology, such as Open Geospatial Consortium (OGC) Web Map Service (WMS) and OGC Web Coverage Service (WCS) standards, to increase the usability and availability of terrestrial ecology data sets. Data sets are standardized into non-proprietary file formats and distributed through OGC Web Service standards. OGC Web services allow the ORNL DAAC to store data sets in a single format and distribute them in multiple ways and formats. Registering the OGC Web services through search catalogues and other spatial data tools allows for publicizing the data sets and makes them more available across the Internet. The ORNL DAAC has also created a Web-based graphical user interface called Spatial Data Access Tool (SDAT) that utilizes OGC Web services standards and allows data distribution and consumption for users not familiar with OGC standards. SDAT also allows for users to visualize the data set prior to download. Google Earth visualizations of the data set are also provided through SDAT. The use of OGC Web service standards at the ORNL DAAC has enabled an increase in data consumption. In one case, a data set had ~10 fold increase in download through OGC Web service in comparison to the conventional FTP and WWW method of access. The increase in download suggests that users are not only finding the data sets they need but also able to consume them readily in the format they need.

Genarris: Random generation of molecular crystal structures and fast screening with a Harris approximation

NASA Astrophysics Data System (ADS)

Li, Xiayue; Curtis, Farren S.; Rose, Timothy; Schober, Christoph; Vazquez-Mayagoitia, Alvaro; Reuter, Karsten; Oberhofer, Harald; Marom, Noa

2018-06-01

We present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations, Genarris employs a Harris approximation, whereby the total density of a molecular crystal is constructed via superposition of single molecule densities. Dispersion-inclusive density functional theory is then used for the Harris density without performing a self-consistency cycle. Genarris uses machine learning for clustering, based on a relative coordinate descriptor developed specifically for molecular crystals, which is shown to be robust in identifying packing motif similarity. In addition to random structure generation, Genarris offers three workflows based on different sequences of successive clustering and selection steps: the "Rigorous" workflow is an exhaustive exploration of the potential energy landscape, the "Energy" workflow produces a set of low energy structures, and the "Diverse" workflow produces a maximally diverse set of structures. The latter is recommended for generating initial populations for genetic algorithms. Here, the implementation of Genarris is reported and its application is demonstrated for three test cases.
The Sign Rule and Beyond: Boundary Effects, Flexibility, and Noise Correlations in Neural Population Codes

PubMed Central

Hu, Yu; Zylberberg, Joel; Shea-Brown, Eric

2014-01-01

Over repeat presentations of the same stimulus, sensory neurons show variable responses. This “noise” is typically correlated between pairs of cells, and a question with rich history in neuroscience is how these noise correlations impact the population's ability to encode the stimulus. Here, we consider a very general setting for population coding, investigating how information varies as a function of noise correlations, with all other aspects of the problem – neural tuning curves, etc. – held fixed. This work yields unifying insights into the role of noise correlations. These are summarized in the form of theorems, and illustrated with numerical examples involving neurons with diverse tuning curves. Our main contributions are as follows. (1) We generalize previous results to prove a sign rule (SR) — if noise correlations between pairs of neurons have opposite signs vs. their signal correlations, then coding performance will improve compared to the independent case. This holds for three different metrics of coding performance, and for arbitrary tuning curves and levels of heterogeneity. This generality is true for our other results as well. (2) As also pointed out in the literature, the SR does not provide a necessary condition for good coding. We show that a diverse set of correlation structures can improve coding. Many of these violate the SR, as do experimentally observed correlations. There is structure to this diversity: we prove that the optimal correlation structures must lie on boundaries of the possible set of noise correlations. (3) We provide a novel set of necessary and sufficient conditions, under which the coding performance (in the presence of noise) will be as good as it would be if there were no noise present at all. PMID:24586128
ADME evaluation in drug discovery. 1. Applications of genetic algorithms to the prediction of blood-brain partitioning of a large set of drugs.

PubMed

Hou, Tingjun; Xu, Xiaojie

2002-12-01

In this study, the relationships between the brain-blood concentration ratio of 96 structurally diverse compounds with a large number of structurally derived descriptors were investigated. The linear models were based on molecular descriptors that can be calculated for any compound simply from a knowledge of its molecular structure. The linear correlation coefficients of the models were optimized by genetic algorithms (GAs), and the descriptors used in the linear models were automatically selected from 27 structurally derived descriptors. The GA optimizations resulted in a group of linear models with three or four molecular descriptors with good statistical significance. The change of descriptor use as the evolution proceeds demonstrates that the octane/water partition coefficient and the partial negative solvent-accessible surface area multiplied by the negative charge are crucial to brain-blood barrier permeability. Moreover, we found that the predictions using multiple QSPR models from GA optimization gave quite good results in spite of the diversity of structures, which was better than the predictions using the best single model. The predictions for the two external sets with 37 diverse compounds using multiple QSPR models indicate that the best linear models with four descriptors are sufficiently effective for predictive use. Considering the ease of computation of the descriptors, the linear models may be used as general utilities to screen the blood-brain barrier partitioning of drugs in a high-throughput fashion.
Zebra: a web server for bioinformatic analysis of diverse protein families.

PubMed

Suplatov, Dmitry; Kirilin, Evgeny; Takhaveev, Vakil; Svedas, Vytas

2014-01-01

During evolution of proteins from a common ancestor, one functional property can be preserved while others can vary leading to functional diversity. A systematic study of the corresponding adaptive mutations provides a key to one of the most challenging problems of modern structural biology - understanding the impact of amino acid substitutions on protein function. The subfamily-specific positions (SSPs) are conserved within functional subfamilies but are different between them and, therefore, seem to be responsible for functional diversity in protein superfamilies. Consequently, a corresponding method to perform the bioinformatic analysis of sequence and structural data has to be implemented in the common laboratory practice to study the structure-function relationship in proteins and develop novel protein engineering strategies. This paper describes Zebra web server - a powerful remote platform that implements a novel bioinformatic analysis algorithm to study diverse protein families. It is the first application that provides specificity determinants at different levels of functional classification, therefore addressing complex functional diversity of large superfamilies. Statistical analysis is implemented to automatically select a set of highly significant SSPs to be used as hotspots for directed evolution or rational design experiments and analyzed studying the structure-function relationship. Zebra results are provided in two ways - (1) as a single all-in-one parsable text file and (2) as PyMol sessions with structural representation of SSPs. Zebra web server is available at http://biokinet.belozersky.msu.ru/zebra .
A new test set for validating predictions of protein-ligand interaction.

PubMed

Nissink, J Willem M; Murray, Chris; Hartshorn, Mike; Verdonk, Marcel L; Cole, Jason C; Taylor, Robin

2002-12-01

We present a large test set of protein-ligand complexes for the purpose of validating algorithms that rely on the prediction of protein-ligand interactions. The set consists of 305 complexes with protonation states assigned by manual inspection. The following checks have been carried out to identify unsuitable entries in this set: (1) assessing the involvement of crystallographically related protein units in ligand binding; (2) identification of bad clashes between protein side chains and ligand; and (3) assessment of structural errors, and/or inconsistency of ligand placement with crystal structure electron density. In addition, the set has been pruned to assure diversity in terms of protein-ligand structures, and subsets are supplied for different protein-structure resolution ranges. A classification of the set by protein type is available. As an illustration, validation results are shown for GOLD and SuperStar. GOLD is a program that performs flexible protein-ligand docking, and SuperStar is used for the prediction of favorable interaction sites in proteins. The new CCDC/Astex test set is freely available to the scientific community (http://www.ccdc.cam.ac.uk). Copyright 2002 Wiley-Liss, Inc.
Molecular characterization of the Gossypium Diversity Reference Set of the US National Cotton Germplasm Collection.

PubMed

Hinze, Lori L; Fang, David D; Gore, Michael A; Scheffler, Brian E; Yu, John Z; Frelichowski, James; Percy, Richard G

2015-02-01

A core marker set containing markers developed to be informative within a single commercial cotton species can elucidate diversity structure within a multi-species subset of the Gossypium germplasm collection. An understanding of the genetic diversity of cotton (Gossypium spp.) as represented in the US National Cotton Germplasm Collection is essential to develop strategies for collecting, conserving, and utilizing these germplasm resources. The US collection is one of the largest world collections and includes not only accessions with improved yield and fiber quality within cultivated species, but also accessions possessing sources of abiotic and biotic stress resistance often found in wild species. We evaluated the genetic diversity of a subset of 272 diploid and 1,984 tetraploid accessions in the collection (designated the Gossypium Diversity Reference Set) using a core set of 105 microsatellite markers. Utility of the core set of markers in differentiating intra-genome variation was much greater in commercial tetraploid genomes (99.7 % polymorphic bands) than in wild diploid genomes (72.7 % polymorphic bands), and may have been influenced by pre-selection of markers for effectiveness in the commercial species. Principal coordinate analyses revealed that the marker set differentiated interspecific variation among tetraploid species, but was only capable of partially differentiating among species and genomes of the wild diploids. Putative species-specific marker bands in G. hirsutum (73) and G. barbadense (81) were identified that could be used for qualitative identification of misclassifications, redundancies, and introgression within commercial tetraploid species. The results of this broad-scale molecular characterization are essential to the management and conservation of the collection and provide insight and guidance in the use of the collection by the cotton research community in their cotton improvement efforts.
Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus.

PubMed

Kashtan, Nadav; Roggensack, Sara E; Berta-Thompson, Jessie W; Grinberg, Maor; Stepanauskas, Ramunas; Chisholm, Sallie W

2017-09-01

The Atlantic and Pacific Oceans represent different biogeochemical regimes in which the abundant marine cyanobacterium Prochlorococcus thrives. We have shown that Prochlorococcus populations in the Atlantic are composed of hundreds of genomically, and likely ecologically, distinct coexisting subpopulations with distinct genomic backbones. Here we ask if differences in the ecology and selection pressures between the Atlantic and Pacific are reflected in the diversity and genomic composition of their indigenous Prochlorococcus populations. We applied large-scale single-cell genomics and compared the cell-by-cell genomic composition of wild populations of co-occurring cells from samples from Station ALOHA off Hawaii, and from Bermuda Atlantic Time Series Station off Bermuda. We reveal fundamental differences in diversity and genomic structure of populations between the sites. The Pacific populations are more diverse than those in the Atlantic, composed of significantly more coexisting subpopulations and lacking dominant subpopulations. Prochlorococcus from the two sites seem to be composed of mostly non-overlapping distinct sets of subpopulations with different genomic backbones-likely reflecting different sets of ocean-specific micro-niches. Furthermore, phylogenetically closely related strains carry ocean-associated nutrient acquisition genes likely reflecting differences in major selection pressures between the oceans. This differential selection, along with geographic separation, clearly has a significant role in shaping these populations.
Prediction of Mutagenicity of Chemicals from Their Calculated Molecular Descriptors: A Case Study with Structurally Homogeneous versus Diverse Datasets.

PubMed

Basak, Subhash C; Majumdar, Subhabrata

2015-01-01

Variation in high-dimensional data is often caused by a few latent factors, and hence dimension reduction or variable selection techniques are often useful in gathering useful information from the data. In this paper we consider two such recent methods: Interrelated two-way clustering and envelope models. We couple these methods with traditional statistical procedures like ridge regression and linear discriminant analysis, and apply them on two data sets which have more predictors than samples (i.e. n < p scenario) and several types of molecular descriptors. One of these datasets consists of a congeneric group of Amines while the other has a much diverse collection compounds. The difference of prediction results between these two datasets for both the methods supports the hypothesis that for a congeneric set of compounds, descriptors of a certain type are enough to provide good QSAR models, but as the data set grows diverse including a variety of descriptors can improve model quality considerably.
Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

PubMed

Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

2015-12-08

Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.
The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers

USDA-ARS?s Scientific Manuscript database

The evolution of animal mitochondrial (mt) genomes has yielded a highly conserved structure: a single circular chromosome approximately 14 to 20 kb long. Within the last two decades, exceptions to this conserved structure have been reported in a diverse set of organisms. One such exception is the di...
From diagnostics to metagenomics: Applications of DNA-based tools in forest pathology

Treesearch

Amy L. Ross-Davis; Mee-Sook Kim; Jane E. Stewart; John W. Hanna; John D. Shaw; Ned B. Klopfenstein

2013-01-01

Advances in molecular technology provide an accessible set of tools to 1) help forest pathologists detect, identify, and monitor forest pathogens, 2) examine the evolutionary relationships and global distributions of forest pathogens and their hosts, 3) assess the diversity and structure of host and pathogen populations, and 4) evaluate the structure and function of...
Temporal turnover and the maintenance of diversity in ecological assemblages

PubMed Central

Magurran, Anne E.; Henderson, Peter A.

2010-01-01

Temporal variation in species abundances occurs in all ecological communities. Here, we explore the role that this temporal turnover plays in maintaining assemblage diversity. We investigate a three-decade time series of estuarine fishes and show that the abundances of the individual species fluctuate asynchronously around their mean levels. We then use a time-series modelling approach to examine the consequences of different patterns of turnover, by asking how the correlation between the abundance of a species in a given year and its abundance in the previous year influences the structure of the overall assemblage. Classical diversity measures that ignore species identities reveal that the observed assemblage structure will persist under all but the most extreme conditions. However, metrics that track species identities indicate a narrower set of turnover scenarios under which the predicted assemblage resembles the natural one. Our study suggests that species diversity metrics are insensitive to change and that measures that track species ranks may provide better early warning that an assemblage is being perturbed. It also highlights the need to incorporate temporal turnover in investigations of assemblage structure and function. PMID:20980310
Robust estimation of microbial diversity in theory and in practice

PubMed Central

Haegeman, Bart; Hamelin, Jérôme; Moriarty, John; Neal, Peter; Dushoff, Jonathan; Weitz, Joshua S

2013-01-01

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics (‘Hill diversities'), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity. PMID:23407313
Transcriptional regulation by the Set7 lysine methyltransferase

PubMed Central

Keating, Samuel; El-Osta, Assam

2013-01-01

Posttranslational histone modifications define chromatin structure and function. In recent years, a number of studies have characterized many of the enzymatic activities and diverse regulatory components required for monomethylation of histone H3 lysine 4 (H3K4me1) and the expression of specific genes. The challenge now is to understand how this specific chemical modification is written and the Set7 methyltransferase has emerged as a key regulatory enzyme mediating methylation of lysine residues of histone and non-histone proteins. In this review, we comprehensively explore the regulatory proteins modified by Set7 and highlight mechanisms of specific co-recruitment of the enzyme to activating promoters. With a focus on signaling and transcriptional control in disease we discuss recent experimental data emphasizing specific components of diverse regulatory complexes that mediate chromatin modification and reinterpretation of Set7-mediated gene expression. PMID:23478572
Electrostatic similarity of proteins: Application of three dimensional spherical harmonic decomposition

PubMed Central

Długosz, Maciej; Trylska, Joanna

2008-01-01

We present a method for describing and comparing global electrostatic properties of biomolecules based on the spherical harmonic decomposition of electrostatic potential data. Unlike other approaches our method does not require any prior three dimensional structural alignment. The electrostatic potential, given as a volumetric data set from a numerical solution of the Poisson or Poisson–Boltzmann equation, is represented with descriptors that are rotation invariant. The method can be applied to large and structurally diverse sets of biomolecules enabling to cluster them according to their electrostatic features. PMID:18624502
Unexpected Diversity during Community Succession in the Apple Flower Microbiome

PubMed Central

Shade, Ashley; McManus, Patricia S.; Handelsman, Jo

2013-01-01

ABSTRACT Despite its importance to the host, the flower microbiome is poorly understood. We report a culture-independent, community-level assessment of apple flower microbial diversity and dynamics. We collected flowers from six apple trees at five time points, starting before flowers opened and ending at petal fall. We applied streptomycin to half of the trees when flowers opened. Assessment of microbial diversity using tag pyrosequencing of 16S rRNA genes revealed that the apple flower communities were rich and diverse and dominated by members of TM7 and Deinococcus-Thermus, phyla about which relatively little is known. From thousands of taxa, we identified six successional groups with coherent dynamics whose abundances peaked at different times before and after bud opening. We designated the groups Pioneer, Early, Mid, Late, Climax, and Generalist communities. The successional pattern was attributed to a set of prevalent taxa that were persistent and gradually changing in abundance. These taxa had significant associations with other community members, as demonstrated with a cooccurrence network based on local similarity analysis. We also detected a set of less-abundant, transient taxa that contributed to general tree-to-tree variability but not to the successional pattern. Communities on trees sprayed with streptomycin had slightly lower phylogenetic diversity than those on unsprayed trees but did not differ in structure or succession. Our results suggest that changes in apple flower microbial community structure are predictable over the life of the flower, providing a basis for ecological understanding and disease management. PMID:23443006
Establishing the A. E. Watkins landrace cultivar collection as a resource for systematic gene discovery in bread wheat.

PubMed

Wingen, Luzie U; Orford, Simon; Goram, Richard; Leverington-Waite, Michelle; Bilham, Lorelei; Patsiou, Theofania S; Ambrose, Mike; Dicks, Jo; Griffiths, Simon

2014-08-01

A high level of genetic diversity was found in the A. E. Watkins bread wheat landrace collection. Genotypic information was used to determine the population structure and to develop germplasm resources. In the 1930s A. E. Watkins acquired landrace cultivars of bread wheat (Triticum aestivum L.) from official channels of the board of Trade in London, many of which originated from local markets in 32 countries. The geographic distribution of the 826 landrace cultivars of the current collection, here called the Watkins collection, covers many Asian and European countries and some from Africa. The cultivars were genotyped with 41 microsatellite markers in order to investigate the genetic diversity and population structure of the collection. A high level of genetic diversity was found, higher than in a collection of modern European winter bread wheat varieties from 1945 to 2000. Furthermore, although weak, the population structure of the Watkins collection reveals nine ancestral geographical groupings. An exchange of genetic material between ancestral groups before commercial wheat-breeding started would be a possible explanation for this. The increased knowledge regarding the diversity of the Watkins collection was used to develop resources for wheat research and breeding, one of them a core set, which captures the majority of the genetic diversity detected. The understanding of genetic diversity and population structure together with the availability of breeding resources should help to accelerate the detection of new alleles in the Watkins collection.
Application of combinatorial biocatalysis for a unique ring expansion of dihydroxymethylzearalenone

USDA-ARS?s Scientific Manuscript database

Combinatorial biocatalysis was applied to generate a diverse set of dihydroxymethylzearalenone derivatives with modified ring structure. In one chemoenzymatic reaction sequence, dihydroxymethylzearalenone was first subjected to a unique enzyme-catalyzed oxidative ring opening reaction that creates ...
Prediction of aquatic toxicity mode of action using linear discriminant and random forest models.

PubMed

Martin, Todd M; Grulke, Christopher M; Young, Douglas M; Russom, Christine L; Wang, Nina Y; Jackson, Crystal R; Barron, Mace G

2013-09-23

The ability to determine the mode of action (MOA) for a diverse group of chemicals is a critical part of ecological risk assessment and chemical regulation. However, existing MOA assignment approaches in ecotoxicology have been limited to a relatively few MOAs, have high uncertainty, or rely on professional judgment. In this study, machine based learning algorithms (linear discriminant analysis and random forest) were used to develop models for assigning aquatic toxicity MOA. These methods were selected since they have been shown to be able to correlate diverse data sets and provide an indication of the most important descriptors. A data set of MOA assignments for 924 chemicals was developed using a combination of high confidence assignments, international consensus classifications, ASTER (ASessment Tools for the Evaluation of Risk) predictions, and weight of evidence professional judgment based an assessment of structure and literature information. The overall data set was randomly divided into a training set (75%) and a validation set (25%) and then used to develop linear discriminant analysis (LDA) and random forest (RF) MOA assignment models. The LDA and RF models had high internal concordance and specificity and were able to produce overall prediction accuracies ranging from 84.5 to 87.7% for the validation set. These results demonstrate that computational chemistry approaches can be used to determine the acute toxicity MOAs across a large range of structures and mechanisms.
Diverse forms of bonding in two-dimensional Si allotropes: Nematic orbitals in the MoS2 structure

NASA Astrophysics Data System (ADS)

Gimbert, Florian; Lee, Chi-Cheng; Friedlein, Rainer; Fleurence, Antoine; Yamada-Takamura, Yukiko; Ozaki, Taisuke

2014-10-01

The interplay of sp2- and sp3-type bonding defines silicon allotropes in two- and three-dimensional forms. A two-dimensional phase bearing structural resemblance to a single MoS2 layer is found to possess a lower total energy than low-buckled silicene and to be stable in terms of its phonon dispersion relations. A set of cigar-shaped nematic orbitals originating from the Si sp2 orbitals realizes bonding with a sixfold coordination of the inner Si atoms of the layer. The identification of these nematic orbitals advocates diverse Si bonding configurations different from those of C atoms.

Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae).

PubMed

Eckert, Andrew J; van Heerwaarden, Joost; Wegrzyn, Jill L; Nelson, C Dana; Ross-Ibarra, Jeffrey; González-Martínez, Santíago C; Neale, David B

2010-07-01

Natural populations of forest trees exhibit striking phenotypic adaptations to diverse environmental gradients, thereby making them appealing subjects for the study of genes underlying ecologically relevant phenotypes. Here, we use a genome-wide data set of single nucleotide polymorphisms genotyped across 3059 functional genes to study patterns of population structure and identify loci associated with aridity across the natural range of loblolly pine (Pinus taeda L.). Overall patterns of population structure, as inferred using principal components and Bayesian cluster analyses, were consistent with three genetic clusters likely resulting from expansions out of Pleistocene refugia located in Mexico and Florida. A novel application of association analysis, which removes the confounding effects of shared ancestry on correlations between genetic and environmental variation, identified five loci correlated with aridity. These loci were primarily involved with abiotic stress response to temperature and drought. A unique set of 24 loci was identified as F(ST) outliers on the basis of the genetic clusters identified previously and after accounting for expansions out of Pleistocene refugia. These loci were involved with a diversity of physiological processes. Identification of nonoverlapping sets of loci highlights the fundamental differences implicit in the use of either method and suggests a pluralistic, yet complementary, approach to the identification of genes underlying ecologically relevant phenotypes.
Investigating Shifts in Diverse Family Structures in Newbery Award and Honor Books Utilizing U.S. Census Data, 1930-2010

ERIC Educational Resources Information Center

Despain, Shannon M.; Tunnell, Michael O.; Wilcox, Brad; Morrison, Timothy G.

2015-01-01

Newbery Award and Honor books are a representation of children's literature, but family structures portrayed in them have not previously been studied. This prescriptive content analysis considered 87 contemporary realistic fiction Newbery winners and runners-up since the 1930s that portray families in English-speaking, Western settings. The family…
Structural and functional diversity of Nematoda in relation with environmental variables in the Setúbal and Cascais canyons, Western Iberian Margin

NASA Astrophysics Data System (ADS)

Ingels, Jeroen; Billett, David S. M.; Kiriakoulakis, Konstadinos; Wolff, George A.; Vanreusel, Ann

2011-12-01

Samples collected at two different depths (ca. 3200 and ca. 4200 m) in the Setúbal and Cascais canyons off the Portuguese coast, during the HERMES RRS Charles Darwin cruise CD179, were analysed for (1) sediment biogeochemistry (TOC, TN) and (2) composition, and structural and trophic diversity of nematode communities. Multivariate PERMANOVA analysis on the nematode community data revealed differences between sediment layers that were greater than differences between canyons, water depths, and stations. This suggests that biogeochemical gradients along the vertical sediment profile are crucial in determining nematode community structure. The interaction between canyon conditions and the nematode community is illustrated by biogeochemical patterns in the sediment and the prevalence of nematode genera that are able to persist in disturbed sediments. Trophic analysis of the nematode community indicated that non-selective deposit feeders are dominant, presumably because of their non-selective feeding behaviour compared to other feeding types, which gives them a competitive advantage in exploiting lower-quality food resources. This study presents a preliminary conceptual scheme for interactions between canyon conditions and the resident fauna.
Successful Students Who Are Deaf or Hard of Hearing and Culturally and/or Linguistically Diverse in Inclusive Settings.

PubMed

Ayantoye, Catherine Adekemi; Luckner, John L

2016-01-01

The population of students who are deaf or hard of hearing is becoming more culturally and/or linguistically diverse. However, there is a paucity of practitioner literature and research available to professionals and families to guide decision making about daily practices with these students and their families. The study identified factors that contribute to the success of students who are deaf or hard of hearing and from culturally and/or linguistically diverse backgrounds who receive the majority of their education in inclusive settings. Students were recruited from two schools in two school districts in a western state. Students, educators, interpreters, and parents participated in individual in-depth, semi-structured interviews. Observations of the students were also done. Analysis of the data included coding the transcribed interviews and the field notes to identify common themes. Seven themes emerged and are reported. Recommendations for future research are provided.
Organizing the HIV vaccine development effort.

PubMed

Voronin, Yegor; Snow, William

2013-09-01

To describe and compare the diverse organizational structures and funding mechanisms applied to advance HIV preventive vaccine research and development and to help explain and inform evolving infrastructures and collaborative funding models. On the basis of models that have been tried, improved or abandoned over three decades, the field seems to have settled into a relatively stable set of diverse initiatives, each with its own organizational signature. At the same time, this set of organizations is forging cross-organizational collaborations, which promise to acquire newly emergent beneficial properties. Strong motivation to expedite HIV vaccine R&D has driven a diversity of customized and inventive organizational approaches, largely government and foundation funded. Although no one approach has proven a panacea, the field has evolved into a constellation of often overlapping organizations that complement or reinforce one another. The Global HIV Vaccine Enterprise, a responsive, rapidly evolving loose infrastructure, is an innovative collaboration to catalyze that evolution.
Organizing the HIV Vaccine Development Effort

PubMed Central

Voronin, Yegor; Snow, William

2014-01-01

Purpose of Review Describe and compare the diverse organizational structures and funding mechanisms applied to advance HIV preventive vaccine research and development, to help explain and inform evolving infrastructures and collaborative funding models. Recent Findings Based on models that have been tried, improved or abandoned over three decades, the field seems to have settled into a relatively stable set of diverse initiatives, each with its own organizational signature. At the same time, this set of organizations is forging cross-organizational collaborations, which promise to acquire newly emergent beneficial properties. Summary Strong motivation to expedite HIV vaccine R&D has driven a diversity of customized and inventive organizational approaches, largely government and foundation funded. While no one approach has proven a panacea, the field has evolved into a constellation of often overlapping organizations that complement or reinforce one another. The Global HIV Vaccine Enterprise, a responsive, rapidly evolving loose infrastructure, is an innovative collaboration to catalyze that evolution. PMID:23924997
"Presumed fair: Ironic effects of organizational diversity structures": Correction to Kaiser et al. (2013).

PubMed

2016-06-01

Reports an error in "Presumed fair: Ironic effects of organizational diversity structures" by Cheryl R. Kaiser, Brenda Major, Ines Jurcevic, Tessa L. Dover, Laura M. Brady and Jenessa R. Shapiro (Journal of Personality and Social Psychology, 2013[Mar], Vol 104[3], 504-519). In the article, a raw data merging error in one racial discrimination claim condition from Experiment 6 inadvertently resulted in data analyses on an inaccurate data set. When the error was discovered by the authors and corrected, all analyses reported in Experiment 6 for claim validity, seriousness of the claim, and support for the claimant were inaccurate and none were statistically significant. The conclusions should be altered to indicate that participants with management experience who reflected on their own workplace diversity policies did not show the predicted effects. The literature review, remaining five studies, and remaining conclusions in the article are unaffected by this error. Experiment 6 should also report that 26.4% (not 26.4.7%) of participants had a graduate degree and eight participants (not 8%) did not provide educational data. Experiment 5 should have referred to the claim validity measure as a six-item measure ( .92) rather than a five-item measure; analyses on claim validity are accurate in text. Table 2's note should have said standard errors, not standard deviations. (The following abstract of the original article appeared in record 2012-31077-001.) This research tests the hypothesis that the presence (vs. absence) of organizational diversity structures causes high-status group members (Whites, men) to perceive organizations with diversity structures as procedurally fairer environments for underrepresented groups (racial minorities, women), even when it is clear that underrepresented groups have been unfairly disadvantaged within these organizations. Furthermore, this illusory sense of fairness derived from the mere presence of diversity structures causes high-status group members to legitimize the status quo by becoming less sensitive to discrimination targeted at underrepresented groups and reacting more harshly toward underrepresented group members who claim discrimination. Six experiments support these hypotheses in designs using 4 types of diversity structures (diversity policies, diversity training, diversity awards, idiosyncratically generated diversity structures from participants' own organizations) among 2 high-status groups in tests involving several types of discrimination (discriminatory promotion practices, adverse impact in hiring, wage discrimination). Implications of these experiments for organizational diversity and employment discrimination law are discussed. (PsycINFO Database Record (c) 2016 APA, all rights reserved).
Genetic diversity and structure of Iberian Peninsula cowpeas compared to world-wide cowpea accessions using high density SNP markers.

PubMed

Carvalho, Márcia; Muñoz-Amatriaín, María; Castro, Isaura; Lino-Neto, Teresa; Matos, Manuela; Egea-Cortines, Marcos; Rosa, Eduardo; Close, Timothy; Carnide, Valdemar

2017-11-21

Cowpea (Vigna unguiculata L. Walp) is an important legume crop due to its high protein content, adaptation to heat and drought and capacity to fix nitrogen. Europe has a deficit of cowpea production. Knowledge of genetic diversity among cowpea landraces is important for the preservation of local varieties and is the basis to obtain improved varieties. The aims of this study were to explore diversity and the genetic structure of a set of Iberian Peninsula cowpea accessions in comparison to a worldwide collection and to infer possible dispersion routes of cultivated cowpea. The Illumina Cowpea iSelect Consortium Array containing 51,128 SNPs was used to genotype 96 cowpea accessions including 43 landraces and cultivars from the Iberian Peninsula, and 53 landraces collected worldwide. Four subpopulations were identified. Most Iberian Peninsula accessions clustered together with those from other southern European and northern African countries. Only one accession belonged to another subpopulation, while two accessions were 'admixed'. A lower genetic diversity level was found in the Iberian Peninsula accessions compared to worldwide cowpeas. The genetic analyses performed in this study brought some insights into worldwide genetic diversity and structure and possible dispersion routes of cultivated cowpea. Also, it provided an in-depth analysis of genetic diversity in Iberian Peninsula cowpeas that will help guide crossing strategies in breeding programs.
Diverse heterocyclic scaffolds as dCTP pyrophosphatase 1 inhibitors. Part 1: Triazoles, triazolopyrimidines, triazinoindoles, quinoline hydrazones and arylpiperazines.

PubMed

Llona-Minguez, Sabin; Häggblad, Maria; Martens, Ulf; Throup, Adam; Loseva, Olga; Jemth, Ann-Sofie; Lundgren, Bo; Scobie, Martin; Helleday, Thomas

2017-08-15

A high-throughput screening campaign using a commercial compound library (ChemBridge DiverSET) revealed diverse chemotypes as inhibitors of the human dCTP pyrophosphatase 1 (dCTPase). Triazole, triazolopyrimidine, triazinoindole, quinoline hydrazone and arylpiperazine hits were clustered, confirmed by IC 50 determinations, and their preliminary structure-activity-relationships (SAR) and ligand efficiency scores are discussed in this letter. Copyright © 2017. Published by Elsevier Ltd.
Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice

PubMed Central

Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai

2016-01-01

Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright’s F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance. PMID:27494320
Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

PubMed

Pradhan, Sharat Kumar; Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai; Pandit, Elssa

2016-01-01

Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.
Predicting "Hot" and "Warm" Spots for Fragment Binding.

PubMed

Rathi, Prakash Chandra; Ludlow, R Frederick; Hall, Richard J; Murray, Christopher W; Mortenson, Paul N; Verdonk, Marcel L

2017-05-11

Computational fragment mapping methods aim to predict hotspots on protein surfaces where small fragments will bind. Such methods are popular for druggability assessment as well as structure-based design. However, to date researchers developing or using such tools have had no clear way of assessing the performance of these methods. Here, we introduce the first diverse, high quality validation set for computational fragment mapping. The set contains 52 diverse examples of fragment binding "hot" and "warm" spots from the Protein Data Bank (PDB). Additionally, we describe PLImap, a novel protocol for fragment mapping based on the Protein-Ligand Informatics force field (PLIff). We evaluate PLImap against the new fragment mapping test set, and compare its performance to that of simple shape-based algorithms and fragment docking using GOLD. PLImap is made publicly available from https://bitbucket.org/AstexUK/pli .
Early Archean stromatolites: Paleoenvironmental setting and controls on formation

NASA Technical Reports Server (NTRS)

Lowe, D. R.

1991-01-01

The earliest record of terrestrial life is contained in thin, silicified sedimentary layers within enormously thick, predominantly volcanic sequences in South Africa and Western Australia. This record includes bacteria-like microfossils, laminated carbonaceous structures resembling flat bacterial mats and stromatolites, and a morphologically diverse assemblage of carbonaceous particles. These structures and particles and their host sediments provide the only direct source of information on the morphology, paleoecology, and biogeochemistry of early life; the nature of interactions between organisms and surface systems on the early earth; and possible settings within which life might have evolved. The three known occurrences of 3.5 to 3.2 billion-year-old stromalites were evaluated in terms of depositional setting and biogenicity.
The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.

PubMed

Tsuchiya, Yuko; Mizuguchi, Kenji

2016-04-01

Of the complementarity-determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen-binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen-binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen-binding tendencies of all the CDR loops. © 2016 The Protein Society.
Constraints on trait combinations explain climatic drivers of biodiversity: the importance of trait covariance in community assembly.

PubMed

Dwyer, John M; Laughlin, Daniel C

2017-07-01

Trade-offs maintain diversity and structure communities along environmental gradients. Theory indicates that if covariance among functional traits sets a limit on the number of viable trait combinations in a given environment, then communities with strong multidimensional trait constraints should exhibit low species diversity. We tested this prediction in winter annual plant assemblages along an aridity gradient using multilevel structural equation modelling. Univariate and multivariate functional diversity measures were poorly explained by aridity, and were surprisingly poor predictors of community richness. By contrast, the covariance between maximum height and seed mass strengthened along the aridity gradient, and was strongly associated with richness declines. Community richness had a positive effect on local neighbourhood richness, indicating that climate effects on trait covariance indirectly influence diversity at local scales. We present clear empirical evidence that declines in species richness along gradients of environmental stress can be due to increasing constraints on multidimensional phenotypes. © 2017 John Wiley & Sons Ltd/CNRS.
Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

PubMed Central

Adriaenssens, Evelien M.

2014-01-01

Viruses (including bacteriophages) are the most abundant biological entities on the planet. As such, they are thought to have a major impact on all aspects of microbial community structure and function. Despite this critical role in ecosystem processes, the study of virus/phage diversity has lagged far behind parallel studies of the bacterial and eukaryotic kingdoms, largely due to the absence of any universal phylogenetic marker. Here we review the development and use of signature genes to investigate viral diversity, as a viable strategy for data sets of specific virus groups. Genes that have been used include those encoding structural proteins, such as portal protein, major capsid protein, and tail sheath protein, auxiliary metabolism genes, such as psbA, psbB, and phoH, and several polymerase genes. These marker genes have been used in combination with PCR-based fingerprinting and/or sequencing strategies to investigate spatial, temporal, and seasonal variations and diversity in a wide range of habitats. PMID:24837394
Dealing with extreme data diversity: extraction and fusion from the growing types of document formats

NASA Astrophysics Data System (ADS)

David, Peter; Hansen, Nichole; Nolan, James J.; Alcocer, Pedro

2015-05-01

The growth in text data available online is accompanied by a growth in the diversity of available documents. Corpora with extreme heterogeneity in terms of file formats, document organization, page layout, text style, and content are common. The absence of meaningful metadata describing the structure of online and open-source data leads to text extraction results that contain no information about document structure and are cluttered with page headers and footers, web navigation controls, advertisements, and other items that are typically considered noise. We describe an approach to document structure and metadata recovery that uses visual analysis of documents to infer the communicative intent of the author. Our algorithm identifies the components of documents such as titles, headings, and body content, based on their appearance. Because it operates on an image of a document, our technique can be applied to any type of document, including scanned images. Our approach to document structure recovery considers a finer-grained set of component types than prior approaches. In this initial work, we show that a machine learning approach to document structure recovery using a feature set based on the geometry and appearance of images of documents achieves a 60% greater F1- score than a baseline random classifier.
Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp).

PubMed

Xiong, Haizheng; Shi, Ainong; Mou, Beiquan; Qin, Jun; Motes, Dennis; Lu, Weiguo; Ma, Jianbing; Weng, Yuejin; Yang, Wei; Wu, Dianxing

2016-01-01

The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.
Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp)

PubMed Central

Xiong, Haizheng; Shi, Ainong; Mou, Beiquan; Qin, Jun; Motes, Dennis; Lu, Weiguo; Ma, Jianbing; Weng, Yuejin; Yang, Wei; Wu, Dianxing

2016-01-01

The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research. PMID:27509049
Contrasting Transmission Dynamics of Co-endemic Plasmodium vivax and P. falciparum: Implications for Malaria Control and Elimination.

PubMed

Noviyanti, Rintis; Coutrier, Farah; Utami, Retno A S; Trimarsanto, Hidayat; Tirta, Yusrifar K; Trianty, Leily; Kusuma, Andreas; Sutanto, Inge; Kosasih, Ayleen; Kusriastuti, Rita; Hawley, William A; Laihad, Ferdinand; Lobo, Neil; Marfurt, Jutta; Clark, Taane G; Price, Ric N; Auburn, Sarah

2015-05-01

Outside of Africa, P. falciparum and P. vivax usually coexist. In such co-endemic regions, successful malaria control programs have a greater impact on reducing falciparum malaria, resulting in P. vivax becoming the predominant species of infection. Adding to the challenges of elimination, the dormant liver stage complicates efforts to monitor the impact of ongoing interventions against P. vivax. We investigated molecular approaches to inform the respective transmission dynamics of P. falciparum and P. vivax and how these could help to prioritize public health interventions. Genotype data generated at 8 and 9 microsatellite loci were analysed in 168 P. falciparum and 166 P. vivax isolates, respectively, from four co-endemic sites in Indonesia (Bangka, Kalimantan, Sumba and West Timor). Measures of diversity, linkage disequilibrium (LD) and population structure were used to gauge the transmission dynamics of each species in each setting. Marked differences were observed in the diversity and population structure of P. vivax versus P. falciparum. In Bangka, Kalimantan and Timor, P. falciparum diversity was low, and LD patterns were consistent with unstable, epidemic transmission, amenable to targeted intervention. In contrast, P. vivax diversity was higher and transmission appeared more stable. Population differentiation was lower in P. vivax versus P. falciparum, suggesting that the hypnozoite reservoir might play an important role in sustaining local transmission and facilitating the spread of P. vivax infections in different endemic settings. P. vivax polyclonality varied with local endemicity, demonstrating potential utility in informing on transmission intensity in this species. Molecular approaches can provide important information on malaria transmission that is not readily available from traditional epidemiological measures. Elucidation of the transmission dynamics circulating in a given setting will have a major role in prioritising malaria control strategies, particularly against the relatively neglected non-falciparum species.

Multicontext Diversity: The critical dimension of diversity that can attract students and help them thrive

NASA Astrophysics Data System (ADS)

Weissmann, G. S.; Ibarra, R.; Howland-Davis, M.

2017-12-01

Diversity programs on college campuses have expanded over the past several decades, bringing a broad range of students to academia; however, these programs have not resulted in diversification of faculty or PhD students. Current diversity programs generally focus on two dimensions of diversity: (1) structural diversity, which aims to bring in students from underrepresented groups to college campuses through scholarships, admissions policies, and targeted marketing; and (2) multicultural diversity, which uses programs designed to give students from underrepresented groups homes on campus and programs designed to study cultural aspects of different groups. Though these programs are important, something else must be controlling the lack of minority participation in STEM at advanced levels. We posit that a third dimension of diversity, context diversity, is lacking in university education, especially in STEM fields, and without accessing this form of diversity, programs will never benefit from the broader diversity of society. Context diversity results through application of Multicontext theory, which both explains and predicts the inclusion of exclusion of people within an institutional culture. It describes how different cultures approach understanding the world around them. This "cultural ways of knowing and doing" has been described using a binary system, consisting of "Low Context" and "High Context" cultures. Ibarra (2001) described how a spectrum exists between these end members, and thus individuals brought up in different cultures will understand the world from somewhere along this context diversity spectrum. Academic culture tends to fall on the low context side of the spectrum. Thus, students (and faculty) who come from cultures that tend toward the high context side of the spectrum often feel excluded from the academic setting, especially in STEM fields which tend to be strongly low context in nature. A high percentage of students from underrepresented groups and women tend to fall on toward the high context side of the spectrum, thus this disproportionately affects women and minorities. Multicontextuality can be readily applied in classroom and research settings, thus leading to helping all students thrive in the academic setting.
Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current.

PubMed

Kharbush, Jenan J; Ugalde, Juan A; Hogle, Shane L; Allen, Eric E; Aluwihare, Lihini I

2013-12-01

Hopanoids are pentacyclic triterpenoid lipids produced by many prokaryotes as cell membrane components. The structural variations of composite hopanoids, or bacteriohopanepolyols (BHPs), produced by various bacterial genera make them potentially useful molecular biomarkers of bacterial communities and metabolic processes in both modern and ancient environments. Building on previous work suggesting that organisms in low-oxygen environments are important contributors to BHP production in the marine water column and that there may be physiological roles for BHPs specific to these environments, this study investigated the relationship between trends in BHP structural diversity and abundance and the genetic diversity of BHP producers for the first time in a low-oxygen environment of the Eastern Tropical North Pacific. Amplification of the hopanoid biosynthesis gene for squalene hopene cyclase (sqhC) indicated far greater genetic diversity than would be predicted by examining BHP structural diversity alone and that greater sqhC genetic diversity exists in the marine environment than is represented by cultured representatives and most marine metagenomes. In addition, the genetic relationships in this data set suggest microaerophilic environments as potential "hot spots" of BHP production. Finally, structural analysis of BHPs showed that an isomer of the commonly observed BHP bacteriohopanetetrol may be linked to a producer that is more abundant in low-oxygen environments. Results of this study increase the known diversity of BHP producers and provide a detailed phylogeny with implications for the role of hopanoids in modern bacteria, as well as the evolutionary history of hopanoid biosynthesis, both of which are important considerations for future interpretations of the marine sedimentary record.
The many blades of the β-propeller proteins: conserved but versatile.

PubMed

Chen, Cammy K-M; Chan, Nei-Li; Wang, Andrew H-J

2011-10-01

The β-propeller is a highly symmetrical structure with 4-10 repeats of a four-stranded antiparallel β-sheet motif. Although β-propeller proteins with different blade numbers all adopt disc-like shapes, they are involved in a diverse set of functions, and defects in this family of proteins have been associated with human diseases. However, it has remained ambiguous how variations in blade number could alter the function of β-propellers. In addition to the regularly arranged β-propeller topology, a recently discovered β-pinwheel propeller has been found. Here, we review the structural and functional diversity of β-propeller proteins, including β-pinwheels, as well as recent advances in the typical and atypical propeller structures. Copyright © 2011 Elsevier Ltd. All rights reserved.
Molecular mimicry between protein and tRNA.

PubMed

Nakamura, Y

2001-01-01

Mimicry is a sophisticated development in animals, fish, and plants that allows them to fool others by imitating a shape or color for diverse purposes, such as to prey, evade, lure, pollinate, or threaten. This is not restricted to the macro-world, but extends to the micro-world as molecular mimicry. Recent advances in structural and molecular biology uncovered a set of translation factors that resembles a tRNA shape and, in one case, even mimics a tRNA function for deciphering the genetic code. Nature must have evolved this art of molecular mimicry between protein and ribonucleic acid by using different protein structures until the translation factors sat in the cockpit of a ribosome machine, on behalf of tRNA, and achieved diverse actions. Structural, functional, and evolutionary aspects of molecular mimicry will be discussed.
Image Search Reranking With Hierarchical Topic Awareness.

PubMed

Tian, Xinmei; Yang, Linjun; Lu, Yijuan; Tian, Qi; Tao, Dacheng

2015-10-01

With much attention from both academia and industrial communities, visual search reranking has recently been proposed to refine image search results obtained from text-based image search engines. Most of the traditional reranking methods cannot capture both relevance and diversity of the search results at the same time. Or they ignore the hierarchical topic structure of search result. Each topic is treated equally and independently. However, in real applications, images returned for certain queries are naturally in hierarchical organization, rather than simple parallel relation. In this paper, a new reranking method "topic-aware reranking (TARerank)" is proposed. TARerank describes the hierarchical topic structure of search results in one model, and seamlessly captures both relevance and diversity of the image search results simultaneously. Through a structured learning framework, relevance and diversity are modeled in TARerank by a set of carefully designed features, and then the model is learned from human-labeled training samples. The learned model is expected to predict reranking results with high relevance and diversity for testing queries. To verify the effectiveness of the proposed method, we collect an image search dataset and conduct comparison experiments on it. The experimental results demonstrate that the proposed TARerank outperforms the existing relevance-based and diversified reranking methods.
Integrating diverse scientific and practitioner knowledge in ecological risk analysis: a case study of biodiversity risk assessment in South Africa.

PubMed

Dana, G V; Kapuscinski, A R; Donaldson, J S

2012-05-15

Ecological risk analysis (ERA) is a structured evaluation of threats to species, natural communities, and ecosystem processes from pollutants and toxicants and more complicated living stressors such as invasive species, genetically modified organisms, and biological control agents. Such analyses are typically conducted by a narrowly-focused group of scientific experts using technical information. We evaluate whether the inclusion of more diverse experts and practitioners in ERA improved the ecological knowledge base about South African biodiversity and the potential impacts of genetically modified (GM) crops. We conducted two participatory ERA workshops in South Africa, analyzing potential impacts of GM maize on biodiversity. The first workshop involved only four biological scientists, who were joined by 18 diverse scientists and practitioners in the second, and we compared the ERA process and results between the two using descriptive statistics and semi-structured interview responses. The addition of diverse experts and practitioners led to a more comprehensive understanding of biological composition of the agro-ecosystem and a more ecologically relevant set of hazards, but impeded hazard prioritization and the generation of precise risk assessment values. Results suggest that diverse participation can improve the scoping or problem formulation of the ERA, by generating an ecologically robust set of information on which to base the subsequent, more technical risk assessment. The participatory ERA process also increased the transparency of the ERA by exposing the logic and rationale for decisions made at each step. Copyright © 2011 Elsevier Ltd. All rights reserved.
Intensive agriculture erodes β-diversity at large scales.

PubMed

Karp, Daniel S; Rominger, Andrew J; Zook, Jim; Ranganathan, Jai; Ehrlich, Paul R; Daily, Gretchen C

2012-09-01

Biodiversity is declining from unprecedented land conversions that replace diverse, low-intensity agriculture with vast expanses under homogeneous, intensive production. Despite documented losses of species richness, consequences for β-diversity, changes in community composition between sites, are largely unknown, especially in the tropics. Using a 10-year data set on Costa Rican birds, we find that low-intensity agriculture sustained β-diversity across large scales on a par with forest. In high-intensity agriculture, low local (α) diversity inflated β-diversity as a statistical artefact. Therefore, at small spatial scales, intensive agriculture appeared to retain β-diversity. Unlike in forest or low-intensity systems, however, high-intensity agriculture also homogenised vegetation structure over large distances, thereby decoupling the fundamental ecological pattern of bird communities changing with geographical distance. This ~40% decline in species turnover indicates a significant decline in β-diversity at large spatial scales. These findings point the way towards multi-functional agricultural systems that maintain agricultural productivity while simultaneously conserving biodiversity. © 2012 Blackwell Publishing Ltd/CNRS.
Genetic diversity of calcareous grassland plant species depends on historical landscape configuration.

PubMed

Reisch, Christoph; Schmidkonz, Sonja; Meier, Katrin; Schöpplein, Quirin; Meyer, Carina; Hums, Christian; Putz, Christina; Schmid, Christoph

2017-04-24

Habitat fragmentation is considered to be a main reason for decreasing genetic diversity of plant species. However, the results of many fragmentation studies are inconsistent. This may be due to the influence of habitat conditions, having an indirect effect on genetic variation via reproduction. Consequently we took a comparative approach to analyse the impact of habitat fragmentation and habitat conditions on the genetic diversity of calcareous grassland species in this study. We selected five typical grassland species (Primula veris, Dianthus carthusianorum, Medicago falcata, Polygala comosa and Salvia pratensis) occurring in 18 fragments of calcareous grasslands in south eastern Germany. We sampled 1286 individuals in 87 populations and analysed genetic diversity using amplified fragment length polymorphisms. Additionally, we collected data concerning habitat fragmentation (historical and present landscape structure) and habitat conditions (vegetation structure, soil conditions) of the selected study sites. The whole data set was analysed using Bayesian multiple regressions. Our investigation indicated a habitat loss of nearly 80% and increasing isolation between grasslands since 1830. Bayesian analysis revealed a significant impact of the historical landscape structure, whereas habitat conditions played no important role for the present-day genetic variation of the studied plant species. Our study indicates that the historical landscape structure may be more important for genetic diversity than present habitat conditions. Populations persisting in abandoned grassland fragments may contribute significantly to the species' variability even under deteriorating habitat conditions. Therefore, these populations should be included in approaches to preserve the genetic variation of calcareous grassland species.
Environmental barriers and enablers to physical activity participation among rural adults: a qualitative study.

PubMed

Cleland, Verity; Hughes, Clarissa; Thornton, Lukar; Squibb, Kathryn; Venn, Alison; Ball, Kylie

2015-08-01

Social-ecological models of health behaviour acknowledge environmental influences, but research examining how the environment shapes physical activity in rural settings is limited. This study aimed to explore the environmental factors that act as barriers or facilitators to physical activity participation among rural adults. Forty-nine adults from three regions of rural Tasmania, Australia, participated in semi-structured interviews that explored features of the environment that supported or hindered physical activity. Interviews were digitally recorded, transcribed verbatim and analysed thematically. Four key themes emerged: functionality, diversity, spaces and places for all and realistic expectations. 'Functionality' included connectivity with other destinations, distance, safety, continuity, supporting infrastructure and surfacing. While there was limited 'diversity' of structured activities and recreational facilities, the importance of easy and convenient access to a natural environment that accommodated physical activity was highlighted. 'Spaces and places for all' highlighted the importance of shared-use areas, particularly those that were family- and dog-friendly. Despite desires for more physical activity opportunities, many participants had 'realistic expectations' of what was feasible in rural settings. Functionality, diversity, spaces and places for all and realistic expectations were identified as considerations important for physical activity among rural adults. Further research using quantitative approaches in larger samples is needed to confirm these findings. SO WHAT? Urban-centric views of environmental influences on physical activity are unlikely to be entirely appropriate for rural areas. Evidence-based recommendations are provided for creating new or modifying existing infrastructure to support active living in rural settings.
Diversity, structure and convergent evolution of the global sponge microbiome

PubMed Central

Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel; Björk, Johannes R.; Easson, Cole; Astudillo-García, Carmen; Olson, Julie B.; Erwin, Patrick M.; López-Legentil, Susanna; Luter, Heidi; Chaves-Fonnegra, Andia; Costa, Rodrigo; Schupp, Peter J.; Steindler, Laura; Erpenbeck, Dirk; Gilbert, Jack; Knight, Rob; Ackermann, Gail; Victor Lopez, Jose; Taylor, Michael W.; Thacker, Robert W.; Montoya, Jose M.; Hentschel, Ute; Webster, Nicole S.

2016-01-01

Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host–microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions. PMID:27306690
Kohonen and counterpropagation neural networks applied for mapping and interpretation of IR spectra.

PubMed

Novic, Marjana

2008-01-01

The principles of learning strategy of Kohonen and counterpropagation neural networks are introduced. The advantages of unsupervised learning are discussed. The self-organizing maps produced in both methods are suitable for a wide range of applications. Here, we present an example of Kohonen and counterpropagation neural networks used for mapping, interpretation, and simulation of infrared (IR) spectra. The artificial neural network models were trained for prediction of structural fragments of an unknown compound from its infrared spectrum. The training set contained over 3,200 IR spectra of diverse compounds of known chemical structure. The structure-spectra relationship was encompassed by the counterpropagation neural network, which assigned structural fragments to individual compounds within certain probability limits, assessed from the predictions of test compounds. The counterpropagation neural network model for prediction of fragments of chemical structure is reversible, which means that, for a given structural domain, limited to the training data set in the study, it can be used to simulate the IR spectrum of a chemical defined with a set of structural fragments.
Predicting acute aquatic toxicity of structurally diverse chemicals in fish using artificial intelligence approaches.

PubMed

Singh, Kunwar P; Gupta, Shikha; Rai, Premanjali

2013-09-01

The research aims to develop global modeling tools capable of categorizing structurally diverse chemicals in various toxicity classes according to the EEC and European Community directives, and to predict their acute toxicity in fathead minnow using set of selected molecular descriptors. Accordingly, artificial intelligence approach based classification and regression models, such as probabilistic neural networks (PNN), generalized regression neural networks (GRNN), multilayer perceptron neural network (MLPN), radial basis function neural network (RBFN), support vector machines (SVM), gene expression programming (GEP), and decision tree (DT) were constructed using the experimental toxicity data. Diversity and non-linearity in the chemicals' data were tested using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. Predictive and generalization abilities of various models constructed here were compared using several statistical parameters. PNN and GRNN models performed relatively better than MLPN, RBFN, SVM, GEP, and DT. Both in two and four category classifications, PNN yielded a considerably high accuracy of classification in training (95.85 percent and 90.07 percent) and validation data (91.30 percent and 86.96 percent), respectively. GRNN rendered a high correlation between the measured and model predicted -log LC50 values both for the training (0.929) and validation (0.910) data and low prediction errors (RMSE) of 0.52 and 0.49 for two sets. Efficiency of the selected PNN and GRNN models in predicting acute toxicity of new chemicals was adequately validated using external datasets of different fish species (fathead minnow, bluegill, trout, and guppy). The PNN and GRNN models showed good predictive and generalization abilities and can be used as tools for predicting toxicities of structurally diverse chemical compounds. Copyright © 2013 Elsevier Inc. All rights reserved.
SEM characterization of anatomical variation in chitin organization in insect and arthropod cuticles.

PubMed

Chandran, Rakkiyappan; Williams, Lee; Hung, Albert; Nowlin, Kyle; LaJeunesse, Dennis

2016-03-01

The cuticles of insects and arthropods have some of the most diverse material properties observed in nature, so much so that it is difficult to imagine that all cutciles are primarily composed of the same two materials: a fibrous chitin network and a matrix composed of cuticle proteins. Various factors contribute to the mechanical and optical properties of an insect or arthropod cuticle including the thickness and composition. In this paper, we also identified another factor that may contribute to the optical, surface, and mechanical properties of a cuticle, i.e. the organization of chitin nanofibers and chitin fiber bundles. Self-assembled chitin nanofibers serve as the foundation for all higher order chitin structures in the cuticles of insects and other arthropods via interactions with structural cuticle proteins. Using a technique that enables the characterization of chitin organization in the cuticle of intact insects and arthropod exoskeletons, we demonstrate a structure/function correlation of chitin organization with larger scale anatomical structures. The chitin scaffolds in cuticles display an extraordinarily diverse set of morphologies that may reflect specific mechanical or physical properties. After removal of the proteinaceous and mineral matrix of a cuticle, we observe using SEM diverse nanoscale and micro scale organization of in-situ chitin in the wing, head, eye, leg, and dorsal and ventral thoracic regions of the periodical cicada Magicicada septendecim and in other insects and arthropods. The organization of chitin also appears to have a significant role in the organization of nanoscale surface structures. While microscale bristles and hairs have long been known to be chitin based materials formed as cellular extensions, we have found a nanostructured layer of chitin in the cuticle of the wing of the dog day annual cicada Tibicen tibicens, which may be the scaffold for the nanocone arrays found on the wing. We also use this process to examine the chitin organizations in the fruit fly, Drosophila melanogaster, and the Atlantic brown shrimp, Farfantepenaeus aztecus. Interestingly many of the homologous anatomical structures from diverse arthropods exhibit similar patterns of chitin organization suggesting that a common set of parameters, govern chitin organization. Copyright © 2016 Elsevier Ltd. All rights reserved.
Genetic diversity and haplotype structure of 21 Y-STRs, including nine noncore loci, in South Tunisian Population: Forensic relevance.

PubMed

Makki-Rmida, Faten; Kammoun, Arwa; Mahfoudh, Nadia; Ayadi, Adnene; Gibriel, Abdullah Ahmed; Mallek, Bakhta; Maalej, Leila; Hammami, Zouheir; Maatoug, Samir; Makni, Hafedh; Masmoudi, Saber

2015-12-01

Y chromosome STRs (Y-STRs) are being used frequently in forensic laboratories. Previous studies of Y-STR polymorphisms in different groups of the Tunisian population identified low levels of diversity and discrimination capacity (DC) using various commercial marker sets. This definitely limits the use of such systems for Y-STRs genotyping in Tunisia. In our investigation on South Tunisia, 200 unrelated males were typed for the 12 conventional Y-STRs included in the PowerPlex® Y System. Additional set of nine noncore Y-STRs including DYS446, DYS456, DYS458, DYS388, DYS444, DYS445, DYS449, DYS710, and DYS464 markers were genotyped and evaluated for their potential in improving DC. Allele frequency, gene diversity, haplotype diversity (HD), and DC calculation revealed that DYS464 was the most diverse marker followed by DYS710 and DYS449 markers. The standard panel of 12 Y-STRs (DC = 80.5%) and the nine markers were combined to obtain DC of 99%. Among the 198 different haplotypes observed, 196 haplotypes were unique (HD = 99.999). Out of the nine noncore set, six Y-STRs (DYS458, DYS456, DYS449, DYS710, DYS444, and DYS464) had the greatest impact on enhancing DC. Our data provided putative Y-STRs combination to be used for genetic and forensic applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Effectiveness of genomic prediction of maize hybrid performance in different breeding populations and environments.

PubMed

Windhausen, Vanessa S; Atlin, Gary N; Hickey, John M; Crossa, Jose; Jannink, Jean-Luc; Sorrells, Mark E; Raman, Babu; Cairns, Jill E; Tarekegne, Amsal; Semagn, Kassa; Beyene, Yoseph; Grudloyma, Pichet; Technow, Frank; Riedelsheimer, Christian; Melchinger, Albrecht E

2012-11-01

Genomic prediction is expected to considerably increase genetic gains by increasing selection intensity and accelerating the breeding cycle. In this study, marker effects estimated in 255 diverse maize (Zea mays L.) hybrids were used to predict grain yield, anthesis date, and anthesis-silking interval within the diversity panel and testcross progenies of 30 F(2)-derived lines from each of five populations. Although up to 25% of the genetic variance could be explained by cross validation within the diversity panel, the prediction of testcross performance of F(2)-derived lines using marker effects estimated in the diversity panel was on average zero. Hybrids in the diversity panel could be grouped into eight breeding populations differing in mean performance. When performance was predicted separately for each breeding population on the basis of marker effects estimated in the other populations, predictive ability was low (i.e., 0.12 for grain yield). These results suggest that prediction resulted mostly from differences in mean performance of the breeding populations and less from the relationship between the training and validation sets or linkage disequilibrium with causal variants underlying the predicted traits. Potential uses for genomic prediction in maize hybrid breeding are discussed emphasizing the need of (1) a clear definition of the breeding scenario in which genomic prediction should be applied (i.e., prediction among or within populations), (2) a detailed analysis of the population structure before performing cross validation, and (3) larger training sets with strong genetic relationship to the validation set.
Selection of representative emerging micropollutants for drinking water treatment studies: a systematic approach.

PubMed

Jin, Xiaohui; Peldszus, Sigrid

2012-01-01

Micropollutants remain of concern in drinking water, and there is a broad interest in the ability of different treatment processes to remove these compounds. To gain a better understanding of treatment effectiveness for structurally diverse compounds and to be cost effective, it is necessary to select a small set of representative micropollutants for experimental studies. Unlike other approaches to-date, in this research micropollutants were systematically selected based solely on their physico-chemical and structural properties that are important in individual water treatment processes. This was accomplished by linking underlying principles of treatment processes such as coagulation/flocculation, oxidation, activated carbon adsorption, and membrane filtration to compound characteristics and corresponding molecular descriptors. A systematic statistical approach not commonly used in water treatment was then applied to a compound pool of 182 micropollutants (identified from the literature) and their relevant calculated molecular descriptors. Principal component analysis (PCA) was used to summarize the information residing in this large dataset. D-optimal onion design was then applied to the PCA results to select structurally representative compounds that could be used in experimental treatment studies. To demonstrate the applicability and flexibility of this selection approach, two sets of 22 representative micropollutants are presented. Compounds in the first set are representative when studying a range of water treatment processes (coagulation/flocculation, oxidation, activated carbon adsorption, and membrane filtration), whereas the second set shows representative compounds for ozonation and advanced oxidation studies. Overall, selected micropollutants in both lists are structurally diverse, have wide-ranging physico-chemical properties and cover a large spectrum of applications. The systematic compound selection approach presented here can also be adjusted to fit individual research needs with respect to type of micropollutants, treatment processes and number of compounds selected. Copyright © 2011 Elsevier B.V. All rights reserved.
Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens

PubMed Central

Albrecht, Elena; Escobar, Miguel; Chetelat, Roger T.

2010-01-01

Background and Aims Two closely related, wild tomato-like nightshade species, Solanum lycopersicoides and Solanum sitiens, inhabit a small area within the Atacama Desert region of Peru and Chile. Each species possesses unique traits, including abiotic and biotic stress tolerances, and can be hybridized with cultivated tomato. Conservation and utilization of these tomato relatives would benefit from an understanding of genetic diversity and relationships within and between populations. Methods Levels of genetic diversity and population genetic structure were investigated by genotyping representative accessions of each species with a set of simple sequence repeat (SSR) and allozyme markers. Key Results As expected for self-incompatible species, populations of S. lycopersicoides and S. sitiens were relatively diverse, but contained less diversity than the wild tomato Solanum chilense, a related allogamous species native to this region. Populations of S. lycopersicoides were slightly more diverse than populations of S. sitiens according to SSRs, but the opposite trend was found with allozymes. A higher coefficient of inbreeding was noted in S. sitiens. A pattern of isolation by distance was evident in both species, consistent with the highly fragmented nature of the populations in situ. The populations of each taxon showed strong geographical structure, with evidence for three major groups, corresponding to the northern, central and southern elements of their respective distributions. Conclusions This information should be useful for optimizing regeneration strategies, for sampling of the populations for genes of interest, and for guiding future in situ conservation efforts. PMID:20154348
Environmental Predictors of Diversity in Recent Planktonic Foraminifera as Recorded in Marine Sediments

PubMed Central

Pearson, Paul N.; Dunkley Jones, Tom; Purvis, Andy

2016-01-01

Global diversity patterns are thought to result from a combination of environmental and historical factors. This study tests the set of ecological and evolutionary hypotheses proposed to explain the global variation in present-day coretop diversity in the macroperforate planktonic foraminifera, a clade with an exceptional fossil record. Within this group, marine surface sediment assemblages are thought to represent an accurate, although centennial to millennial time-averaged, representation of recent diversity patterns. Environmental variables chosen to capture ocean temperature, structure, productivity and seasonality were used to model a range of diversity measures across the world’s oceans. Spatial autoregressive models showed that the same broad suite of environmental variables were important in shaping each of the four largely independent diversity measures (rarefied species richness, Simpson’s evenness, functional richness and mean evolutionary age). Sea-surface temperature explains the largest portion of diversity in all four diversity measures, but not in the way predicted by the metabolic theory of ecology. Vertical structure could be linked to increased diversity through the strength of stratification, but not through the depth of the mixed layer. There is limited evidence that seasonal turnover explains diversity patterns. There is evidence for functional redundancy in the low-latitude sites. The evolutionary mechanism of deep-time stability finds mixed support whilst there is relatively little evidence for an out-of-the-tropics model. These results suggest the diversity patterns of planktonic foraminifera cannot be explained by any one environmental variable or proposed mechanism, but instead reflect multiple processes acting in concert. PMID:27851751
Environmental Predictors of Diversity in Recent Planktonic Foraminifera as Recorded in Marine Sediments.

PubMed

Fenton, Isabel S; Pearson, Paul N; Dunkley Jones, Tom; Purvis, Andy

2016-01-01

Global diversity patterns are thought to result from a combination of environmental and historical factors. This study tests the set of ecological and evolutionary hypotheses proposed to explain the global variation in present-day coretop diversity in the macroperforate planktonic foraminifera, a clade with an exceptional fossil record. Within this group, marine surface sediment assemblages are thought to represent an accurate, although centennial to millennial time-averaged, representation of recent diversity patterns. Environmental variables chosen to capture ocean temperature, structure, productivity and seasonality were used to model a range of diversity measures across the world's oceans. Spatial autoregressive models showed that the same broad suite of environmental variables were important in shaping each of the four largely independent diversity measures (rarefied species richness, Simpson's evenness, functional richness and mean evolutionary age). Sea-surface temperature explains the largest portion of diversity in all four diversity measures, but not in the way predicted by the metabolic theory of ecology. Vertical structure could be linked to increased diversity through the strength of stratification, but not through the depth of the mixed layer. There is limited evidence that seasonal turnover explains diversity patterns. There is evidence for functional redundancy in the low-latitude sites. The evolutionary mechanism of deep-time stability finds mixed support whilst there is relatively little evidence for an out-of-the-tropics model. These results suggest the diversity patterns of planktonic foraminifera cannot be explained by any one environmental variable or proposed mechanism, but instead reflect multiple processes acting in concert.
Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

PubMed Central

Eckert, Andrew J.; van Heerwaarden, Joost; Wegrzyn, Jill L.; Nelson, C. Dana; Ross-Ibarra, Jeffrey; González-Martínez, Santíago C.; Neale, David. B.

2010-01-01

Natural populations of forest trees exhibit striking phenotypic adaptations to diverse environmental gradients, thereby making them appealing subjects for the study of genes underlying ecologically relevant phenotypes. Here, we use a genome-wide data set of single nucleotide polymorphisms genotyped across 3059 functional genes to study patterns of population structure and identify loci associated with aridity across the natural range of loblolly pine (Pinus taeda L.). Overall patterns of population structure, as inferred using principal components and Bayesian cluster analyses, were consistent with three genetic clusters likely resulting from expansions out of Pleistocene refugia located in Mexico and Florida. A novel application of association analysis, which removes the confounding effects of shared ancestry on correlations between genetic and environmental variation, identified five loci correlated with aridity. These loci were primarily involved with abiotic stress response to temperature and drought. A unique set of 24 loci was identified as FST outliers on the basis of the genetic clusters identified previously and after accounting for expansions out of Pleistocene refugia. These loci were involved with a diversity of physiological processes. Identification of nonoverlapping sets of loci highlights the fundamental differences implicit in the use of either method and suggests a pluralistic, yet complementary, approach to the identification of genes underlying ecologically relevant phenotypes. PMID:20439779

Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing.

PubMed

Malmberg, M Michelle; Shi, Fan; Spangenberg, German C; Daetwyler, Hans D; Cogan, Noel O I

2018-01-01

Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD). Complexity reduction genotyping-by-sequencing (GBS) methods, including GBS-transcriptomics (GBS-t), enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR) delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs), and identify structural variants (SVs). Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.
Diversity of Algerian oases date palm (Phoenix dactylifera L., Arecaceae): Heterozygote excess and cryptic structure suggest farmer management had a major impact on diversity.

PubMed

Moussouni, Souhila; Pintaud, Jean-Christophe; Vigouroux, Yves; Bouguedoura, Nadia

2017-01-01

Date palm (Phoenix dactyliferaL.) is the mainstay of oasis agriculture in the Saharan region. It is cultivated in a large part of the Mediterranean coastal area of the Sahara and in most isolated oases in the Algerian desert. We sampled 10 oases in Algeria to understand the structure of date palm diversity from the coastal area to a very isolated desert location. We used 18 microsatellite markers and a chloroplast minisatellite to characterize 414 individual palm trees corresponding to 114 named varieties. We found a significant negative inbreeding coefficient, suggesting active farmer selection for heterozygous individuals. Three distinct genetic clusters were identified, a ubiquitous set of varieties found across the different oases, and two clusters, one of which was specific to the northern area, and the other to the drier southern area of the Algerian Sahara. The ubiquitous cluster presented very striking chloroplast diversity, signing the frequency of haplotypes found in Saudi Arabia, the most eastern part of the date palm range. Exchanges of Middle Eastern and Algerian date palms are known to have occurred and could have led to the introduction of this particular chlorotype. However, Algerian nuclear diversity was not of eastern origin. Our study strongly suggests that the peculiar chloroplastic diversity of date palm is maintained by farmers and could originate from date palms introduced from the Middle East a long time ago, which since then, hasbeen strongly introgressed. This study illustrates the complex structure of date palm diversity in Algerian oases and the role of farmers in shaping such cryptic diversity.
Theory-Based Causal Induction

ERIC Educational Resources Information Center

Griffiths, Thomas L.; Tenenbaum, Joshua B.

2009-01-01

Inducing causal relationships from observations is a classic problem in scientific inference, statistics, and machine learning. It is also a central part of human learning, and a task that people perform remarkably well given its notorious difficulties. People can learn causal structure in various settings, from diverse forms of data: observations…
STEM Studio: Where Innovation Generates Innovation

ERIC Educational Resources Information Center

Plonczak, Irene; Brooks, Jacqueline Grennon; Wilson, Gloria Lodato; Elijah, Rosebud; Caliendo, Julia

2014-01-01

STEM Studio at Hofstra University is a clinical practice site that brings together public school pupils and preservice teachers in settings with three features that lead to enhanced learning of all participants: classroom structures using multidisciplinary STEM tasks as platforms for learning; design challenge templates for diverse student…
Empirical scoring functions for advanced protein-ligand docking with PLANTS.

PubMed

Korb, Oliver; Stützle, Thomas; Exner, Thomas E

2009-01-01

In this paper we present two empirical scoring functions, PLANTS(CHEMPLP) and PLANTS(PLP), designed for our docking algorithm PLANTS (Protein-Ligand ANT System), which is based on ant colony optimization (ACO). They are related, regarding their functional form, to parts of already published scoring functions and force fields. The parametrization procedure described here was able to identify several parameter settings showing an excellent performance for the task of pose prediction on two test sets comprising 298 complexes in total. Up to 87% of the complexes of the Astex diverse set and 77% of the CCDC/Astex clean listnc (noncovalently bound complexes of the clean list) could be reproduced with root-mean-square deviations of less than 2 A with respect to the experimentally determined structures. A comparison with the state-of-the-art docking tool GOLD clearly shows that this is, especially for the druglike Astex diverse set, an improvement in pose prediction performance. Additionally, optimized parameter settings for the search algorithm were identified, which can be used to balance pose prediction reliability and search speed.
Genetic diversity trend in Indian rice varieties: an analysis using SSR markers.

PubMed

Singh, Nivedita; Choudhury, Debjani Roy; Tiwari, Gunjan; Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R K; Sharma, A D; Singh, N K; Singh, Rakesh

2016-09-05

The knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diversity especially after green revolution. However, a detailed study of the trend of diversity in Indian rice varieties is lacking. SSR markers have proven to be a marker of choice for studying the genetic diversity. Therefore, the present study was undertaken with the aim to characterize and assess trends of genetic diversity in a large set of Indian rice varieties (released between 1940-2013), conserved in the National Gene Bank of India using SSR markers. A set of 729 Indian rice varieties were genotyped using 36 HvSSR markers to assess the genetic diversity and genetic relationship. A total of 112 alleles was amplified with an average of 3.11 alleles per locus with mean Polymorphic Information Content (PIC) value of 0.29. Cluster analysis grouped these varieties into two clusters whereas the model based population structure divided them into three populations. AMOVA study based on hierarchical cluster and model based approach showed 3 % and 11 % variation between the populations, respectively. Decadal analysis for gene diversity and PIC showed increasing trend from 1940 to 2005, thereafter values for both the parameters showed decreasing trend between years 2006-2013. In contrast to this, allele number demonstrated increasing trend in these varieties released and notified between1940 to 1985, it remained nearly constant during 1986 to 2005 and again showed an increasing trend. Our results demonstrated that the Indian rice varieties harbors huge amount of genetic diversity. However, the trait based improvement program in the last decades forced breeders to rely on few parents, which resulted in loss of gene diversity during 2006 to 2013. The present study indicates the need for broadening the genetic base of Indian rice varieties through the use of diverse parents in the current breeding program.
NEP: web server for epitope prediction based on antibody neutralization of viral strains with diverse sequences

PubMed Central

Chuang, Gwo-Yu; Liou, David; Kwong, Peter D.; Georgiev, Ivelin S.

2014-01-01

Delineation of the antigenic site, or epitope, recognized by an antibody can provide clues about functional vulnerabilities and resistance mechanisms, and can therefore guide antibody optimization and epitope-based vaccine design. Previously, we developed an algorithm for antibody-epitope prediction based on antibody neutralization of viral strains with diverse sequences and validated the algorithm on a set of broadly neutralizing HIV-1 antibodies. Here we describe the implementation of this algorithm, NEP (Neutralization-based Epitope Prediction), as a web-based server. The users must supply as input: (i) an alignment of antigen sequences of diverse viral strains; (ii) neutralization data for the antibody of interest against the same set of antigen sequences; and (iii) (optional) a structure of the unbound antigen, for enhanced prediction accuracy. The prediction results can be downloaded or viewed interactively on the antigen structure (if supplied) from the web browser using a JSmol applet. Since neutralization experiments are typically performed as one of the first steps in the characterization of an antibody to determine its breadth and potency, the NEP server can be used to predict antibody-epitope information at no additional experimental costs. NEP can be accessed on the internet at http://exon.niaid.nih.gov/nep. PMID:24782517
Geocoded data structures and their applications to Earth science investigations

NASA Technical Reports Server (NTRS)

Goldberg, M.

1984-01-01

A geocoded data structure is a means for digitally representing a geographically referenced map or image. The characteristics of representative cellular, linked, and hybrid geocoded data structures are reviewed. The data processing requirements of Earth science projects at the Goddard Space Flight Center and the basic tools of geographic data processing are described. Specific ways that new geocoded data structures can be used to adapt these tools to scientists' needs are presented. These include: expanding analysis and modeling capabilities; simplifying the merging of data sets from diverse sources; and saving computer storage space.
Phylogenetic and structural response of heterotrophic bacteria to dissolved organic matter of different chemical composition in a continuous culture study.

PubMed

Landa, M; Cottrell, M T; Kirchman, D L; Kaiser, K; Medeiros, P M; Tremblay, L; Batailler, N; Caparros, J; Catala, P; Escoubeyrou, K; Oriol, L; Blain, S; Obernosterer, I

2014-06-01

Dissolved organic matter (DOM) and heterotrophic bacteria are highly diverse components of the ocean system, and their interactions are key in regulating the biogeochemical cycles of major elements. How chemical and phylogenetic diversity are linked remains largely unexplored to date. To investigate interactions between bacterial diversity and DOM, we followed the response of natural bacterial communities to two sources of phytoplankton-derived DOM over six bacterial generation times in continuous cultures. Analyses of total hydrolysable neutral sugars and amino acids, and ultrahigh resolution mass spectrometry revealed large differences in the chemical composition of the two DOM sources. According to 454 pyrosequences of 16S ribosomal ribonucleic acid genes, diatom-derived DOM sustained higher levels of bacterial richness, evenness and phylogenetic diversity than cyanobacteria-derived DOM. These distinct community structures were, however, not associated with specific taxa. Grazing pressure affected bacterial community composition without changing the overall pattern of bacterial diversity levels set by DOM. Our results demonstrate that resource composition can shape several facets of bacterial diversity without influencing the phylogenetic composition of bacterial communities, suggesting functional redundancy at different taxonomic levels for the degradation of phytoplankton-derived DOM. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.
The impact of the board's strategy-setting role on board-management relations and hospital performance.

PubMed

Büchner, Vera Antonia; Schreyögg, Jonas; Schultz, Carsten

2014-01-01

The appropriate governance of hospitals largely depends on effective cooperation between governing boards and hospital management. Governing boards play an important role in strategy-setting as part of their support for hospital management. However, in certain situations, this active strategic role may also generate discord within this relationship. The objective of this study is to investigate the impact of the roles, attributes, and processes of governing boards on hospital performance. We examine the impact of the governing board's strategy-setting role on board-management collaboration quality and on financial performance while also analyzing the interaction effects of board diversity and board activity level. The data are derived from a survey that was sent simultaneously to German hospitals and their associated governing board, combined with objective performance information from annual financial statements and quality reports. We use a structural equation modeling approach to test the model. The results indicate that different board characteristics have a significant impact on hospital performance (R = .37). The strategy-setting role and board-management collaboration quality have a positive effect on hospital performance, whereas the impact of strategy-setting on collaboration quality is negative. We find that the positive effect of strategy-setting on performance increases with decreasing board diversity. When board members have more homogeneous backgrounds and exhibit higher board activity levels, the negative effect of the strategy-setting on collaboration quality also increases. Active strategy-setting by a governing board may generally improve hospital performance. Diverse members of governing boards should be involved in strategy-setting for hospitals. However, high board-management collaboration quality may be compromised if managerial autonomy is too highly restricted. Consequently, hospitals should support board-management collaboration about empowered contrasting board roles.
Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

PubMed Central

Hager, Kevin W.; Fullerton, Heather; Butterfield, David A.; Moyer, Craig L.

2017-01-01

The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity. PMID:28970817
DOE Office of Scientific and Technical Information (OSTI.GOV)

Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor

The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimalmore » frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism.« less
Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein

PubMed Central

Hopkins, Max; Kailasan, Shweta; Cohen, Allison; Roux, Simon; Tucker, Kimberly Pause; Shevenell, Amelia; Agbandje-McKenna, Mavis; Breitbart, Mya

2014-01-01

The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein–protein or viral–host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles. PMID:24694711
The extramedical use and diversion of opioid substitution medications and other medications in prison settings in Australia following the introduction of buprenorphine-naloxone film.

PubMed

White, Nancy; Ali, Robert; Larance, Briony; Zador, Deborah; Mattick, Richard P; Degenhardt, Louisa

2016-01-01

Around 65% of people incarcerated in prisons in Australia, America and Europe have a history of drug dependence, sometimes treated with opioid substitution treatment (OST) medications. Studies report that those in treatment in prison do engage in some level of diversion to others, whether on a voluntary or coerced basis. We aimed to examine the use of prescribed and non-prescribed OST medications by those in prisons, especially buprenorphine-naloxone film (BNX-F); the extent of non-adherence and diversion and reasons for such practices; and the impact of the introduction of BNX-F into the prison system. Mixed methods study drawing on: (i) structured interviews with current OST clients (n = 60) who reported being incarcerated in the 12 months prior to being interviewed and (ii) qualitative interviews with key experts working in corrections and prison (or justice) health settings. The majority were prescribed OST medications in prison, with 25% removing all or part of their supervised dose on at least one occasion, and 44% reporting use of non-prescribed medications. Some reported intravenous use (14% injected). One-third of OST recipients reported selling/sharing OST medications with others in prison. The introduction of BNX-F into the prison system saw different diversion methods used and removal from dosing within prison. Despite prison being a highly regulated and controlled environment, some level of diversion and sharing of psychoactive medication occurs among prisoners. The buprenorphine formulations used in OST present particular challenges with respect to supervised dosing in this setting. [White N, Ali R, Larance B, Zador D, Mattick RP, Degenhardt L. The extramedical use and diversion of opioid substitution medications and other medications in prison settings in Australia following the introduction of buprenorphine-naloxone film. Drug Alcohol Rev 2015;●●:●●-●●]. © 2015 Australasian Professional Society on Alcohol and other Drugs.
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
Toward the Structural Transformation of Schools: Innovations in Staffing

ERIC Educational Resources Information Center

Coggshall, Jane; Lasagna, Molly; Laine, Sabrina

2009-01-01

The troubled economy is driving school organizations to become more efficient and driving the business community to demand that schools produce graduates with different sets of skills. States are finally uniting around common student learning standards as the student population grows more diverse. And the new administration is pouring an…
Race, Sex, and Discrimination in School Settings: A Multilevel Analysis of Associations with Delinquency

ERIC Educational Resources Information Center

Chambers, Brittany D.; Erausquin, Jennifer Toller

2018-01-01

Background: Adolescence is a critical phase of development and experimentation with delinquent behaviors. There is a growing body of literature exploring individual and structural impacts of discrimination on health outcomes and delinquent behaviors. However, there is limited research assessing how school diversity and discrimination impact…
The National Health Educator Job Analysis 2010: Process and Outcomes

ERIC Educational Resources Information Center

Doyle, Eva I.; Caro, Carla M.; Lysoby, Linda; Auld, M. Elaine; Smith, Becky J.; Muenzen, Patricia M.

2012-01-01

The National Health Educator Job Analysis 2010 was conducted to update the competencies model for entry- and advanced-level health educators. Qualitative and quantitative methods were used. Structured interviews, focus groups, and a modified Delphi technique were implemented to engage 59 health educators from diverse work settings and experience…
Estimation of Henry's Law Constant for a Diverse Set of Organic Compounds from Molecular Structure

EPA Science Inventory

The SPARC (SPARC Performs Automated Reasoning in Chemistry) vapor pressure and activity coefficient models were coupled to estimate Henry’s Law Constant (HLC) in water and in hexadecane for a wide range of non-polar and polar organic compounds without modification or additional p...
The evolution of Lachancea thermotolerans is driven by geographical determination, anthropisation and flux between different ecosystems

PubMed Central

Bely, Marina; Masneuf-Pomarede, Isabelle; Jiranek, Vladimir; Albertin, Warren

2017-01-01

The yeast Lachancea thermotolerans (formerly Kluyveromyces thermotolerans) is a species with remarkable, yet underexplored, biotechnological potential. This ubiquist occupies a range of natural and anthropic habitats covering a wide geographic span. To gain an insight into L. thermotolerans population diversity and structure, 172 isolates sourced from diverse habitats worldwide were analysed using a set of 14 microsatellite markers. The resultant clustering revealed that the evolution of L. thermotolerans has been driven by the geography and ecological niche of the isolation sources. Isolates originating from anthropic environments, in particular grapes and wine, were genetically close, thus suggesting domestication events within the species. The observed clustering was further validated by several means including, population structure analysis, F-statistics, Mantel’s test and the analysis of molecular variance (AMOVA). Phenotypic performance of isolates was tested using several growth substrates and physicochemical conditions, providing added support for the clustering. Altogether, this study sheds light on the genotypic and phenotypic diversity of L. thermotolerans, contributing to a better understanding of the population structure, ecology and evolution of this non-Saccharomyces yeast. PMID:28910346

Genetic structure in village dogs reveals a Central Asian domestication origin.

PubMed

Shannon, Laura M; Boyko, Ryan H; Castelhano, Marta; Corey, Elizabeth; Hayward, Jessica J; McLean, Corin; White, Michelle E; Abi Said, Mounir; Anita, Baddley A; Bondjengo, Nono Ikombe; Calero, Jorge; Galov, Ana; Hedimbi, Marius; Imam, Bulu; Khalap, Rajashree; Lally, Douglas; Masta, Andrew; Oliveira, Kyle C; Pérez, Lucía; Randall, Julia; Tam, Nguyen Minh; Trujillo-Cornejo, Francisco J; Valeriano, Carlos; Sutter, Nathan B; Todhunter, Rory J; Bustamante, Carlos D; Boyko, Adam R

2015-11-03

Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups--a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations--including those of Vietnam, India, and Egypt-show minimal evidence of European admixture. These populations exhibit a clear gradient of short--range linkage disequilibrium consistent with a Central Asian domestication origin.
Genetic structure in village dogs reveals a Central Asian domestication origin

PubMed Central

Shannon, Laura M.; Boyko, Ryan H.; Castelhano, Marta; Corey, Elizabeth; Hayward, Jessica J.; McLean, Corin; White, Michelle E.; Abi Said, Mounir; Anita, Baddley A.; Bondjengo, Nono Ikombe; Calero, Jorge; Galov, Ana; Hedimbi, Marius; Imam, Bulu; Khalap, Rajashree; Lally, Douglas; Masta, Andrew; Oliveira, Kyle C.; Pérez, Lucía; Randall, Julia; Tam, Nguyen Minh; Trujillo-Cornejo, Francisco J.; Valeriano, Carlos; Sutter, Nathan B.; Todhunter, Rory J.; Bustamante, Carlos D.; Boyko, Adam R.

2015-01-01

Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations—including those of Vietnam, India, and Egypt—show minimal evidence of European admixture. These populations exhibit a clear gradient of short-range linkage disequilibrium consistent with a Central Asian domestication origin. PMID:26483491
The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies.

PubMed

Muñoz-Amatriaín, María; Cuesta-Marcos, Alfonso; Endelman, Jeffrey B; Comadran, Jordi; Bonman, John M; Bockelman, Harold E; Chao, Shiaoman; Russell, Joanne; Waugh, Robbie; Hayes, Patrick M; Muehlbauer, Gary J

2014-01-01

New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections.
4D-Fingerprint Categorical QSAR Models for Skin Sensitization Based on Classification Local Lymph Node Assay Measures

PubMed Central

Li, Yi; Tseng, Yufeng J.; Pan, Dahua; Liu, Jianzhong; Kern, Petra S.; Gerberick, G. Frank; Hopfinger, Anton J.

2008-01-01

Currently, the only validated methods to identify skin sensitization effects are in vivo models, such as the Local Lymph Node Assay (LLNA) and guinea pig studies. There is a tremendous need, in particular due to novel legislation, to develop animal alternatives, eg. Quantitative Structure-Activity Relationship (QSAR) models. Here, QSAR models for skin sensitization using LLNA data have been constructed. The descriptors used to generate these models are derived from the 4D-molecular similarity paradigm and are referred to as universal 4D-fingerprints. A training set of 132 structurally diverse compounds and a test set of 15 structurally diverse compounds were used in this study. The statistical methodologies used to build the models are logistic regression (LR), and partial least square coupled logistic regression (PLS-LR), which prove to be effective tools for studying skin sensitization measures expressed in the two categorical terms of sensitizer and non-sensitizer. QSAR models with low values of the Hosmer-Lemeshow goodness-of-fit statistic, χHL2, are significant and predictive. For the training set, the cross-validated prediction accuracy of the logistic regression models ranges from 77.3% to 78.0%, while that of PLS-logistic regression models ranges from 87.1% to 89.4%. For the test set, the prediction accuracy of logistic regression models ranges from 80.0%-86.7%, while that of PLS-logistic regression models ranges from 73.3%-80.0%. The QSAR models are made up of 4D-fingerprints related to aromatic atoms, hydrogen bond acceptors and negatively partially charged atoms. PMID:17226934
Genomic Prediction of Gene Bank Wheat Landraces

PubMed Central

Crossa, José; Jarquín, Diego; Franco, Jorge; Pérez-Rodríguez, Paulino; Burgueño, Juan; Saint-Pierre, Carolina; Vikram, Prashant; Sansaloni, Carolina; Petroli, Cesar; Akdemir, Deniz; Sneller, Clay; Reynolds, Matthew; Tattaris, Maria; Payne, Thomas; Guzman, Carlos; Peña, Roberto J.; Wenzl, Peter; Singh, Sukhwinder

2016-01-01

This study examines genomic prediction within 8416 Mexican landrace accessions and 2403 Iranian landrace accessions stored in gene banks. The Mexican and Iranian collections were evaluated in separate field trials, including an optimum environment for several traits, and in two separate environments (drought, D and heat, H) for the highly heritable traits, days to heading (DTH), and days to maturity (DTM). Analyses accounting and not accounting for population structure were performed. Genomic prediction models include genotype × environment interaction (G × E). Two alternative prediction strategies were studied: (1) random cross-validation of the data in 20% training (TRN) and 80% testing (TST) (TRN20-TST80) sets, and (2) two types of core sets, “diversity” and “prediction”, including 10% and 20%, respectively, of the total collections. Accounting for population structure decreased prediction accuracy by 15–20% as compared to prediction accuracy obtained when not accounting for population structure. Accounting for population structure gave prediction accuracies for traits evaluated in one environment for TRN20-TST80 that ranged from 0.407 to 0.677 for Mexican landraces, and from 0.166 to 0.662 for Iranian landraces. Prediction accuracy of the 20% diversity core set was similar to accuracies obtained for TRN20-TST80, ranging from 0.412 to 0.654 for Mexican landraces, and from 0.182 to 0.647 for Iranian landraces. The predictive core set gave similar prediction accuracy as the diversity core set for Mexican collections, but slightly lower for Iranian collections. Prediction accuracy when incorporating G × E for DTH and DTM for Mexican landraces for TRN20-TST80 was around 0.60, which is greater than without the G × E term. For Iranian landraces, accuracies were 0.55 for the G × E model with TRN20-TST80. Results show promising prediction accuracies for potential use in germplasm enhancement and rapid introgression of exotic germplasm into elite materials. PMID:27172218
Congestion game scheduling for virtual drug screening optimization

NASA Astrophysics Data System (ADS)

Nikitina, Natalia; Ivashko, Evgeny; Tchernykh, Andrei

2018-02-01

In virtual drug screening, the chemical diversity of hits is an important factor, along with their predicted activity. Moreover, interim results are of interest for directing the further research, and their diversity is also desirable. In this paper, we consider a problem of obtaining a diverse set of virtual screening hits in a short time. To this end, we propose a mathematical model of task scheduling for virtual drug screening in high-performance computational systems as a congestion game between computational nodes to find the equilibrium solutions for best balancing the number of interim hits with their chemical diversity. The model considers the heterogeneous environment with workload uncertainty, processing time uncertainty, and limited knowledge about the input dataset structure. We perform computational experiments and evaluate the performance of the developed approach considering organic molecules database GDB-9. The used set of molecules is rich enough to demonstrate the feasibility and practicability of proposed solutions. We compare the algorithm with two known heuristics used in practice and observe that game-based scheduling outperforms them by the hit discovery rate and chemical diversity at earlier steps. Based on these results, we use a social utility metric for assessing the efficiency of our equilibrium solutions and show that they reach greatest values.
Clinical use of the Kessler psychological distress scales with culturally diverse groups.

PubMed

Stolk, Yvonne; Kaplan, Ida; Szwarc, Josef

2014-06-01

The Kessler 10 (K10) and embedded Kessler 6 (K6) was developed to screen for non-specific psychological distress and serious mental illness in mental health surveys of English-speaking populations, but has been adopted in Western and non-Western countries as a screening and outcome measure in primary care and mental health settings. This review examines whether the original K6/K10's validity for culturally diverse populations was established, and whether the cultural equivalence, and sensitivity to change of translated or culturally adapted K6/K10s, has been demonstrated with culturally diverse client groups. Evidence for the original K6/K10's validity for culturally diverse populations is limited. Questions about the conceptual and linguistic equivalence of translated/adapted K6/K10s arise from reports of changes in item connotation and differential item functioning. Evidence for structural equivalence is inconsistent, as is support for criterion equivalence, with the majority of studies compromising on accuracy in case prediction. Research demonstrating sensitivity to change with culturally diverse groups is lacking. Inconsistent evidence for the K6/K10's cultural appropriateness in clinical settings, and a lack of clinical norms for either majority or culturally diverse groups, indicate the importance of further research into the psychological distress construct with culturally diverse clients, and the need for caution in interpreting K6/K10 scores. Copyright © 2014 John Wiley & Sons, Ltd.
QSAR models for thiophene and imidazopyridine derivatives inhibitors of the Polo-Like Kinase 1.

PubMed

Comelli, Nieves C; Duchowicz, Pablo R; Castro, Eduardo A

2014-10-01

The inhibitory activity of 103 thiophene and 33 imidazopyridine derivatives against Polo-Like Kinase 1 (PLK1) expressed as pIC50 (-logIC50) was predicted by QSAR modeling. Multivariate linear regression (MLR) was employed to model the relationship between 0D and 3D molecular descriptors and biological activities of molecules using the replacement method (MR) as variable selection tool. The 136 compounds were separated into several training and test sets. Two splitting approaches, distribution of biological data and structural diversity, and the statistical experimental design procedure D-optimal distance were applied to the dataset. The significance of the training set models was confirmed by statistically higher values of the internal leave one out cross-validated coefficient of determination (Q2) and external predictive coefficient of determination for the test set (Rtest2). The model developed from a training set, obtained with the D-optimal distance protocol and using 3D descriptor space along with activity values, separated chemical features that allowed to distinguish high and low pIC50 values reasonably well. Then, we verified that such model was sufficient to reliably and accurately predict the activity of external diverse structures. The model robustness was properly characterized by means of standard procedures and their applicability domain (AD) was analyzed by leverage method. Copyright © 2014 Elsevier B.V. All rights reserved.
Use of an airborne lidar system to model plant species composition and diversity of Mediterranean oak forests.

PubMed

Simonson, William D; Allen, Harriet D; Coomes, David A

2012-10-01

Airborne lidar is a remote-sensing tool of increasing importance in ecological and conservation research due to its ability to characterize three-dimensional vegetation structure. If different aspects of plant species diversity and composition can be related to vegetation structure, landscape-level assessments of plant communities may be possible. We examined this possibility for Mediterranean oak forests in southern Portugal, which are rich in biological diversity but also threatened. We compared data from a discrete, first-and-last return lidar data set collected for 31 plots of cork oak (Quercus suber) and Algerian oak (Quercus canariensis) forest with field data to test whether lidar can be used to predict the vertical structure of vegetation, diversity of plant species, and community type. Lidar- and field-measured structural data were significantly correlated (up to r= 0.85). Diversity of forest species was significantly associated with lidar-measured vegetation height (R(2) = 0.50, p < 0.001). Clustering and ordination of the species data pointed to the presence of 2 main forest classes that could be discriminated with an accuracy of 89% on the basis of lidar data. Lidar can be applied widely for mapping of habitat and assessments of habitat condition (e.g., in support of the European Species and Habitats Directive [92/43/EEC]). However, particular attention needs to be paid to issues of survey design: density of lidar points and geospatial accuracy of ground-truthing and its timing relative to acquisition of lidar data. ©2012 Society for Conservation Biology.
Ecological and genetic determinants of plasmid distribution in Escherichia coli.

PubMed

Medaney, Frances; Ellis, Richard J; Raymond, Ben

2016-11-01

Bacterial plasmids are important carriers of virulence and antibiotic resistance genes. Nevertheless, little is known of the determinants of plasmid distribution in bacterial populations. Here the factors affecting the diversity and distribution of the large plasmids of Escherichia coli were explored in cattle grazing on semi-natural grassland, a set of populations with low frequencies of antibiotic resistance genes. Critically, the population genetic structure of bacterial hosts was chararacterized. This revealed structured E. coli populations with high diversity between sites and individuals but low diversity within cattle hosts. Plasmid profiles, however, varied considerably within the same E. coli genotype. Both ecological and genetic factors affected plasmid distribution: plasmid profiles were affected by site, E. coli diversity, E. coli genotype and the presence of other large plasmids. Notably 3/26 E. coli serotypes accounted for half the observed plasmid-free isolates indicating that within species variation can substantially affect carriage of the major conjugative plasmids. The observed population structure suggest that most of the opportunities for within species plasmid transfer occur between different individuals of the same genotype and support recent experimental work indicating that plasmid-host coevolution, and epistatic interactions on fitness costs are likely to be important in determining occupancy. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.
Polydopamine and eumelanin molecular structures investigated with ab initio calculations† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04692d Click here for additional data file.

PubMed Central

Chen, Chun-Teh; Martin-Martinez, Francisco J.; Jung, Gang Seob

2017-01-01

A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin. All probable early-polymerized 5,6-dihydroxyindole (DHI) oligomers, ranging from dimers to tetramers, have been systematically analyzed to find the most stable geometry connections as well as to propose a set of molecular models that represents the chemically diverse nature of PDA and eumelanin. Our results indicate that more planar oligomers have a tendency to be more stable. This finding is in good agreement with recent experimental observations, which suggested that PDA and eumelanin are composed of nearly planar oligomers that appear to be stacked together via π–π interactions to form graphite-like layered aggregates. We also show that there is a group of tetramers notably more stable than the others, implying that even though there is an inherent chemical diversity in PDA and eumelanin, the molecular structures of the majority of the species are quite repetitive. Our results also suggest that larger oligomers are less likely to form. This observation is also consistent with experimental measurements, supporting the existence of small oligomers instead of large polymers as main components of PDA and eumelanin. In summary, this work brings an insight into the controversial structure of PDA and eumelanin, explaining some of the most important structural features, and providing a set of molecular models for more accurate modeling of eumelanin-like materials. PMID:28451292
Effectiveness of Genomic Prediction of Maize Hybrid Performance in Different Breeding Populations and Environments

PubMed Central

Windhausen, Vanessa S.; Atlin, Gary N.; Hickey, John M.; Crossa, Jose; Jannink, Jean-Luc; Sorrells, Mark E.; Raman, Babu; Cairns, Jill E.; Tarekegne, Amsal; Semagn, Kassa; Beyene, Yoseph; Grudloyma, Pichet; Technow, Frank; Riedelsheimer, Christian; Melchinger, Albrecht E.

2012-01-01

Genomic prediction is expected to considerably increase genetic gains by increasing selection intensity and accelerating the breeding cycle. In this study, marker effects estimated in 255 diverse maize (Zea mays L.) hybrids were used to predict grain yield, anthesis date, and anthesis-silking interval within the diversity panel and testcross progenies of 30 F2-derived lines from each of five populations. Although up to 25% of the genetic variance could be explained by cross validation within the diversity panel, the prediction of testcross performance of F2-derived lines using marker effects estimated in the diversity panel was on average zero. Hybrids in the diversity panel could be grouped into eight breeding populations differing in mean performance. When performance was predicted separately for each breeding population on the basis of marker effects estimated in the other populations, predictive ability was low (i.e., 0.12 for grain yield). These results suggest that prediction resulted mostly from differences in mean performance of the breeding populations and less from the relationship between the training and validation sets or linkage disequilibrium with causal variants underlying the predicted traits. Potential uses for genomic prediction in maize hybrid breeding are discussed emphasizing the need of (1) a clear definition of the breeding scenario in which genomic prediction should be applied (i.e., prediction among or within populations), (2) a detailed analysis of the population structure before performing cross validation, and (3) larger training sets with strong genetic relationship to the validation set. PMID:23173094
Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections

PubMed Central

Kaga, Akito; Shimizu, Takehiko; Watanabe, Satoshi; Tsubokura, Yasutaka; Katayose, Yuichi; Harada, Kyuya; Vaughan, Duncan A.; Tomooka, Norihiko

2012-01-01

Genetic variation and population structure among 1603 soybean accessions, consisted of 832 Japanese landraces, 109 old and 57 recent Japanese varieties, 341 landrace from 16 Asian countries and 264 wild soybean accessions, were characterized using 191 SNP markers. Although gene diversity of Japanese soybean germplasm was slight lower than that of exotic soybean germplasm, population differentiation and clustering analyses indicated clear genetic differentiation among Japanese cultivated soybeans, exotic cultivated soybeans and wild soybeans. Nine hundred ninety eight Japanese accessions were separated to a certain extent into groups corresponding to their agro-morphologic characteristics such as photosensitivity and seed characteristics rather than their geographical origin. Based on the assessment of the SNP markers and several agro-morphologic traits, accessions that retain gene diversity of the whole collection were selected to develop several soybean sets of different sizes using an heuristic approach; a minimum of 12 accessions can represent the observed gene diversity; a mini-core collection of 96 accession can represent a major proportion of both geographic origin and agro-morphologic trait variation. These selected sets of germplasm will provide an effective platform for enhancing soybean diversity studies and assist in finding novel traits for crop improvement. PMID:23136496
GUDM: Automatic Generation of Unified Datasets for Learning and Reasoning in Healthcare.

PubMed

Ali, Rahman; Siddiqi, Muhammad Hameed; Idris, Muhammad; Ali, Taqdir; Hussain, Shujaat; Huh, Eui-Nam; Kang, Byeong Ho; Lee, Sungyoung

2015-07-02

A wide array of biomedical data are generated and made available to healthcare experts. However, due to the diverse nature of data, it is difficult to predict outcomes from it. It is therefore necessary to combine these diverse data sources into a single unified dataset. This paper proposes a global unified data model (GUDM) to provide a global unified data structure for all data sources and generate a unified dataset by a "data modeler" tool. The proposed tool implements user-centric priority based approach which can easily resolve the problems of unified data modeling and overlapping attributes across multiple datasets. The tool is illustrated using sample diabetes mellitus data. The diverse data sources to generate the unified dataset for diabetes mellitus include clinical trial information, a social media interaction dataset and physical activity data collected using different sensors. To realize the significance of the unified dataset, we adopted a well-known rough set theory based rules creation process to create rules from the unified dataset. The evaluation of the tool on six different sets of locally created diverse datasets shows that the tool, on average, reduces 94.1% time efforts of the experts and knowledge engineer while creating unified datasets.
GUDM: Automatic Generation of Unified Datasets for Learning and Reasoning in Healthcare

PubMed Central

Ali, Rahman; Siddiqi, Muhammad Hameed; Idris, Muhammad; Ali, Taqdir; Hussain, Shujaat; Huh, Eui-Nam; Kang, Byeong Ho; Lee, Sungyoung

2015-01-01

A wide array of biomedical data are generated and made available to healthcare experts. However, due to the diverse nature of data, it is difficult to predict outcomes from it. It is therefore necessary to combine these diverse data sources into a single unified dataset. This paper proposes a global unified data model (GUDM) to provide a global unified data structure for all data sources and generate a unified dataset by a “data modeler” tool. The proposed tool implements user-centric priority based approach which can easily resolve the problems of unified data modeling and overlapping attributes across multiple datasets. The tool is illustrated using sample diabetes mellitus data. The diverse data sources to generate the unified dataset for diabetes mellitus include clinical trial information, a social media interaction dataset and physical activity data collected using different sensors. To realize the significance of the unified dataset, we adopted a well-known rough set theory based rules creation process to create rules from the unified dataset. The evaluation of the tool on six different sets of locally created diverse datasets shows that the tool, on average, reduces 94.1% time efforts of the experts and knowledge engineer while creating unified datasets. PMID:26147731
Sexual recombination is a signature of a persisting malaria epidemic in Peru

PubMed Central

2011-01-01

Background The aim of this study was to consider the impact that multi-clone, complex infections have on a parasite population structure in a low transmission setting. In general, complexity of infection (minimum number of clones within an infection) and the overall population level diversity is expected to be minimal in low transmission settings. Additionally, the parasite population structure is predicted to be clonal, rather than sexual due to infrequent parasite inoculation and lack of recombination between genetically distinct clones. However, in this low transmission of the Peruvian Amazon, complex infections are becoming more frequent, in spite of decreasing infection prevalence. In this study, it was hypothesized that sexual recombination between distinct clonal lineages of Plasmodium falciparum parasites were altering the subpopulation structure and effectively maintaining the population-level diversity. Methods Fourteen microsatellite markers were chosen to describe the genetic diversity in 313 naturally occurring P. falciparum infections from Peruvian Amazon. The population and subpopulation structure was characterized by measuring: clusteredness, expected heterozygosity (He), allelic richness, private allelic richness, and linkage disequilibrium. Next, microsatellite haplotypes and alleles were correlated with P. falciparum merozoite surface protein 1 Block 2 (Pfmsp1-B2) to examine the presence of recombinant microsatellite haplotypes. Results The parasite population structure consists of six genetically diverse subpopulations of clones, called "clusters". Clusters 1, 3, 4, and 6 have unique haplotypes that exceed 70% of the total number of clones within each cluster, while Clusters 2 and 5 have a lower proportion of unique haplotypes, but still exceed 46%. By measuring the He, allelic richness, and private allelic richness within each of the six subpopulations, relatively low levels of genetic diversity within each subpopulation (except Cluster 4) are observed. This indicated that the number of alleles, and not the combination of alleles, are limited. Next, the standard index of association (IAS) was measured, which revealed a significant decay in linkage disequilibrium (LD) associated with Cluster 6, which is indicative of independent assortment of alleles. This decay in LD is a signature of this subpopulation approaching linkage equilibrium by undergoing sexual recombination. To trace possible recombination events, the two most frequent microsatellite haplotypes observed over time (defined by either a K1 or Mad20) were selected as the progenitors and then potential recombinants were identified in within the natural population. Conclusions Contrary to conventional low transmission models, this study provides evidence of a parasite population structure that is superficially defined by a clonal backbone. Sexual recombination does occur and even arguably is responsible for maintaining the substructure of this population. PMID:22039962
Genetic structure of the carnivorous plant Pinguicula moranensis (Lentibulariaceae) on the transvolcanic Mexican belt.

PubMed

Alcalá, Raúl E; Domínguez, César A

2012-06-01

Most species of Pinguicula present a montane distribution with populations located at high altitudes. In this context, we proposed that populations of Pinguicula species could be genetically differentiated even at a local scale. This study supported that prediction, as a RAPD-based analysis of molecular variance revealed a high degree of genetic structure (Φ (st) = 0.157, P = 0.001) and low gene flow (Nm = 1.0) among four central populations of Pinguicula moranensis in Mexico, with a maximum geographic separation of about 140 km. The four populations also exhibited high levels of genetic diversity (mean Nei's genetic diversity = 0.3716; % polymorphism = 95.45%). The evolutionary implications of the genetic structure found in P. moranensis for other species in the genus are discussed in the context of the naturally fragmented distribution and a set of life history traits shared by most Pinguicula species that could promote geographic isolation and limited gene flow.
The Black Community: Diversity and Unity.

ERIC Educational Resources Information Center

Blackwell, James E.

The black community is defined in this book as a diversified set of interrelated structures and aggregates of people who are held together by the forces of racism. The need for theoretical perspectives for understanding black-white relations and for analyzing the nature of the black community is explained. The black family, patterns of family…
The Western Sydney Rustbelt: Recognizing and Building on Strengths in Pre-Service Teacher Education

ERIC Educational Resources Information Center

Naidoo, Loshini; D'warte, Jacqueline Ann

2017-01-01

Preparing pre-service teachers to address the disparities in educational attainment that occur in settings with complex demographics such as high poverty and super diversity (Vertovec, 2007) require a theoretically driven contextual and spacial (Soja, 1996) understanding of disadvantage. This understanding highlights the structural and systemic…
Making a Broader Case for the Narrow View: Where to Begin?

ERIC Educational Resources Information Center

Wallach, Geraldine P.; Charlton, Stephen; Christie, Julie

2009-01-01

Purpose: This final article covering the topic of the interplay between decoding, comprehension, and content versus structure knowledge describes a set of language initiatives that are focused toward content area learning. Inspired by the work of their colleagues from diverse fields and their own work, the authors offer suggestions to clinicians…

An Analysis of the Structure and Evolution of Networks

ERIC Educational Resources Information Center

Hua, Guangying

2011-01-01

As network research receives more and more attention from both academic researchers and practitioners, network analysis has become a fast growing field attracting many researchers from diverse fields such as physics, computer science, and sociology. This dissertation provides a review of theory and research on different real data sets from the…
Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)

NASA Astrophysics Data System (ADS)

Jin, Yuqing; Ma, Yongpeng; Wang, Shun; Hu, Xian-Ge; Huang, Li-Sha; Li, Yue; Wang, Xiao-Ru; Mao, Jian-Feng

2016-10-01

Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.
Discrete Fourier Transform-Based Multivariate Image Analysis: Application to Modeling of Aromatase Inhibitory Activity.

PubMed

Barigye, Stephen J; Freitas, Matheus P; Ausina, Priscila; Zancan, Patricia; Sola-Penna, Mauro; Castillo-Garit, Juan A

2018-02-12

We recently generalized the formerly alignment-dependent multivariate image analysis applied to quantitative structure-activity relationships (MIA-QSAR) method through the application of the discrete Fourier transform (DFT), allowing for its application to noncongruent and structurally diverse chemical compound data sets. Here we report the first practical application of this method in the screening of molecular entities of therapeutic interest, with human aromatase inhibitory activity as the case study. We developed an ensemble classification model based on the two-dimensional (2D) DFT MIA-QSAR descriptors, with which we screened the NCI Diversity Set V (1593 compounds) and obtained 34 chemical compounds with possible aromatase inhibitory activity. These compounds were docked into the aromatase active site, and the 10 most promising compounds were selected for in vitro experimental validation. Of these compounds, 7419 (nonsteroidal) and 89 201 (steroidal) demonstrated satisfactory antiproliferative and aromatase inhibitory activities. The obtained results suggest that the 2D-DFT MIA-QSAR method may be useful in ligand-based virtual screening of new molecular entities of therapeutic utility.
New insights into the stereochemical requirements of the bradykinin B2 receptor antagonists binding

NASA Astrophysics Data System (ADS)

Lupala, Cecylia S.; Gomez-Gutierrez, Patricia; Perez, Juan J.

2016-01-01

Bradykinin (BK) is a member of the kinin family, released in response to inflammation, trauma, burns, shock, allergy and some cardiovascular diseases, provoking vasodilatation and increased vascular permeability among other effects. Their actions are mediated through at least two G-protein coupled receptors, B1 a receptor up-regulated during inflammation episodes or tissue trauma and B2 that is constitutively expressed in a variety of cell types. The goal of the present work is to carry out a structure-activity study of BK B2 antagonism, taking into account the stereochemical features of diverse non-peptide antagonists and the way these features translate into ligand anchoring points to complementary regions of the receptor, through the analysis of the respective ligand-receptor complex. For this purpose an atomistic model of the BK B2 receptor was built by homology modeling and subsequently refined embedded in a lipid bilayer by means of a 600 ns molecular dynamics trajectory. The average structure from the last hundred nanoseconds of the molecular dynamics trajectory was energy minimized and used as model of the receptor for docking studies. For this purpose, a set of compounds with antagonistic profile, covering maximal diversity were selected from the literature. Specifically, the set of compounds include Fasitibant, FR173657, Anatibant, WIN64338, Bradyzide, CHEMBL442294, and JSM10292. Molecules were docked into the BK B2 receptor model and the corresponding complexes analyzed to understand ligand-receptor interactions. The outcome of this study is summarized in a 3D pharmacophore that explains the observed structure-activity results and provides insight into the design of novel molecules with antagonistic profile. To prove the validity of the pharmacophore hypothesized a virtual screening process was also carried out. The pharmacophore was used as query to identify new hits using diverse databases of molecules. The results of this study revealed a set of new hits with structures not connected to the molecules used for pharmacophore development. A few of these structures were purchased and tested. The results of the binding studies show about a 33 % success rate with a correlation between the number of pharmacophore points fulfilled and their antagonistic potency. Some of these structures are disclosed in the present work.
Influence of biotic variables on invertebrate size structure and diversity in coastal wetlands of Southeastern Spain

NASA Astrophysics Data System (ADS)

Antón-Pardo, María; Armengol, Xavier

2016-10-01

Biomass and size-based estimations provide relevant information regarding ecosystem functioning and biotic interactions. Our aims were to study the effect of fish and macrophytes on the size structure of invertebrate assemblages (from rotifers to insects) in a set of coastal water bodies, estimating the biomass (total and main invertebrate groups), the biomass-size spectra (model of Pareto) and size diversity. In fishless ponds, cladoceran and ostracod biomass were higher, and they presented greater size diversity. In fish ponds, rotifer biomass presented greater proportion; while in fishless ponds, cladocerans were usually the most abundant taxa and the largest organisms. The biomass size spectra showed more irregularities in fishless ponds, due to the low densities of small taxa (rotifers and copepod juveniles) and big taxa (malacostraceans or insects). Differences is size structure and diversity were also observed between spring and summer, suggesting a higher recruitment of juveniles in spring, and thus, a higher predation pressure upon zooplankton at that moment. Macrophyte cover did not apparently influence those parameters, except for the biomass of ostracods, copepods, and insects. Therefore, predation by fish strongly affected invertebrate biomass, reflecting their selective feeding, and allowing high densities of small taxa. Predation pressure decreased size diversity, by limiting the abundance of vulnerable taxa of specific size. Seasonal changes were likely related to the spring recruitment of fish juveniles. The presence of small fish and invertebrate predator taxa among the macrophytes, restrict their role as refuges for prey invertebrates.
Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs

PubMed Central

Saxena, Rachit K.; von Wettberg, Eric; Upadhyaya, Hari D.; Sanchez, Vanessa; Songok, Serah; Saxena, Kulbhushan; Kimurto, Paul; Varshney, Rajeev K.

2014-01-01

Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively. PMID:24533111
The effect of range changes on the functional turnover, structure and diversity of bird assemblages under future climate scenarios.

PubMed

Barbet-Massin, Morgane; Jetz, Walter

2015-08-01

Animal assemblages fulfill a critical set of ecological functions for ecosystems that may be altered substantially as climate change-induced distribution changes lead to community disaggregation and reassembly. We combine species and community perspectives to assess the consequences of projected geographic range changes for the diverse functional attributes of avian assemblages worldwide. Assemblage functional structure is projected to change highly unevenly across space. These differences arise from both changes in the number of species and changes in species' relative local functional redundancy or distinctness. They sometimes result in substantial losses of functional diversity that could have severe consequences for ecosystem health. Range expansions may counter functional losses in high-latitude regions, but offer little compensation in many tropical and subtropical biomes. Future management of local community function and ecosystem services thus relies on understanding the global dynamics of species distributions and multiscale approaches that include the biogeographic context of species traits. © 2015 John Wiley & Sons Ltd.
Contrasting Transmission Dynamics of Co-endemic Plasmodium vivax and P. falciparum: Implications for Malaria Control and Elimination

PubMed Central

Noviyanti, Rintis; Coutrier, Farah; Utami, Retno A. S.; Trimarsanto, Hidayat; Tirta, Yusrifar K.; Trianty, Leily; Kusuma, Andreas; Sutanto, Inge; Kosasih, Ayleen; Kusriastuti, Rita; Hawley, William A.; Laihad, Ferdinand; Lobo, Neil; Marfurt, Jutta; Clark, Taane G.; Price, Ric N.; Auburn, Sarah

2015-01-01

Background Outside of Africa, P. falciparum and P. vivax usually coexist. In such co-endemic regions, successful malaria control programs have a greater impact on reducing falciparum malaria, resulting in P. vivax becoming the predominant species of infection. Adding to the challenges of elimination, the dormant liver stage complicates efforts to monitor the impact of ongoing interventions against P. vivax. We investigated molecular approaches to inform the respective transmission dynamics of P. falciparum and P. vivax and how these could help to prioritize public health interventions. Methodology/ Principal Findings Genotype data generated at 8 and 9 microsatellite loci were analysed in 168 P. falciparum and 166 P. vivax isolates, respectively, from four co-endemic sites in Indonesia (Bangka, Kalimantan, Sumba and West Timor). Measures of diversity, linkage disequilibrium (LD) and population structure were used to gauge the transmission dynamics of each species in each setting. Marked differences were observed in the diversity and population structure of P. vivax versus P. falciparum. In Bangka, Kalimantan and Timor, P. falciparum diversity was low, and LD patterns were consistent with unstable, epidemic transmission, amenable to targeted intervention. In contrast, P. vivax diversity was higher and transmission appeared more stable. Population differentiation was lower in P. vivax versus P. falciparum, suggesting that the hypnozoite reservoir might play an important role in sustaining local transmission and facilitating the spread of P. vivax infections in different endemic settings. P. vivax polyclonality varied with local endemicity, demonstrating potential utility in informing on transmission intensity in this species. Conclusions/ Significance Molecular approaches can provide important information on malaria transmission that is not readily available from traditional epidemiological measures. Elucidation of the transmission dynamics circulating in a given setting will have a major role in prioritising malaria control strategies, particularly against the relatively neglected non-falciparum species. PMID:25951184
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

PubMed Central

Ravindranath, Pradeep Anand; Forli, Stefano; Goodsell, David S.; Olson, Arthur J.; Sanner, Michel F.

2015-01-01

Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains a-priori. The challenges of this approach include the: 1) exponential growth of the search space, demanding more efficient search methods; and 2) increased number of false positives, calling for scoring functions tailored for flexible receptor docking. We present AutoDockFR–AutoDock for Flexible Receptors (ADFR), a new docking engine based on the AutoDock4 scoring function, which addresses the aforementioned challenges with a new Genetic Algorithm (GA) and customized scoring function. We validate ADFR using the Astex Diverse Set, demonstrating an increase in efficiency and reliability of its GA over the one implemented in AutoDock4. We demonstrate greatly increased success rates when cross-docking ligands into apo receptors that require side-chain conformational changes for ligand binding. These cross-docking experiments are based on two datasets: 1) SEQ17 –a receptor diversity set containing 17 pairs of apo-holo structures; and 2) CDK2 –a ligand diversity set composed of one CDK2 apo structure and 52 known bound inhibitors. We show that, when cross-docking ligands into the apo conformation of the receptors with up to 14 flexible side-chains, ADFR reports more correctly cross-docked ligands than AutoDock Vina on both datasets with solutions found for 70.6% vs. 35.3% systems on SEQ17, and 76.9% vs. 61.5% on CDK2. ADFR also outperforms AutoDock Vina in number of top ranking solutions on both datasets. Furthermore, we show that correctly docked CDK2 complexes re-create on average 79.8% of all pairwise atomic interactions between the ligand and moving receptor atoms in the holo complexes. Finally, we show that down-weighting the receptor internal energy improves the ranking of correctly docked poses and that runtime for AutoDockFR scales linearly when side-chain flexibility is added. PMID:26629955
Climatic niche and neutral genetic diversity of the six Iberian pine species: a retrospective and prospective view.

PubMed

Soto, A; Robledo-Arnuncio, J J; González-Martínez, S C; Smouse, P E; Alía, R

2010-04-01

Quaternary climatic fluctuations have left contrasting historical footprints on the neutral genetic diversity patterns of existing populations of different tree species. We should expect the demography, and consequently the neutral genetic structure, of taxa less tolerant to particular climatic extremes to be more sensitive to long-term climate fluctuations. We explore this hypothesis here by sampling all six pine species found in the Iberian Peninsula (2464 individuals, 105 populations), using a common set of chloroplast microsatellite markers, and by looking at the association between neutral genetic diversity and species-specific climatic requirements. We found large variation in neutral genetic diversity and structure among Iberian pines, with cold-enduring mountain species (Pinus uncinata, P. sylvestris and P. nigra) showing substantially greater diversity than thermophilous taxa (P. pinea and P. halepensis). Within species, we observed a significant positive correlation between population genetic diversity and summer precipitation for some of the mountain pines. The observed pattern is consistent with the hypotheses that: (i) more thermophilous species have been subjected to stronger demographic fluctuations in the past, as a consequence of their maladaptation to recurrent glacial cold stages; and (ii) altitudinal migrations have allowed the maintenance of large effective population sizes and genetic variation in cold-tolerant species, especially in more humid regions. In the light of these results and hypotheses, we discuss some potential genetic consequences of impending climate change.
Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish.

PubMed

Coleman, R A; Gauffre, B; Pavlova, A; Beheregaray, L B; Kearns, J; Lyon, J; Sasaki, M; Leblois, R; Sgro, C; Sunnucks, P

2018-06-01

Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fishes, they are less understood in low-mobility species. We estimated impacts of instream barriers on genetic structure and diversity of the low-mobility river blackfish (Gadopsis marmoratus) within five streams separated by weirs or dams constructed 45-120 years ago. We found evidence of small-scale (<13 km) genetic structure within reaches unimpeded by barriers, as expected for a fish with low mobility. Genetic diversity was lower above barriers in small streams only, regardless of barrier age. In particular, one isolated population showed evidence of a recent bottleneck and inbreeding. Differentiation above and below the barrier (F ST = 0.13) was greatest in this stream, but in other streams did not differ from background levels. Spatially explicit simulations suggest that short-term barrier effects would not be detected with our data set unless effective population sizes were very small (<100). Our study highlights that, in structured populations, the ability to detect short-term genetic effects from barriers is reduced and requires more genetic markers compared to panmictic populations. We also demonstrate the importance of accounting for natural population genetic structure in fragmentation studies.
Evaluation and optimization of virtual screening workflows with DEKOIS 2.0--a public library of challenging docking benchmark sets.

PubMed

Bauer, Matthias R; Ibrahim, Tamer M; Vogel, Simon M; Boeckler, Frank M

2013-06-24

The application of molecular benchmarking sets helps to assess the actual performance of virtual screening (VS) workflows. To improve the efficiency of structure-based VS approaches, the selection and optimization of various parameters can be guided by benchmarking. With the DEKOIS 2.0 library, we aim to further extend and complement the collection of publicly available decoy sets. Based on BindingDB bioactivity data, we provide 81 new and structurally diverse benchmark sets for a wide variety of different target classes. To ensure a meaningful selection of ligands, we address several issues that can be found in bioactivity data. We have improved our previously introduced DEKOIS methodology with enhanced physicochemical matching, now including the consideration of molecular charges, as well as a more sophisticated elimination of latent actives in the decoy set (LADS). We evaluate the docking performance of Glide, GOLD, and AutoDock Vina with our data sets and highlight existing challenges for VS tools. All DEKOIS 2.0 benchmark sets will be made accessible at http://www.dekois.com.
The Effects of Educational Diversity in a National Sample of Law Students: Fitting Multilevel Latent Variable Models in Data With Categorical Indicators.

PubMed

Gottfredson, Nisha C; Panter, A T; Daye, Charles E; Allen, Walter F; Wightman, Linda F

2009-01-01

Controversy surrounding the use of race-conscious admissions can be partially resolved with improved empirical knowledge of the effects of racial diversity in educational settings. We use a national sample of law students nested in 64 law schools to test the complex and largely untested theory regarding the effects of educational diversity on student outcomes. Social scientists who study these outcomes frequently encounter both latent variables and nested data within a single analysis. Yet, until recently, an appropriate modeling technique has been computationally infeasible, and consequently few applied researchers have estimated appropriate models to test their theories, sometimes limiting the scope of their research question. Our results, based on disaggregated multilevel structural equation models, show that racial diversity is related to a reduction in prejudiced attitudes and increased perceived exposure to diverse ideas and that these effects are mediated by more frequent interpersonal contact with diverse peers. These findings provide support for the idea that administrative manipulation of educational diversity may lead to improved student outcomes. Admitting a racially/ethnically diverse student body provides an educational experience that encourages increased exposure to diverse ideas and belief systems.
How diverse is the asteroid belt?

NASA Technical Reports Server (NTRS)

Burbine, Thomas H.; Bell, Jeffrey F.

1993-01-01

For approximately twenty years, many different asteroid taxonomies, which used many different observational data sets, have been developed to try to group asteroids into classes that contain members with similar spectral characteristics. However, to understand the structure of the asteroid belt, the resulting classes are only useful if they are grouping together asteroids with somewhat similar mineralogies and thermal histories. Until recently, these taxonomies have focused on spectral reflectance data from 0.3 to 1.1 microns and visual albedo. But in the last five years, observational data sets (e.g., 0.8 to 2.5 microns spectra, CCD spectra, 3 microns spectra, and radar albedos) for a small number of asteroids were compiled that can give a better mineralogical interpretation, but whose use in asteroid taxonomy was relatively limited. Analyses of these 'supplementary' data sets show that most asteroid classes contain members with different compositions and/or thermal histories. To understand the diversity of the asteroid belt, the number of objects with these observations must be expanded and used in the next generation of taxonomies.
Combinatorial Pharmacophore-Based 3D-QSAR Analysis and Virtual Screening of FGFR1 Inhibitors

PubMed Central

Zhou, Nannan; Xu, Yuan; Liu, Xian; Wang, Yulan; Peng, Jianlong; Luo, Xiaomin; Zheng, Mingyue; Chen, Kaixian; Jiang, Hualiang

2015-01-01

The fibroblast growth factor/fibroblast growth factor receptor (FGF/FGFR) signaling pathway plays crucial roles in cell proliferation, angiogenesis, migration, and survival. Aberration in FGFRs correlates with several malignancies and disorders. FGFRs have proved to be attractive targets for therapeutic intervention in cancer, and it is of high interest to find FGFR inhibitors with novel scaffolds. In this study, a combinatorial three-dimensional quantitative structure-activity relationship (3D-QSAR) model was developed based on previously reported FGFR1 inhibitors with diverse structural skeletons. This model was evaluated for its prediction performance on a diverse test set containing 232 FGFR inhibitors, and it yielded a SD value of 0.75 pIC50 units from measured inhibition affinities and a Pearson’s correlation coefficient R2 of 0.53. This result suggests that the combinatorial 3D-QSAR model could be used to search for new FGFR1 hit structures and predict their potential activity. To further evaluate the performance of the model, a decoy set validation was used to measure the efficiency of the model by calculating EF (enrichment factor). Based on the combinatorial pharmacophore model, a virtual screening against SPECS database was performed. Nineteen novel active compounds were successfully identified, which provide new chemical starting points for further structural optimization of FGFR1 inhibitors. PMID:26110383
Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations

PubMed Central

Zehdi-Azouzi, Salwa; Cherif, Emira; Moussouni, Souhila; Gros-Balthazard, Muriel; Abbas Naqvi, Summar; Ludeña, Bertha; Castillo, Karina; Chabrillange, Nathalie; Bouguedoura, Nadia; Bennaceur, Malika; Si-Dehbi, Farida; Abdoulkader, Sabira; Daher, Abdourahman; Terral, Jean-Frederic; Santoni, Sylvain; Ballardini, Marco; Mercuri, Antonio; Ben Salah, Mohamed; Kadri, Karim; Othmani, Ahmed; Littardi, Claudio; Salhi-Hannachi, Amel; Pintaud, Jean-Christophe; Aberlenc-Bertossi, Frédérique

2015-01-01

Background and Aims Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species. Methods Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite. Key Results Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species. Conclusions This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool. PMID:26113618
Taxonomic and functional trait diversity of wild bees in different urban settings.

PubMed

Normandin, Étienne; Vereecken, Nicolas J; Buddle, Christopher M; Fournier, Valérie

2017-01-01

Urbanization is one of the major anthropogenic processes contributing to local habitat loss and extirpation of numerous species, including wild bees, the most widespread pollinators. Little is known about the mechanisms through which urbanization impacts wild bee communities, or the types of urban green spaces that best promote their conservation in cities. The main objective of this study was to describe and compare wild bee community diversity, structure, and dynamics in two Canadian cities, Montreal and Quebec City. A second objective was to compare functional trait diversity among three habitat types (cemeteries, community gardens and urban parks) within each city. Bees were collected using pan traps and netting on the same 46 sites, multiple times, over the active season in 2012 and 2013. A total of 32,237 specimens were identified, representing 200 species and 6 families, including two new continental records, Hylaeus communis Nylander (1852) and Anthidium florentinum (Fabricius, 1775). Despite high community evenness, we found significant abundance of diverse species, including exotic ones. Spatio-temporal analysis showed higher stability in the most urbanized city (Montreal) but low nestedness of species assemblages among the three urban habitats in both cities. Our study demonstrates that cities are home to diverse communities of wild bees, but in turn affect bee community structure and dynamics. We also found that community gardens harbour high levels of functional trait diversity. Urban agriculture therefore contributes substantially to the provision of functionally diverse bee communities and possibly to urban pollination services.
Taxonomic and functional trait diversity of wild bees in different urban settings

PubMed Central

Buddle, Christopher M.; Fournier, Valérie

2017-01-01

Urbanization is one of the major anthropogenic processes contributing to local habitat loss and extirpation of numerous species, including wild bees, the most widespread pollinators. Little is known about the mechanisms through which urbanization impacts wild bee communities, or the types of urban green spaces that best promote their conservation in cities. The main objective of this study was to describe and compare wild bee community diversity, structure, and dynamics in two Canadian cities, Montreal and Quebec City. A second objective was to compare functional trait diversity among three habitat types (cemeteries, community gardens and urban parks) within each city. Bees were collected using pan traps and netting on the same 46 sites, multiple times, over the active season in 2012 and 2013. A total of 32,237 specimens were identified, representing 200 species and 6 families, including two new continental records, Hylaeus communis Nylander (1852) and Anthidium florentinum (Fabricius, 1775). Despite high community evenness, we found significant abundance of diverse species, including exotic ones. Spatio-temporal analysis showed higher stability in the most urbanized city (Montreal) but low nestedness of species assemblages among the three urban habitats in both cities. Our study demonstrates that cities are home to diverse communities of wild bees, but in turn affect bee community structure and dynamics. We also found that community gardens harbour high levels of functional trait diversity. Urban agriculture therefore contributes substantially to the provision of functionally diverse bee communities and possibly to urban pollination services. PMID:28286711
Accessing genetic diversity for crop improvement.

PubMed

Glaszmann, J C; Kilian, B; Upadhyaya, H D; Varshney, R K

2010-04-01

Vast germplasm collections are accessible but their use for crop improvement is limited-efficiently accessing genetic diversity is still a challenge. Molecular markers have clarified the structure of genetic diversity in a broad range of crops. Recent developments have made whole-genome surveys and gene-targeted surveys possible, shedding light on population dynamics and on the impact of selection during domestication. Thanks to this new precision, germplasm description has gained analytical power for resolving the genetic basis of trait variation and adaptation in crops such as major cereals, chickpea, grapevine, cacao, or banana. The challenge now is to finely characterize all the facets of plant behavior in carefully chosen materials. We suggest broadening the use of 'core reference sets' so as to facilitate material sharing within the scientific community.
Outlier Loci and Selection Signatures of Simple Sequence Repeats (SSRs) in Flax (Linum usitatissimum L.).

PubMed

Soto-Cerda, Braulio J; Cloutier, Sylvie

2013-01-01

Genomic microsatellites (gSSRs) and expressed sequence tag-derived SSRs (EST-SSRs) have gained wide application for elucidating genetic diversity and population structure in plants. Both marker systems are assumed to be selectively neutral when making demographic inferences, but this assumption is rarely tested. In this study, three neutrality tests were assessed for identifying outlier loci among 150 SSRs (85 gSSRs and 65 EST-SSRs) that likely influence estimates of population structure in three differentiated flax sub-populations ( F ST = 0.19). Moreover, the utility of gSSRs, EST-SSRs, and the combined sets of SSRs was also evaluated in assessing genetic diversity and population structure in flax. Six outlier loci were identified by at least two neutrality tests showing footprints of balancing selection. After removing the outlier loci, the STRUCTURE analysis and the dendrogram topology of EST-SSRs improved. Conversely, gSSRs and combined SSRs results did not change significantly, possibly as a consequence of the higher number of neutral loci assessed. Taken together, the genetic structure analyses established the superiority of gSSRs to determine the genetic relationships among flax accessions, although the combined SSRs produced the best results. Genetic diversity parameters did not differ statistically ( P > 0.05) between gSSRs and EST-SSRs, an observation partially explained by the similar number of repeat motifs. Our study provides new insights into the ability of gSSRs and EST-SSRs to measure genetic diversity and structure in flax and confirms the importance of testing for the occurrence of outlier loci to properly assess natural and breeding populations, particularly in studies considering only few loci.

Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets.

PubMed

Cortes-Ciriano, Isidro

2016-01-01

Assessing compound toxicity at early stages of the drug discovery process is a crucial task to dismiss drug candidates likely to fail in clinical trials. Screening drug candidates against structural alerts, i.e. chemical fragments associated to a toxicological response prior or after being metabolized (bioactivation), has proved a valuable approach for this task. During the last decades, diverse algorithms have been proposed for the automatic derivation of structural alerts from categorical toxicity data sets. Here, the python library bioalerts is presented, which comprises functionalities for the automatic derivation of structural alerts from categorical (dichotomous), e.g. toxic/non-toxic, and continuous bioactivity data sets, e.g. [Formula: see text] or [Formula: see text] values. The library bioalerts relies on the RDKit implementation of the circular Morgan fingerprint algorithm to compute chemical substructures, which are derived by considering radial atom neighbourhoods of increasing bond radius. In addition to the derivation of structural alerts, bioalerts provides functionalities for the calculation of unhashed (keyed) Morgan fingerprints, which can be used in predictive bioactivity modelling with the advantage of allowing for a chemically meaningful deconvolution of the chemical space. Finally, bioalerts provides functionalities for the easy visualization of the derived structural alerts.
Strategy to discover diverse optimal molecules in the small molecule universe.

PubMed

Rupakheti, Chetan; Virshup, Aaron; Yang, Weitao; Beratan, David N

2015-03-23

The small molecule universe (SMU) is defined as a set of over 10(60) synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 , 7296 - 7303 ) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 10(5) molecules.
Strategy To Discover Diverse Optimal Molecules in the Small Molecule Universe

PubMed Central

2015-01-01

The small molecule universe (SMU) is defined as a set of over 1060 synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework (Virshup et al. J. Am. Chem. Soc.2013, 135, 7296–730323548177) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 105 molecules. PMID:25594586
Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design.

PubMed

Ludwiczak, Jan; Jarmula, Adam; Dunin-Horkawicz, Stanislaw

2018-07-01

Computational protein design is a set of procedures for computing amino acid sequences that will fold into a specified structure. Rosetta Design, a commonly used software for protein design, allows for the effective identification of sequences compatible with a given backbone structure, while molecular dynamics (MD) simulations can thoroughly sample near-native conformations. We benchmarked a procedure in which Rosetta design is started on MD-derived structural ensembles and showed that such a combined approach generates 20-30% more diverse sequences than currently available methods with only a slight increase in computation time. Importantly, the increase in diversity is achieved without a loss in the quality of the designed sequences assessed by their resemblance to natural sequences. We demonstrate that the MD-based procedure is also applicable to de novo design tasks started from backbone structures without any sequence information. In addition, we implemented a protocol that can be used to assess the stability of designed models and to select the best candidates for experimental validation. In sum our results demonstrate that the MD ensemble-based flexible backbone design can be a viable method for protein design, especially for tasks that require a large pool of diverse sequences. Copyright © 2018 Elsevier Inc. All rights reserved.
A strategy to find minimal energy nanocluster structures.

PubMed

Rogan, José; Varas, Alejandro; Valdivia, Juan Alejandro; Kiwi, Miguel

2013-11-05

An unbiased strategy to search for the global and local minimal energy structures of free standing nanoclusters is presented. Our objectives are twofold: to find a diverse set of low lying local minima, as well as the global minimum. To do so, we use massively the fast inertial relaxation engine algorithm as an efficient local minimizer. This procedure turns out to be quite efficient to reach the global minimum, and also most of the local minima. We test the method with the Lennard-Jones (LJ) potential, for which an abundant literature does exist, and obtain novel results, which include a new local minimum for LJ13 , 10 new local minima for LJ14 , and thousands of new local minima for 15≤N≤65. Insights on how to choose the initial configurations, analyzing the effectiveness of the method in reaching low-energy structures, including the global minimum, are developed as a function of the number of atoms of the cluster. Also, a novel characterization of the potential energy surface, analyzing properties of the local minima basins, is provided. The procedure constitutes a promising tool to generate a diverse set of cluster conformations, both two- and three-dimensional, that can be used as an input for refinement by means of ab initio methods. Copyright © 2013 Wiley Periodicals, Inc.
Comparative analysis of diguanylate cyclase and phosphodiesterase genes in Klebsiella pneumoniae.

PubMed

Cruz, Diana P; Huertas, Mónica G; Lozano, Marcela; Zárate, Lina; Zambrano, María Mercedes

2012-07-09

Klebsiella pneumoniae can be found in environmental habitats as well as in hospital settings where it is commonly associated with nosocomial infections. One of the factors that contribute to virulence is its capacity to form biofilms on diverse biotic and abiotic surfaces. The second messenger Bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) is a ubiquitous signal in bacteria that controls biofilm formation as well as several other cellular processes. The cellular levels of this messenger are controlled by c-di-GMP synthesis and degradation catalyzed by diguanylate cyclase (DGC) and phophodiesterase (PDE) enzymes, respectively. Many bacteria contain multiple copies of these proteins with diverse organizational structure that highlight the complex regulatory mechanisms of this signaling network. This work was undertaken to identify DGCs and PDEs and analyze the domain structure of these proteins in K. pneumoniae. A search for conserved GGDEF and EAL domains in three sequenced K. pneumoniae genomes showed that there were multiple copies of GGDEF and EAL containing proteins. Both single domain and hybrid GGDEF proteins were identified: 21 in K. pneumoniae Kp342, 18 in K. pneumoniae MGH 78578 and 17 in K. pneumoniae NTUH-K2044. The majority had only the GGDEF domain, most with the GGEEF motif, and hybrid proteins containing both GGDEF and EAL domains were also found. The I site for allosteric control was identified only in single GGDEF domain proteins and not in hybrid proteins. EAL-only proteins, containing either intact or degenerate domains, were also identified: 15 in Kp342, 15 in MGH 78578 and 10 in NTUH-K2044. Several input sensory domains and transmembrane segments were identified, which together indicate complex regulatory circuits that in many cases can be membrane associated. The comparative analysis of proteins containing GGDEF/EAL domains in K. pneumoniae showed that most copies were shared among the three strains and that some were unique to a particular strain. The multiplicity of these proteins and the diversity of structural characteristics suggest that the c-di-GMP network in this enteric bacterium is highly complex and reflects the importance of having diverse mechanisms to control cellular processes in environments as diverse as soils or plants and clinical settings.
Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm.

PubMed

Abdurakhmonov, I Y; Kohel, R J; Yu, J Z; Pepper, A E; Abdullaev, A A; Kushanov, F N; Salakhutdinov, I B; Buriev, Z T; Saha, S; Scheffler, B E; Jenkins, J N; Abdukarimov, A

2008-12-01

The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still 'lagging' cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11-12% of SSR loci pairs revealed a significant LD. At the significance threshold (r(2)>/=0.1), a genome-wide average of LD declines within the genetic distance at <10 cM in the landrace stocks germplasm and >30 cM in variety germplasm. Genome wide LD at r(2)>/=0.2 was reduced on average to approximately 1-2 cM in the landrace stock germplasm and 6-8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and stratification existing in cotton germplasm resources. The number of SSR markers associated with fiber quality traits in diverse cotton germplasm, which broadly covered many historical meiotic events, should be useful to effectively exploit potentially new genetic variation by using MAS programs.
Structural diversity promotes productivity of mixed, uneven-aged forests in southwestern Germany.

PubMed

Dănescu, Adrian; Albrecht, Axel T; Bauhus, Jürgen

2016-10-01

Forest diversity-productivity relationships have been intensively investigated in recent decades. However, few studies have considered the interplay between species and structural diversity in driving productivity. We analyzed these factors using data from 52 permanent plots in southwestern Germany with more than 53,000 repeated tree measurements. We used basal area increment as a proxy for productivity and hypothesized that: (1) structural diversity would increase tree and stand productivity, (2) diversity-productivity relationships would be weaker for species diversity than for structural diversity, and (3) species diversity would also indirectly impact stand productivity via changes in size structure. We measured diversity using distance-independent indices. We fitted separate linear mixed-effects models for fir, spruce and beech at the tree level, whereas at the stand level we pooled all available data. We tested our third hypothesis using structural equation modeling. Structural and species diversity acted as direct and independent drivers of stand productivity, with structural diversity being a slightly better predictor. Structural diversity, but not species diversity, had a significant, albeit asymmetric, effect on tree productivity. The functioning of structurally diverse, mixed forests is influenced by both structural and species diversity. These sources of trait diversity contribute to increased vertical stratification and crown plasticity, which in turn diminish competitive interferences and lead to more densely packed canopies per unit area. Our research highlights the positive effects of species diversity and structural diversity on forest productivity and ecosystem dynamics.
Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean[W][OPEN

PubMed Central

Bellucci, Elisa; Bitocchi, Elena; Ferrarini, Alberto; Benazzo, Andrea; Biagetti, Eleonora; Klie, Sebastian; Minio, Andrea; Rau, Domenico; Rodriguez, Monica; Panziera, Alex; Venturini, Luca; Attene, Giovanna; Albertini, Emidio; Jackson, Scott A.; Nanni, Laura; Fernie, Alisdair R.; Nikoloski, Zoran; Bertorelle, Giorgio; Delledonne, Massimo; Papa, Roberto

2014-01-01

Using RNA sequencing technology and de novo transcriptome assembly, we compared representative sets of wild and domesticated accessions of common bean (Phaseolus vulgaris) from Mesoamerica. RNA was extracted at the first true-leaf stage, and de novo assembly was used to develop a reference transcriptome; the final data set consists of ∼190,000 single nucleotide polymorphisms from 27,243 contigs in expressed genomic regions. A drastic reduction in nucleotide diversity (∼60%) is evident for the domesticated form, compared with the wild form, and almost 50% of the contigs that are polymorphic were brought to fixation by domestication. In parallel, the effects of domestication decreased the diversity of gene expression (18%). While the coexpression networks for the wild and domesticated accessions demonstrate similar seminal network properties, they show distinct community structures that are enriched for different molecular functions. After simulating the demographic dynamics during domestication, we found that 9% of the genes were actively selected during domestication. We also show that selection induced a further reduction in the diversity of gene expression (26%) and was associated with 5-fold enrichment of differentially expressed genes. While there is substantial evidence of positive selection associated with domestication, in a few cases, this selection has increased the nucleotide diversity in the domesticated pool at target loci associated with abiotic stress responses, flowering time, and morphology. PMID:24850850
Introgression from cultivated rice alters genetic structures of wild relative populations: implications for in situ conservation

PubMed Central

Jin, Xin; Chen, Yu; Liu, Ping; Li, Chen; Cai, Xingxing; Rong, Jun

2018-01-01

Abstract Maintaining genetic integrity is essential for in situ and ex situ conservation of crop wild relative (CWR) species. However, introgression of crop alleles into CWR species/populations may change their genetic structure and diversity, resulting in more invasive weeds or, in contrast, the extinction of endangered populations. To determine crop-wild introgression and its consequences, we examined the genetic structure and diversity of six wild rice (Oryza rufipogon) populations under in situ conservation in China. Thirty-four simple sequence repeat (SSR) and 34 insertion/deletion markers were used to genotype the wild rice populations and two sets of rice cultivars (O. sativa), corresponding to the two types of molecular markers. Shared alleles and STRUCTURE analyses suggested a variable level of crop-wild introgression and admixture. Principal coordinates and cluster analyses indicated differentiation of wild rice populations, which was associated with the spatial distances to cultivated rice fields. The level of overall genetic diversity was comparable between wild rice populations and rice cultivars, but a great number of wild-specific alleles was detected in the wild populations. We conclude based on the results that crop-wild introgression can considerably alter the pattern of genetic structure and relationships of CWR populations. Appropriate measures should be taken for effective in situ conservation of CWR species under the scenario of crop-wild introgression. PMID:29308123
Introgression from cultivated rice alters genetic structures of wild relative populations: implications for in situ conservation.

PubMed

Jin, Xin; Chen, Yu; Liu, Ping; Li, Chen; Cai, Xingxing; Rong, Jun; Lu, Bao-Rong

2018-02-01

Maintaining genetic integrity is essential for in situ and ex situ conservation of crop wild relative (CWR) species. However, introgression of crop alleles into CWR species/populations may change their genetic structure and diversity, resulting in more invasive weeds or, in contrast, the extinction of endangered populations. To determine crop-wild introgression and its consequences, we examined the genetic structure and diversity of six wild rice ( Oryza rufipogon ) populations under in situ conservation in China. Thirty-four simple sequence repeat (SSR) and 34 insertion/deletion markers were used to genotype the wild rice populations and two sets of rice cultivars ( O. sativa ), corresponding to the two types of molecular markers. Shared alleles and STRUCTURE analyses suggested a variable level of crop-wild introgression and admixture. Principal coordinates and cluster analyses indicated differentiation of wild rice populations, which was associated with the spatial distances to cultivated rice fields. The level of overall genetic diversity was comparable between wild rice populations and rice cultivars, but a great number of wild-specific alleles was detected in the wild populations. We conclude based on the results that crop-wild introgression can considerably alter the pattern of genetic structure and relationships of CWR populations. Appropriate measures should be taken for effective in situ conservation of CWR species under the scenario of crop-wild introgression.
Breast Cancer Nodes Detection Using Ultrasonic Microscale Subarrayed MIMO RADAR

PubMed Central

Siwamogsatham, Siwaruk; Pomalaza-Ráez, Carlos

2014-01-01

This paper proposes the use of ultrasonic microscale subarrayed MIMO RADARs to estimate the position of breast cancer nodes. The transmit and receive antenna arrays are divided into subarrays. In order to increase the signal diversity each subarray is assigned a different waveform from an orthogonal set. High-frequency ultrasonic transducers are used since a breast is considered to be a superficial structure. Closed form expressions for the optimal Neyman-Pearson detector are derived. The combination of the waveform diversity present in the subarrayed deployment and traditional phased-array RADAR techniques provides promising results. PMID:25309591
Assessing the Regioselectivity of OleD-Catalyzed Glycosylation with a Diverse Set of Acceptors

PubMed Central

Zhou, Maoquan; Hamza, Adel; Zhan, Chang-Guo; Thorson, Jon S.

2013-01-01

To explore the acceptor regioselectivity of OleD-catalyzed glucosylation, the products of OleD-catalyzed reactions with the six structurally diverse acceptors - flavones (daidzein), isoflavones (flavopiridol), stilbenes (resveratrol), indole alkaloids (10-hydroxycamptothecin), and steroids (2-methoxyestradiol) - were determined. This study highlights the first synthesis of flavopiridol and 2-methoxyestradiol glucosides and confirms the ability of OleD to glucosylate both aromatic and aliphatic nucleophiles. In all cases, molecular dynamics simulations were consistent with the determined product distribution and suggest the potential to develop a virtual screening model to identify additional OleD substrates. PMID:23360118
Picante: R tools for integrating phylogenies and ecology.

PubMed

Kembel, Steven W; Cowan, Peter D; Helmus, Matthew R; Cornwell, William K; Morlon, Helene; Ackerly, David D; Blomberg, Simon P; Webb, Campbell O

2010-06-01

Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities. The package calculates phylogenetic diversity metrics, performs trait comparative analyses, manipulates phenotypic and phylogenetic data, and performs tests for phylogenetic signal in trait distributions, community structure and species interactions. Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante.r-forge.r-project.org) and from CRAN (http://cran.r-project.org).
Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23.

PubMed

Barkan, David T; Cheng, Xiao-Li; Celino, Herodion; Tran, Tran T; Bhandari, Ashok; Craik, Charles S; Sali, Andrej; Smythe, Mark L

2016-11-23

Disulfide-rich peptides (DRPs) are found throughout nature. They are suitable scaffolds for drug development due to their small cores, whose disulfide bonds impart extraordinary chemical and biological stability. A challenge in developing a DRP therapeutic is to engineer binding to a specific target. This challenge can be overcome by (i) sampling the large sequence space of a given scaffold through a phage display library and by (ii) panning multiple libraries encoding structurally distinct scaffolds. Here, we implement a protocol for defining these diverse scaffolds, based on clustering structurally defined DRPs according to their conformational similarity. We developed and applied a hierarchical clustering protocol based on DRP structural similarity, followed by two post-processing steps, to classify 806 unique DRP structures into 81 clusters. The 20 most populated clusters comprised 85% of all DRPs. Representative scaffolds were selected from each of these clusters; the representatives were structurally distinct from one another, but similar to other DRPs in their respective clusters. To demonstrate the utility of the clusters, phage libraries were constructed for three of the representative scaffolds and panned against interleukin-23. One library produced a peptide that bound to this target with an IC 50 of 3.3 μM. Most DRP clusters contained members that were diverse in sequence, host organism, and interacting proteins, indicating that cluster members were functionally diverse despite having similar structure. Only 20 peptide scaffolds accounted for most of the natural DRP structural diversity, providing suitable starting points for seeding phage display experiments. Through selection of the scaffold surface to vary in phage display, libraries can be designed that present sequence diversity in architecturally distinct, biologically relevant combinations of secondary structures. We supported this hypothesis with a proof-of-concept experiment in which three phage libraries were constructed and panned against the IL-23 target, resulting in a single-digit μM hit and suggesting that a collection of libraries based on the full set of 20 scaffolds increases the potential to identify efficiently peptide binders to a protein target in a drug discovery program.
Genetic Diversity of Blumeria graminis f. sp. hordei in Central Europe and Its Comparison with Australian Population

PubMed Central

Komínková, Eva; Dreiseitl, Antonín; Malečková, Eva; Doležel, Jaroslav

2016-01-01

Population surveys of Blumeria graminis f. sp. hordei (Bgh), a causal agent of more than 50% of barley fungal infections in the Czech Republic, have been traditionally based on virulence tests, at times supplemented with non-specific Restriction fragment length polymorphism or Random amplified polymorphic DNA markers. A genomic sequence of Bgh, which has become available recently, enables identification of potential markers suitable for population genetics studies. Two major strategies relying on transposable elements and microsatellites were employed in this work to develop a set of Repeat junction markers, Single sequence repeat and Single nucleotide polymorphism markers. A resolution power of the new panel of markers comprising 33 polymorphisms was demonstrated by a phylogenetic analysis of 158 Bgh isolates. A core set of 97 Czech isolates was compared to a set 50 Australian isolates on the background of 11 diverse isolates collected throughout the world. 73.2% of Czech isolates were found to be genetically unique. An extreme diversity of this collection was in strong contrast with the uniformity of the Australian one. This work paves the way for studies of population structure and dynamics based on genetic variability among different Bgh isolates originating from geographically limited regions. PMID:27875588
Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors

NASA Astrophysics Data System (ADS)

Kalid, Ori; Toledo Warshaviak, Dora; Shechter, Sharon; Sherman, Woody; Shacham, Sharon

2012-11-01

We present the Consensus Induced Fit Docking (cIFD) approach for adapting a protein binding site to accommodate multiple diverse ligands for virtual screening. This novel approach results in a single binding site structure that can bind diverse chemotypes and is thus highly useful for efficient structure-based virtual screening. We first describe the cIFD method and its validation on three targets that were previously shown to be challenging for docking programs (COX-2, estrogen receptor, and HIV reverse transcriptase). We then demonstrate the application of cIFD to the challenging discovery of irreversible Crm1 inhibitors. We report the identification of 33 novel Crm1 inhibitors, which resulted from the testing of 402 purchased compounds selected from a screening set containing 261,680 compounds. This corresponds to a hit rate of 8.2 %. The novel Crm1 inhibitors reveal diverse chemical structures, validating the utility of the cIFD method in a real-world drug discovery project. This approach offers a pragmatic way to implicitly account for protein flexibility without the additional computational costs of ensemble docking or including full protein flexibility during virtual screening.
Delineating Substrate Diversity of Disparate Short-Chain Dehydrogenase Reductase from Debaryomyces hansenii.

PubMed

Ghatak, Arindam; Bharatham, Nagakumar; Shanbhag, Anirudh P; Datta, Santanu; Venkatraman, Janani

2017-01-01

Short-chain dehydrogenase reductases (SDRs) have been utilized for catalyzing the reduction of many aromatic/aliphatic prochiral ketones to their respective alcohols. However, there is a paucity of data that elucidates their innate biological role and diverse substrate space. In this study, we executed an in-depth biochemical characterization and substrate space mapping (with 278 prochiral ketones) of an unannotated SDR (DHK) from Debaryomyces hansenii and compared it with structurally and functionally characterized SDR Synechococcus elongatus. PCC 7942 FabG to delineate its industrial significance. It was observed that DHK was significantly more efficient than FabG, reducing a diverse set of ketones albeit at higher conversion rates. Comparison of the FabG structure with a homology model of DHK and a docking of substrate to both structures revealed the presence of additional flexible loops near the substrate binding site of DHK. The comparative elasticity of the cofactor and substrate binding site of FabG and DHK was experimentally substantiated using differential scanning fluorimetry. It is postulated that the loop flexibility may account for the superior catalytic efficiency of DHK although the positioning of the catalytic triad is conserved.
Delineating Substrate Diversity of Disparate Short-Chain Dehydrogenase Reductase from Debaryomyces hansenii

PubMed Central

Ghatak, Arindam; Bharatham, Nagakumar; Shanbhag, Anirudh P.; Datta, Santanu; Venkatraman, Janani

2017-01-01

Short-chain dehydrogenase reductases (SDRs) have been utilized for catalyzing the reduction of many aromatic/aliphatic prochiral ketones to their respective alcohols. However, there is a paucity of data that elucidates their innate biological role and diverse substrate space. In this study, we executed an in-depth biochemical characterization and substrate space mapping (with 278 prochiral ketones) of an unannotated SDR (DHK) from Debaryomyces hansenii and compared it with structurally and functionally characterized SDR Synechococcus elongatus. PCC 7942 FabG to delineate its industrial significance. It was observed that DHK was significantly more efficient than FabG, reducing a diverse set of ketones albeit at higher conversion rates. Comparison of the FabG structure with a homology model of DHK and a docking of substrate to both structures revealed the presence of additional flexible loops near the substrate binding site of DHK. The comparative elasticity of the cofactor and substrate binding site of FabG and DHK was experimentally substantiated using differential scanning fluorimetry. It is postulated that the loop flexibility may account for the superior catalytic efficiency of DHK although the positioning of the catalytic triad is conserved. PMID:28107498
Multiple solvent crystal structures of ribonuclease A: An assessment of the method

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

Dechene, Michelle; Wink, Glenna; Smith, Mychal

2010-11-12

The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) andmore » with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.« less

Long-term stability in the richness and structure of helminth communities in eels, Anguilla anguilla, in Lough Derg, River Shannon, Ireland.

PubMed

Kennedy, C R; Moriarty, C

2002-12-01

A data set on intestinal helminth parasites was collected in the course of an 18 year investigation into the biology of eels in Meelick Bay, Lough Derg, River Shannon. This was used to test two hypotheses relating to the composition and structure of intestinal helminth communities, namely that eels in large rivers do not harbour richer and more diverse communities than those in small rivers but that community composition and structure are more stable over time than in small rivers. The helminth community was species poor, with only six species comprising the component community and a maximum infracommunity richness of three species. The community was overwhelmingly dominated by the acanthocephalan Acanthocephalus lucii, reflecting the importance of its intermediate host Asellus aquaticus in the eels' diet. The remaining helminth species contributed to species richness but made very little contribution to community diversity. Population levels of Acanthocephalus lucii fell and remained low between 1992 and 2000, probably reflecting increased movement of eels from other parts of the lough into Meelick Bay. Diversity values were low, but similar to those reported from other rivers in Britain and Europe. The results provided support for both hypotheses and indicated that in respect of richness, diversity and dominance, the helminth communities of eels in the River Shannon were typical of, and comparable to, those of other large rivers throughout Europe.
Genetic diversity, population structure, and traditional culture of Camellia reticulata.

PubMed

Xin, Tong; Huang, Weijuan; De Riek, Jan; Zhang, Shuang; Ahmed, Selena; Van Huylenbroeck, Johan; Long, Chunlin

2017-11-01

Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio-economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi-structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material ( n = 190 individuals) from five populations at study sites using single-dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species ( H sp = 0.3397, I sp = 0.5236) and population (percentage of polymorphic loci = 85.63%, H pop = 0.2937, I pop = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio-economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.
Image Re-Ranking Based on Topic Diversity.

PubMed

Qian, Xueming; Lu, Dan; Wang, Yaxiong; Zhu, Li; Tang, Yuan Yan; Wang, Meng

2017-08-01

Social media sharing Websites allow users to annotate images with free tags, which significantly contribute to the development of the web image retrieval. Tag-based image search is an important method to find images shared by users in social networks. However, how to make the top ranked result relevant and with diversity is challenging. In this paper, we propose a topic diverse ranking approach for tag-based image retrieval with the consideration of promoting the topic coverage performance. First, we construct a tag graph based on the similarity between each tag. Then, the community detection method is conducted to mine the topic community of each tag. After that, inter-community and intra-community ranking are introduced to obtain the final retrieved results. In the inter-community ranking process, an adaptive random walk model is employed to rank the community based on the multi-information of each topic community. Besides, we build an inverted index structure for images to accelerate the searching process. Experimental results on Flickr data set and NUS-Wide data sets show the effectiveness of the proposed approach.
Emerging Topics and Innovative Methodologies in Cannabis Research

PubMed Central

Albright, Victoria A; Johnson, Eric Otto

2018-01-01

Aims And Scope: Cannabis use is ascendant in our society, affecting the health of our citizens, our social norms and social structures, and our economies. This special issue brings together a diverse set of research manuscripts that push the borders of our understanding of burgeoning cannabis use and displays innovative methods developed to study these phenomena. PMID:29795983
The Teacher as an Agent of Meaningful Educational Change

ERIC Educational Resources Information Center

Vandeyar, Saloshna

2017-01-01

This paper peers through the window to look at how a teacher brings about meaningful educational change in a diverse classroom. Utilizing three sets of arguments from the field of educational change, I traced educational change within a teacher during the course of an academic year. Data capture comprised a mix of semi-structured interviews and…
Identification and Analysis of the Alternatives for Achieving Greater Television Program Diversity in the United States.

ERIC Educational Resources Information Center

Dimling, John A., Jr.; And Others

Several alternatives to the present television industry structure are considered in this study. They are: continuation of present policies, satellite-to-home broadcasting, and cable distribution of television. Trends noted are: the growth of commercial UHF (Ultra High Frequency) stations, the introduction of all-channel sets, population growth,…
The Transformative Potential of Humanizing Pedagogy: Addressing the Diverse Needs of Chicano/Mexicano Students

ERIC Educational Resources Information Center

Franquiz, Maria E.; Salazar, Maria del Carmen

2004-01-01

The purpose of this paper is to present an argument for understanding the factors that support or constrain the development of Chicana/o students' academic identities and consequently, their academic resiliency in high school. The article draws on a larger study investigating ways that schooling structures and teacher mind-sets can sustain…
Culture creates genetic structure in the Caucasus: Autosomal, mitochondrial, and Y-chromosomal variation in Daghestan

PubMed Central

Marchani, Elizabeth E; Watkins, W Scott; Bulayeva, Kazima; Harpending, Henry C; Jorde, Lynn B

2008-01-01

Background Near the junction of three major continents, the Caucasus region has been an important thoroughfare for human migration. While the Caucasus Mountains have diverted human traffic to the few lowland regions that provide a gateway from north to south between the Caspian and Black Seas, highland populations have been isolated by their remote geographic location and their practice of patrilocal endogamy. We investigate how these cultural and historical differences between highland and lowland populations have affected patterns of genetic diversity. We test 1) whether the highland practice of patrilocal endogamy has generated sex-specific population relationships, and 2) whether the history of migration and military conquest associated with the lowland populations has left Central Asian genes in the Caucasus, by comparing genetic diversity and pairwise population relationships between Daghestani populations and reference populations throughout Europe and Asia for autosomal, mitochondrial, and Y-chromosomal markers. Results We found that the highland Daghestani populations had contrasting histories for the mitochondrial DNA and Y-chromosome data sets. Y-chromosomal haplogroup diversity was reduced among highland Daghestani populations when compared to other populations and to highland Daghestani mitochondrial DNA haplogroup diversity. Lowland Daghestani populations showed Turkish and Central Asian affinities for both mitochondrial and Y-chromosomal data sets. Autosomal population histories are strongly correlated to the pattern observed for the mitochondrial DNA data set, while the correlation between the mitochondrial DNA and Y-chromosome distance matrices was weak and not significant. Conclusion The reduced Y-chromosomal diversity exhibited by highland Daghestani populations is consistent with genetic drift caused by patrilocal endogamy. Mitochondrial and Y-chromosomal phylogeographic comparisons indicate a common Near Eastern origin of highland populations. Lowland Daghestani populations show varying influence from Near Eastern and Central Asian populations. PMID:18637195
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.
Ecospaces occupied by Homo erectus and Homo sapiens in insular Southeast Asia in the Pleistocene

NASA Astrophysics Data System (ADS)

Hertler, Christine; Haupt, Susanne; Volmer, Rebekka; Bruch, Angela

2014-05-01

Hominins migrated to the islands of the Sunda Shelf multiple times. At least two immigration events are evident, an early immigration of Homo erectus in the late Early Pleistocene and a second immigration of Homo sapiens during the Late Pleistocene. Regional environments changed considerably in the Pleistocene. Expansion patterns among hominins are at least co-determined by their ecologies and environmental change. We examine these expansion patterns on the basis of habitat reconstructions. Mammalian communities provide a geographically extensive record and permit to assess hominin ecospaces. Although chronological resolution is low, they represent the most complete record of habitat changes associated with hominin expansion patterns. In order to reconstruct and compare hominin ecospaces on a quantitative scale, we set up a reference sample consisting of mammalian communities of 117 national parks in South Asia and Sub-Saharan Africa. The diversity of such communities is assessed by ecological profiling of specialized herbivore taxa. Moreover, datasets on climate and vegetation correlate with the diversity structure of such specialized herbivore communities. Reconstructing the diversity structure of communities at key sites in Pleistocene Southeast Asia permits to infer features of the climatic and vegetation framework associated with different hominin taxa. Our results show that Homo erectus and Homo sapiens did not occupy similar ecospaces. The ecospace of Homo erectus is characterized by comparatively low diversity among frugivorous and folivorous taxa, while obligate grazers are part of the assemblages. Specialized herbivore communities with such a diversity structure occur at present in East Africa, while they are absent in Southeast Asia. In the reference sample, this type of ecospace corresponds to seasonal wetlands. Although Homo sapiens still inhabits this type of environment in Southeast Asia, his ecospace is wider. Homo sapiens is associated with specialized herbivore communities dominated by frugivorous and folivorous taxa. Specialized herbivore communities with such a diversity structure occur at present in rainforests on the Sunda Shelf.
Influence of Ethnolinguistic Diversity on the Sorghum Genetic Patterns in Subsistence Farming Systems in Eastern Kenya

PubMed Central

Labeyrie, Vanesse; Deu, Monique; Barnaud, Adeline; Calatayud, Caroline; Buiron, Marylène; Wambugu, Peterson; Manel, Stéphanie; Glaszmann, Jean-Christophe; Leclerc, Christian

2014-01-01

Understanding the effects of actions undertaken by human societies on crop evolution processes is a major challenge for the conservation of genetic resources. This study investigated the mechanisms whereby social boundaries associated with patterns of ethnolinguistic diversity have influenced the on-farm distribution of sorghum diversity. Social boundaries limit the diffusion of planting material, practices and knowledge, thus shaping crop diversity in situ. To assess the effect of social boundaries, this study was conducted in the contact zone between the Chuka, Mbeere and Tharaka ethnolinguistic groups in eastern Kenya. Sorghum varieties were inventoried and samples collected in 130 households. In all, 297 individual plants derived from seeds collected under sixteen variety names were characterized using a set of 18 SSR molecular markers and 15 morphological descriptors. The genetic structure was investigated using both a Bayesian assignment method and distance-based clustering. Principal Coordinates Analysis was used to describe the structure of the morphological diversity of the panicles. The distribution of the varieties and the main genetic clusters across ethnolinguistic groups was described using a non-parametric MANOVA and pairwise Fisher tests. The spatial distribution of landrace names and the overall genetic spatial patterns were significantly correlated with ethnolinguistic partition. However, the genetic structure inferred from molecular makers did not discriminate the short-cycle landraces despite their morphological distinctness. The cases of two improved varieties highlighted possible fates of improved materials. The most recent one was often given the name of local landraces. The second one, that was introduced a dozen years ago, displays traces of admixture with local landraces with differential intensity among ethnic groups. The patterns of congruence or discordance between the nomenclature of farmers’ varieties and the structure of both genetic and morphological diversity highlight the effects of the social organization of communities on the diffusion of seed, practices, and variety nomenclature. PMID:24637745
Accurate Classification of RNA Structures Using Topological Fingerprints

PubMed Central

Li, Kejie; Gribskov, Michael

2016-01-01

While RNAs are well known to possess complex structures, functionally similar RNAs often have little sequence similarity. While the exact size and spacing of base-paired regions vary, functionally similar RNAs have pronounced similarity in the arrangement, or topology, of base-paired stems. Furthermore, predicted RNA structures often lack pseudoknots (a crucial aspect of biological activity), and are only partially correct, or incomplete. A topological approach addresses all of these difficulties. In this work we describe each RNA structure as a graph that can be converted to a topological spectrum (RNA fingerprint). The set of subgraphs in an RNA structure, its RNA fingerprint, can be compared with the fingerprints of other RNA structures to identify and correctly classify functionally related RNAs. Topologically similar RNAs can be identified even when a large fraction, up to 30%, of the stems are omitted, indicating that highly accurate structures are not necessary. We investigate the performance of the RNA fingerprint approach on a set of eight highly curated RNA families, with diverse sizes and functions, containing pseudoknots, and with little sequence similarity–an especially difficult test set. In spite of the difficult test set, the RNA fingerprint approach is very successful (ROC AUC > 0.95). Due to the inclusion of pseudoknots, the RNA fingerprint approach both covers a wider range of possible structures than methods based only on secondary structure, and its tolerance for incomplete structures suggests that it can be applied even to predicted structures. Source code is freely available at https://github.rcac.purdue.edu/mgribsko/XIOS_RNA_fingerprint. PMID:27755571
Hierarchical drivers of reef-fish metacommunity structure.

PubMed

MacNeil, M Aaron; Graham, Nicholas A J; Polunin, Nicholas V C; Kulbicki, Michel; Galzin, René; Harmelin-Vivien, Mireille; Rushton, Steven P

2009-01-01

Coral reefs are highly complex ecological systems, where multiple processes interact across scales in space and time to create assemblages of exceptionally high biodiversity. Despite the increasing frequency of hierarchically structured sampling programs used in coral-reef science, little progress has been made in quantifying the relative importance of processes operating across multiple scales. The vast majority of reef studies are conducted, or at least analyzed, at a single spatial scale, ignoring the implicitly hierarchical structure of the overall system in favor of small-scale experiments or large-scale observations. Here we demonstrate how alpha (mean local number of species), beta diversity (degree of species dissimilarity among local sites), and gamma diversity (overall species richness) vary with spatial scale, and using a hierarchical, information-theoretic approach, we evaluate the relative importance of site-, reef-, and atoll-level processes driving the fish metacommunity structure among 10 atolls in French Polynesia. Process-based models, representing well-established hypotheses about drivers of reef-fish community structure, were assembled into a candidate set of 12 hierarchical linear models. Variation in fish abundance, biomass, and species richness were unevenly distributed among transect, reef, and atoll levels, establishing the relative contribution of variation at these spatial scales to the structure of the metacommunity. Reef-fish biomass, species richness, and the abundance of most functional-groups corresponded primarily with transect-level habitat diversity and atoll-lagoon size, whereas detritivore and grazer abundances were largely correlated with potential covariates of larval dispersal. Our findings show that (1) within-transect and among-atoll factors primarily drive the relationship between alpha and gamma diversity in this reef-fish metacommunity; (2) habitat is the primary correlate with reef-fish metacommunity structure at multiple spatial scales; and (3) inter-atoll connectedness was poorly correlated with the nonrandom clustering of reef-fish species. These results demonstrate the importance of modeling hierarchical data and processes in understanding reef-fish metacommunity structure.
Structural similarity based kriging for quantitative structure activity and property relationship modeling.

PubMed

Teixeira, Ana L; Falcao, Andre O

2014-07-28

Structurally similar molecules tend to have similar properties, i.e. closer molecules in the molecular space are more likely to yield similar property values while distant molecules are more likely to yield different values. Based on this principle, we propose the use of a new method that takes into account the high dimensionality of the molecular space, predicting chemical, physical, or biological properties based on the most similar compounds with measured properties. This methodology uses ordinary kriging coupled with three different molecular similarity approaches (based on molecular descriptors, fingerprints, and atom matching) which creates an interpolation map over the molecular space that is capable of predicting properties/activities for diverse chemical data sets. The proposed method was tested in two data sets of diverse chemical compounds collected from the literature and preprocessed. One of the data sets contained dihydrofolate reductase inhibition activity data, and the second molecules for which aqueous solubility was known. The overall predictive results using kriging for both data sets comply with the results obtained in the literature using typical QSPR/QSAR approaches. However, the procedure did not involve any type of descriptor selection or even minimal information about each problem, suggesting that this approach is directly applicable to a large spectrum of problems in QSAR/QSPR. Furthermore, the predictive results improve significantly with the similarity threshold between the training and testing compounds, allowing the definition of a confidence threshold of similarity and error estimation for each case inferred. The use of kriging for interpolation over the molecular metric space is independent of the training data set size, and no reparametrizations are necessary when more compounds are added or removed from the set, and increasing the size of the database will consequentially improve the quality of the estimations. Finally it is shown that this model can be used for checking the consistency of measured data and for guiding an extension of the training set by determining the regions of the molecular space for which new experimental measurements could be used to maximize the model's predictive performance.
Unexpected diversity during community succession in the apple flower microbiome.

PubMed

Shade, Ashley; McManus, Patricia S; Handelsman, Jo

2013-02-26

Despite its importance to the host, the flower microbiome is poorly understood. We report a culture-independent, community-level assessment of apple flower microbial diversity and dynamics. We collected flowers from six apple trees at five time points, starting before flowers opened and ending at petal fall. We applied streptomycin to half of the trees when flowers opened. Assessment of microbial diversity using tag pyrosequencing of 16S rRNA genes revealed that the apple flower communities were rich and diverse and dominated by members of TM7 and Deinococcus-Thermus, phyla about which relatively little is known. From thousands of taxa, we identified six successional groups with coherent dynamics whose abundances peaked at different times before and after bud opening. We designated the groups Pioneer, Early, Mid, Late, Climax, and Generalist communities. The successional pattern was attributed to a set of prevalent taxa that were persistent and gradually changing in abundance. These taxa had significant associations with other community members, as demonstrated with a cooccurrence network based on local similarity analysis. We also detected a set of less-abundant, transient taxa that contributed to general tree-to-tree variability but not to the successional pattern. Communities on trees sprayed with streptomycin had slightly lower phylogenetic diversity than those on unsprayed trees but did not differ in structure or succession. Our results suggest that changes in apple flower microbial community structure are predictable over the life of the flower, providing a basis for ecological understanding and disease management. Flowering plants (angiosperms) represent a diverse group of an estimated 400,000 species, and their successful cultivation is essential to agriculture. Yet fundamental knowledge of flower-associated microbiotas remains largely unknown. Even less well understood are the changes that flower microbial communities experience through time. Flowers are particularly conducive to comprehensive temporal studies because they are, by nature, ephemeral organs. Here, we present the first culture-independent time series of bacterial and archaeal communities associated with the flowers of apple, an economically important crop. We found unexpected diversity on apple flowers, including a preponderance of taxa affiliated with Deinococcus-Thermus and TM7, phyla that are understudied but thought to be tolerant to an array of environmental stresses. Our results also suggest that changes in microbial community structure on the apple flower may be predictable over the life of the flower, providing the basis for ecological understanding and disease management.
Diversity of Bats in Contrasting Habitats of Hulu Terengganu Dipterocarp Forest and Setiu Wetland BRIS Forest with a Note on Preliminary Study of Vertical Stratification of Pteropodid Bats.

PubMed

Pounsin, Grace; Wahab, Nur Syahirah; Roslan, Azuan; Zahidin, Muhamad Aidil; Pesiu, Elizabeth; Tamrin, Nur Aida Md; Abdullah, M T

2018-03-01

A study of the bat diversity was conducted in Hulu Terengganu dipterocarp forest and Setiu Wetland Beach Ridges Interspersed with Swales (BRIS) forest in Terengganu, to study the species diversity, composition and stratification of fruit bats from the understorey to the forest canopy. Mist nets were set up at the understorey, sub-canopy and canopy layer while harp traps were set up at the understorey layer. We recorded 170 individuals from six families' compromised 21 species from Hulu Terengganu dipterocarp forests and four species from Setiu Wetland BRIS forests throughout the sampling period. Megaerops ecaudatus and Cynopterus brachyotis were the most dominant species in Hulu Terengganu dipterocarp forest and Setiu Wetland BRIS forests. Our study also recorded two species with new distributional records for the east coast of Peninsular Malaysia, namely, Rhinolophus chiewkweeae and Chaerephon johorensis in Hulu Terengganu dipterocarp forests. Potential factors that might influence the results were in terms of the canopy covers, the structural complexity of canopy, food availability and spatial characteristics. This study was able to increase the knowledge on the species diversity and composition of bats in Hulu Terengganu dipterocarp forest and Setiu Wetland BRIS forest, thus, further aid in the effort of bat conservation in both areas.
Microbial Diversity in Deep-sea Methane Seep Sediments Presented by SSU rRNA Gene Tag Sequencing

PubMed Central

Nunoura, Takuro; Takaki, Yoshihiro; Kazama, Hiromi; Hirai, Miho; Ashi, Juichiro; Imachi, Hiroyuki; Takai, Ken

2012-01-01

Microbial community structures in methane seep sediments in the Nankai Trough were analyzed by tag-sequencing analysis for the small subunit (SSU) rRNA gene using a newly developed primer set. The dominant members of Archaea were Deep-sea Hydrothermal Vent Euryarchaeotic Group 6 (DHVEG 6), Marine Group I (MGI) and Deep Sea Archaeal Group (DSAG), and those in Bacteria were Alpha-, Gamma-, Delta- and Epsilonproteobacteria, Chloroflexi, Bacteroidetes, Planctomycetes and Acidobacteria. Diversity and richness were examined by 8,709 and 7,690 tag-sequences from sediments at 5 and 25 cm below the seafloor (cmbsf), respectively. The estimated diversity and richness in the methane seep sediment are as high as those in soil and deep-sea hydrothermal environments, although the tag-sequences obtained in this study were not sufficient to show whole microbial diversity in this analysis. We also compared the diversity and richness of each taxon/division between the sediments from the two depths, and found that the diversity and richness of some taxa/divisions varied significantly along with the depth. PMID:22510646
Visualization of diversity in large multivariate data sets.

PubMed

Pham, Tuan; Hess, Rob; Ju, Crystal; Zhang, Eugene; Metoyer, Ronald

2010-01-01

Understanding the diversity of a set of multivariate objects is an important problem in many domains, including ecology, college admissions, investing, machine learning, and others. However, to date, very little work has been done to help users achieve this kind of understanding. Visual representation is especially appealing for this task because it offers the potential to allow users to efficiently observe the objects of interest in a direct and holistic way. Thus, in this paper, we attempt to formalize the problem of visualizing the diversity of a large (more than 1000 objects), multivariate (more than 5 attributes) data set as one worth deeper investigation by the information visualization community. In doing so, we contribute a precise definition of diversity, a set of requirements for diversity visualizations based on this definition, and a formal user study design intended to evaluate the capacity of a visual representation for communicating diversity information. Our primary contribution, however, is a visual representation, called the Diversity Map, for visualizing diversity. An evaluation of the Diversity Map using our study design shows that users can judge elements of diversity consistently and as or more accurately than when using the only other representation specifically designed to visualize diversity.
Pharmacophore modeling of diverse classes of p38 MAP kinase inhibitors.

PubMed

Sarma, Rituparna; Sinha, Sharat; Ravikumar, Muttineni; Kishore Kumar, Madala; Mahmood, S K

2008-12-01

Mitogen-activated protein (MAP) p38 kinase is a serine-threonine protein kinase and its inhibitors are useful in the treatment of inflammatory diseases. Pharmacophore models were developed using HypoGen program of Catalyst with diverse classes of p38 MAP kinase inhibitors. The best pharmacophore hypothesis (Hypo1) with hydrogen-bond acceptor (HBA), hydrophobic (HY), hydrogen-bond donor (HBD), and ring aromatic (RA) as features has correlation coefficient of 0.959, root mean square deviation (RMSD) of 1.069 and configuration cost of 14.536. The model was validated using test set containing 119 compounds and had high correlation coefficient of 0.851. The results demonstrate that results obtained in this study can be considered to be useful and reliable tools in identifying structurally diverse compounds with desired biological activity.
Development of eighteen microsatellite loci in walleye (Sander vitreus)

USGS Publications Warehouse

Coykendall, D. Katharine; Morrison, Cheryl L.; Stott, Wendylee; Springmann, Marcus J.

2014-01-01

A suite of tri- and tetra-nucleotide microsatellite loci were developed for walleye (Sander vitreus) from 454 pyrosequencing data. Eighteen of the 50 primer sets tested amplified consistently in 35 walleye from two lakes on Isle Royale, Lake Superior: Chickenbone Lake and Whittlesey Lake. The loci displayed moderate levels of allelic diversity (average 5.5 alleles/locus) and heterozygosity (average 35.8 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and detect phylogeographic structuring as individuals assigned back to their population of origin. Cross-species amplification within S. canadensis(sauger) was successful for 15 loci, and 11 loci were diagnostic to species. The loci characterized here will be useful for detecting fine-scale spatial structuring, resolving the taxonomic status of Sander species and sub-species, and detecting walleye/sauger hybrids.

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

Burnett, R.A.

A major goal of the Analysis of Large Data Sets (ALDS) research project at Pacific Northwest Laboratory (PNL) is to provide efficient data organization, storage, and access capabilities for statistical applications involving large amounts of data. As part of the effort to achieve this goal, a self-describing binary (SDB) data file structure has been designed and implemented together with a set of basic data manipulation functions and supporting SDB data access routines. Logical and physical data descriptors are stored in SDB files preceding the data values. SDB files thus provide a common data representation for interfacing diverse software components. Thismore » paper describes the various types of data descriptors and data structures permitted by the file design. Data buffering, file segmentation, and a segment overflow handler are also discussed.« less
Host and geographic structure of endophytic and endolichenic fungi at a continental scale.

PubMed

U'Ren, Jana M; Lutzoni, François; Miadlikowska, Jolanta; Laetsch, Alexander D; Arnold, A Elizabeth

2012-05-01

Endophytic and endolichenic fungi occur in healthy tissues of plants and lichens, respectively, playing potentially important roles in the ecology and evolution of their hosts. However, previous sampling has not comprehensively evaluated the biotic, biogeographic, and abiotic factors that structure their communities. Using molecular data we examined the diversity, composition, and distributions of 4154 endophytic and endolichenic Ascomycota cultured from replicate surveys of ca. 20 plant and lichen species in each of five North American sites (Madrean coniferous forest, Arizona; montane semideciduous forest, North Carolina; scrub forest, Florida; Beringian tundra and forest, western Alaska; subalpine tundra, eastern central Alaska). Endolichenic fungi were more abundant and diverse per host species than endophytes, but communities of endophytes were more diverse overall, reflecting high diversity in mosses and lycophytes. Endophytes of vascular plants were largely distinct from fungal communities that inhabit mosses and lichens. Fungi from closely related hosts from different regions were similar in higher taxonomy, but differed at shallow taxonomic levels. These differences reflected climate factors more strongly than geographic distance alone. Our study provides a first evaluation of endophytic and endolichenic fungal associations with their hosts at a continental scale. Both plants and lichens harbor abundant and diverse fungal communities whose incidence, diversity, and composition reflect the interplay of climatic patterns, geographic separation, host type, and host lineage. Although culture-free methods will inform future work, our study sets the stage for empirical assessments of ecological specificity, metabolic capability, and comparative genomics.
An orthogonal system for heterologous expression of actinobacterial lasso peptides in Streptomyces hosts.

PubMed

Mevaere, Jimmy; Goulard, Christophe; Schneider, Olha; Sekurova, Olga N; Ma, Haiyan; Zirah, Séverine; Afonso, Carlos; Rebuffat, Sylvie; Zotchev, Sergey B; Li, Yanyan

2018-05-29

Lasso peptides are ribosomally synthesized and post-translationally modified peptides produced by bacteria. They are characterized by an unusual lariat-knot structure. Targeted genome scanning revealed a wide diversity of lasso peptides encoded in actinobacterial genomes, but cloning and heterologous expression of these clusters turned out to be problematic. To circumvent this, we developed an orthogonal expression system for heterologous production of actinobacterial lasso peptides in Streptomyces hosts based on a newly-identified regulatory circuit from Actinoalloteichus fjordicus. Six lasso peptide gene clusters, mainly originating from marine Actinobacteria, were chosen for proof-of-concept studies. By varying the Streptomyces expression hosts and a small set of culture conditions, three new lasso peptides were successfully produced and characterized by tandem MS. The newly developed expression system thus sets the stage to uncover and bioengineer the chemo-diversity of actinobacterial lasso peptides. Moreover, our data provide some considerations for future bioprospecting efforts for such peptides.
A Low-Cost, Hands-on Module to Characterize Antimicrobial Compounds Using an Interdisciplinary, Biophysical Approach

PubMed Central

Kaushik, Karishma S.; Kessel, Ashley; Ratnayeke, Nalin; Gordon, Vernita D.

2015-01-01

We have developed a hands-on experimental module that combines biology experiments with a physics-based analytical model in order to characterize antimicrobial compounds. To understand antibiotic resistance, participants perform a disc diffusion assay to test the antimicrobial activity of different compounds and then apply a diffusion-based analytical model to gain insights into the behavior of the active antimicrobial component. In our experience, this module was robust, reproducible, and cost-effective, suggesting that it could be implemented in diverse settings such as undergraduate research, STEM (science, technology, engineering, and math) camps, school programs, and laboratory training workshops. By providing valuable interdisciplinary research experience in science outreach and education initiatives, this module addresses the paucity of structured training or education programs that integrate diverse scientific fields. Its low-cost requirements make it especially suitable for use in resource-limited settings. PMID:25602254
Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

PubMed

Cabana, Graciela S; Lewis, Cecil M; Tito, Raúl Y; Covey, R Alan; Cáceres, Angela M; Cruz, Augusto F De La; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I; Iannacone, Gian Carlo; López, Paul W; Martínez, Rolando; Medina, Ángel; Dávila, Olimpio Ortega; Pinto, Karla Paloma Osorio; Santillán, Susan I Polo; Domínguez, Percy Rojas; Rubel, Meagan; Smith, Heather F; Smith, Silvia E; Massa, Verónica Rubín de Celis; Lizárraga, Beatriz; Stone, Anne C

2014-01-01

Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored. Here we examine population genetic diversity in the Peruvian Central Andes using data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations differed from coastal and lowland populations in mtDNA genetic structure only; highland groups also showed strong evidence of female-biased gene flow and/or effective sizes relative to other Peruvian ecozones. Taken together, these findings indicate that population genetic structure in the Peruvian Central Andes is considerably more complex than previously reported and that characterizations of and explanations for genetic variation may be best pursued within more localized regions and defined time periods.
Metacommunity ecology meets biogeography: effects of geographical region, spatial dynamics and environmental filtering on community structure in aquatic organisms.

PubMed

Heino, Jani; Soininen, Janne; Alahuhta, Janne; Lappalainen, Jyrki; Virtanen, Risto

2017-01-01

Metacommunity patterns and underlying processes in aquatic organisms have typically been studied within a drainage basin. We examined variation in the composition of six freshwater organismal groups across various drainage basins in Finland. We first modelled spatial structures within each drainage basin using Moran eigenvector maps. Second, we partitioned variation in community structure among three groups of predictors using constrained ordination: (1) local environmental variables, (2) spatial variables, and (3) dummy variable drainage basin identity. Third, we examined turnover and nestedness components of multiple-site beta diversity, and tested the best fit patterns of our datasets using the "elements of metacommunity structure" analysis. Our results showed that basin identity and local environmental variables were significant predictors of community structure, whereas within-basin spatial effects were typically negligible. In half of the organismal groups (diatoms, bryophytes, zooplankton), basin identity was a slightly better predictor of community structure than local environmental variables, whereas the opposite was true for the remaining three organismal groups (insects, macrophytes, fish). Both pure basin and local environmental fractions were, however, significant after accounting for the effects of the other predictor variable sets. All organismal groups exhibited high levels of beta diversity, which was mostly attributable to the turnover component. Our results showed consistent Clementsian-type metacommunity structures, suggesting that subgroups of species responded similarly to environmental factors or drainage basin limits. We conclude that aquatic communities across large scales are mostly determined by environmental and basin effects, which leads to high beta diversity and prevalence of Clementsian community types.
Influence of Traditional Management and Environmental Variables on Mediterranean Saproxylic Beetle Assemblages.

PubMed

Ramilo, P; Martínez-Falcón, A P; García-López, A; Brustel, H; Galante, E; Micó, E

2017-12-08

Mediterranean oak forests of the Iberian Peninsula host a great diversity of saproxylic beetles. For centuries, humans have carried out traditional management practices in this area, at both habitat and tree level, causing changes in forest structure. The aim of this study was to evaluate the anthropic effect of these traditional practices on saproxylic beetle diversity by measuring a set of environmental variables related to forest structure at both plot and tree level. Fauna was collected using window traps over a period of 12 mo. Multiple regression procedures showed which variables significantly affected the diversity of the studied assemblage. Our results demonstrated that the different metrics used to assess the diversity of assemblages responded variably depending on the management strategies applied and the level at which they were carried out. Certain management practices that disrupted the landscape from its natural state, such as the introduction of livestock or the local removal of particular trees, maximized species richness but, nevertheless, had a negative effect on the rest of diversity metrics analyzed. However, other practices such as pollarding, which involves the suppression of the main branch of the tree, had a positive effect on all diversity metrics evaluated as it promoted the formation of potential microhabitats for saproxylic fauna. We concluded that not all types and degrees of traditional forest management favor saproxylic beetle diversity and that different diversity metrics should be taken into consideration in future strategies for the protection and conservation of this fauna. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization.

PubMed

Libbrecht, Maxwell W; Bilmes, Jeffrey A; Noble, William Stafford

2018-04-01

Selecting a non-redundant representative subset of sequences is a common step in many bioinformatics workflows, such as the creation of non-redundant training sets for sequence and structural models or selection of "operational taxonomic units" from metagenomics data. Previous methods for this task, such as CD-HIT, PISCES, and UCLUST, apply a heuristic threshold-based algorithm that has no theoretical guarantees. We propose a new approach based on submodular optimization. Submodular optimization, a discrete analogue to continuous convex optimization, has been used with great success for other representative set selection problems. We demonstrate that the submodular optimization approach results in representative protein sequence subsets with greater structural diversity than sets chosen by existing methods, using as a gold standard the SCOPe library of protein domain structures. In this setting, submodular optimization consistently yields protein sequence subsets that include more SCOPe domain families than sets of the same size selected by competing approaches. We also show how the optimization framework allows us to design a mixture objective function that performs well for both large and small representative sets. The framework we describe is the best possible in polynomial time (under some assumptions), and it is flexible and intuitive because it applies a suite of generic methods to optimize one of a variety of objective functions. © 2018 Wiley Periodicals, Inc.
A Personalised Needs-Led Group Approach to Induction: Perceptions of Early Academics in a University School of Education

ERIC Educational Resources Information Center

Jarvis, Joy; Dickerson, Claire; Chivers, Leo; Collins, Chris; Lee, Libby; Levy, Roger; Solly, Dianne

2012-01-01

Members of staff joining a school of education often have extensive experience in practice but not in academia and the university setting may present a complex diversity of roles, ways of working, values and goals. Colleagues may face issues of understanding the organisational structure and culture, changing identities, and concerns about their…
Hydrogeomorphic (HGM) Approach to Assessing Wetland Functions: Guidelines for Developing Guidebooks (Version 2)

DTIC Science & Technology

2013-06-01

setting, landscape position, watershed size), the structural components of the wetland ecosystem (e.g., plants , animals, soil , water, and the...Community Support Characteristic Invertebrate Community Support Landscape/Regional Biodiversity Diversity of native plant species (index, H’) Number of...Flagging GPS and Digital Camera / Spare Batteries Clipboard, Calculator, and Pencils County Soil Survey Plant Identification Keys Munsell
NEP: web server for epitope prediction based on antibody neutralization of viral strains with diverse sequences.

PubMed

Chuang, Gwo-Yu; Liou, David; Kwong, Peter D; Georgiev, Ivelin S

2014-07-01

Delineation of the antigenic site, or epitope, recognized by an antibody can provide clues about functional vulnerabilities and resistance mechanisms, and can therefore guide antibody optimization and epitope-based vaccine design. Previously, we developed an algorithm for antibody-epitope prediction based on antibody neutralization of viral strains with diverse sequences and validated the algorithm on a set of broadly neutralizing HIV-1 antibodies. Here we describe the implementation of this algorithm, NEP (Neutralization-based Epitope Prediction), as a web-based server. The users must supply as input: (i) an alignment of antigen sequences of diverse viral strains; (ii) neutralization data for the antibody of interest against the same set of antigen sequences; and (iii) (optional) a structure of the unbound antigen, for enhanced prediction accuracy. The prediction results can be downloaded or viewed interactively on the antigen structure (if supplied) from the web browser using a JSmol applet. Since neutralization experiments are typically performed as one of the first steps in the characterization of an antibody to determine its breadth and potency, the NEP server can be used to predict antibody-epitope information at no additional experimental costs. NEP can be accessed on the internet at http://exon.niaid.nih.gov/nep. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.
WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets

PubMed Central

2014-01-01

Background Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software. Results We here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages. Conclusions With these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called “Smiley2png 1.0”) can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu. PMID:24886360
Activity Settings and Daily Routines in Preschool Classrooms: Diverse Experiences in Early Learning Settings for Low-Income Children.

PubMed

Fuligni, Allison Sidle; Howes, Carollee; Huang, Yiching; Hong, Sandra Soliday; Lara-Cinisomo, Sandraluz

2012-06-01

This paper examines activity settings and daily classroom routines experienced by 3- and 4-year-old low-income children in public center-based preschool programs, private center-based programs, and family child care homes. Two daily routine profiles were identified using a time-sampling coding procedure: a High Free-Choice pattern in which children spent a majority of their day engaged in child-directed free-choice activity settings combined with relatively low amounts of teacher-directed activity, and a Structured-Balanced pattern in which children spent relatively equal proportions of their day engaged in child-directed free-choice activity settings and teacher-directed small- and whole-group activities. Daily routine profiles were associated with program type and curriculum use but not with measures of process quality. Children in Structured-Balanced classrooms had more opportunities to engage in language and literacy and math activities, whereas children in High Free-Choice classrooms had more opportunities for gross motor and fantasy play. Being in a Structured-Balanced classroom was associated with children's language scores but profiles were not associated with measures of children's math reasoning or socio-emotional behavior. Consideration of teachers' structuring of daily routines represents a valuable way to understand nuances in the provision of learning experiences for young children in the context of current views about developmentally appropriate practice and school readiness.
Activity Settings and Daily Routines in Preschool Classrooms: Diverse Experiences in Early Learning Settings for Low-Income Children

PubMed Central

Fuligni, Allison Sidle; Howes, Carollee; Huang, Yiching; Hong, Sandra Soliday; Lara-Cinisomo, Sandraluz

2011-01-01

This paper examines activity settings and daily classroom routines experienced by 3- and 4-year-old low-income children in public center-based preschool programs, private center-based programs, and family child care homes. Two daily routine profiles were identified using a time-sampling coding procedure: a High Free-Choice pattern in which children spent a majority of their day engaged in child-directed free-choice activity settings combined with relatively low amounts of teacher-directed activity, and a Structured-Balanced pattern in which children spent relatively equal proportions of their day engaged in child-directed free-choice activity settings and teacher-directed small- and whole-group activities. Daily routine profiles were associated with program type and curriculum use but not with measures of process quality. Children in Structured-Balanced classrooms had more opportunities to engage in language and literacy and math activities, whereas children in High Free-Choice classrooms had more opportunities for gross motor and fantasy play. Being in a Structured-Balanced classroom was associated with children’s language scores but profiles were not associated with measures of children’s math reasoning or socio-emotional behavior. Consideration of teachers’ structuring of daily routines represents a valuable way to understand nuances in the provision of learning experiences for young children in the context of current views about developmentally appropriate practice and school readiness. PMID:22665945
On the Improvement of Convergence Performance for Integrated Design of Wind Turbine Blade Using a Vector Dominating Multi-objective Evolution Algorithm

NASA Astrophysics Data System (ADS)

Wang, L.; Wang, T. G.; Wu, J. H.; Cheng, G. P.

2016-09-01

A novel multi-objective optimization algorithm incorporating evolution strategies and vector mechanisms, referred as VD-MOEA, is proposed and applied in aerodynamic- structural integrated design of wind turbine blade. In the algorithm, a set of uniformly distributed vectors is constructed to guide population in moving forward to the Pareto front rapidly and maintain population diversity with high efficiency. For example, two- and three- objective designs of 1.5MW wind turbine blade are subsequently carried out for the optimization objectives of maximum annual energy production, minimum blade mass, and minimum extreme root thrust. The results show that the Pareto optimal solutions can be obtained in one single simulation run and uniformly distributed in the objective space, maximally maintaining the population diversity. In comparison to conventional evolution algorithms, VD-MOEA displays dramatic improvement of algorithm performance in both convergence and diversity preservation for handling complex problems of multi-variables, multi-objectives and multi-constraints. This provides a reliable high-performance optimization approach for the aerodynamic-structural integrated design of wind turbine blade.
Multilocus Phylogeography and Species Delimitation in the Cumberland Plateau Salamander, Plethodon kentucki: Incongruence among Data Sets and Methods

PubMed Central

Kuchta, Shawn R.; Brown, Ashley D.; Converse, Paul E.; Highton, Richard

2016-01-01

Species are a fundamental unit of biodiversity, yet can be challenging to delimit objectively. This is particularly true of species complexes characterized by high levels of population genetic structure, hybridization between genetic groups, isolation by distance, and limited phenotypic variation. Previous work on the Cumberland Plateau Salamander, Plethodon kentucki, suggested that it might constitute a species complex despite occupying a relatively small geographic range. To examine this hypothesis, we sampled 135 individuals from 43 populations, and used four mitochondrial loci and five nuclear loci (5693 base pairs) to quantify phylogeographic structure and probe for cryptic species diversity. Rates of evolution for each locus were inferred using the multidistribute package, and time calibrated gene trees and species trees were inferred using BEAST 2 and *BEAST 2, respectively. Because the parameter space relevant for species delimitation is large and complex, and all methods make simplifying assumptions that may lead them to fail, we conducted an array of analyses. Our assumption was that strongly supported species would be congruent across methods. Putative species were first delimited using a Bayesian implementation of the GMYC model (bGMYC), Geneland, and Brownie. We then validated these species using the genealogical sorting index and BPP. We found substantial phylogeographic diversity using mtDNA, including four divergent clades and an inferred common ancestor at 14.9 myr (95% HPD: 10.8–19.7 myr). By contrast, this diversity was not corroborated by nuclear sequence data, which exhibited low levels of variation and weak phylogeographic structure. Species trees estimated a far younger root than did the mtDNA data, closer to 1.0 myr old. Mutually exclusive putative species were identified by the different approaches. Possible causes of data set discordance, and the problem of species delimitation in complexes with high levels of population structure and introgressive hybridization, are discussed. PMID:26974148
Heathlands confronting global change: drivers of biodiversity loss from past to future scenarios

PubMed Central

Fagúndez, Jaime

2013-01-01

Background Heathlands are dynamic plant communities characterized by a high cover of sclerophyllous, ericoid shrubs that develop over nutrient-poor soils. Interest in the preservation of these habitats in Europe has increased over the last decades, but over this time there has been a general decline in habitat quality, affecting community structure, ecosystem functions and biodiversity. Negative drivers that trigger these changes include land-use changes (i.e. habitat destruction and fragmentation), pollution, climate change, natural succession and human management, as well as the presence of invasive exotic species. Scope Based on recent scientific literature, the effect of each of these potential drivers on a wide set of factors, including physiological traits, species richness and diversity, community structure, ecosystem functions and soil conditions, is reviewed. The effects of these drivers are generally understood, but the direction and magnitude of factor interactions, whenever studied, have shown high variability. Conclusions Habitat loss and fragmentation affect sensitive species and ecosystem functions. The nature of the surrounding area will condition the quality of the heathland remnants by, for example, propagule pressure from invasive species. The dominant ericoid shrubs can be out-competed by vigorous perennial grasses with increased atmospheric nitrogen deposition, although interactions with climate and management practices may either counteract or enhance this process. Grazing or periodic burning promotes heath loss but site-specific combined treatments maintain species diversity and community structure. Climate change alone moderately affects plant diversity, community structure and ecosystem functions. Combined with other factors, climatic changes will condition heath development, mainly with regard to key aspects such as seed set and seedling establishment, rare species occurrence and nutrient cycling in the soil. It is essential to address the effects of not only individual factors, but their interactions, together with land-use history, on heathland development and conservation in order to predict habitat response to future scenarios. PMID:23223202
Heathlands confronting global change: drivers of biodiversity loss from past to future scenarios.

PubMed

Fagúndez, Jaime

2013-02-01

Heathlands are dynamic plant communities characterized by a high cover of sclerophyllous, ericoid shrubs that develop over nutrient-poor soils. Interest in the preservation of these habitats in Europe has increased over the last decades, but over this time there has been a general decline in habitat quality, affecting community structure, ecosystem functions and biodiversity. Negative drivers that trigger these changes include land-use changes (i.e. habitat destruction and fragmentation), pollution, climate change, natural succession and human management, as well as the presence of invasive exotic species. Based on recent scientific literature, the effect of each of these potential drivers on a wide set of factors, including physiological traits, species richness and diversity, community structure, ecosystem functions and soil conditions, is reviewed. The effects of these drivers are generally understood, but the direction and magnitude of factor interactions, whenever studied, have shown high variability. Habitat loss and fragmentation affect sensitive species and ecosystem functions. The nature of the surrounding area will condition the quality of the heathland remnants by, for example, propagule pressure from invasive species. The dominant ericoid shrubs can be out-competed by vigorous perennial grasses with increased atmospheric nitrogen deposition, although interactions with climate and management practices may either counteract or enhance this process. Grazing or periodic burning promotes heath loss but site-specific combined treatments maintain species diversity and community structure. Climate change alone moderately affects plant diversity, community structure and ecosystem functions. Combined with other factors, climatic changes will condition heath development, mainly with regard to key aspects such as seed set and seedling establishment, rare species occurrence and nutrient cycling in the soil. It is essential to address the effects of not only individual factors, but their interactions, together with land-use history, on heathland development and conservation in order to predict habitat response to future scenarios.
Stand structural diversity rather than species diversity enhances aboveground carbon storage in secondary subtropical forests in Eastern China

NASA Astrophysics Data System (ADS)

Ali, Arshad; Yan, En-Rong; Chen, Han Y. H.; Chang, Scott X.; Zhao, Yan-Tao; Yang, Xiao-Dong; Xu, Ming-Shan

2016-08-01

Stand structural diversity, typically characterized by variances in tree diameter at breast height (DBH) and total height, plays a critical role in influencing aboveground carbon (C) storage. However, few studies have considered the multivariate relationships of aboveground C storage with stand age, stand structural diversity, and species diversity in natural forests. In this study, aboveground C storage, stand age, tree species, DBH and height diversity indices, were determined across 80 subtropical forest plots in Eastern China. We employed structural equation modelling (SEM) to test for the direct and indirect effects of stand structural diversity, species diversity, and stand age on aboveground C storage. The three final SEMs with different directions for the path between species diversity and stand structural diversity had a similar goodness of fit to the data. They accounted for 82 % of the variation in aboveground C storage, 55-59 % of the variation in stand structural diversity, and 0.1 to 9 % of the variation in species diversity. Stand age demonstrated strong positive total effects, including a positive direct effect (β = 0.41), and a positive indirect effect via stand structural diversity (β = 0.41) on aboveground C storage. Stand structural diversity had a positive direct effect on aboveground C storage (β = 0.56), whereas there was little total effect of species diversity as it had a negative direct association with, but had a positive indirect effect, via stand structural diversity, on aboveground C storage. The negligible total effect of species diversity on aboveground C storage in the forests under study may have been attributable to competitive exclusion with high aboveground biomass, or a historical logging preference for productive species. Our analyses suggested that stand structural diversity was a major determinant for variations in aboveground C storage in the secondary subtropical forests in Eastern China. Hence, maintaining tree DBH and height diversity through silvicultural operations might constitute an effective approach for enhancing aboveground C storage in these forests.
Structural and conformational determinants of macrocycle cell permeability.

PubMed

Over, Björn; Matsson, Pär; Tyrchan, Christian; Artursson, Per; Doak, Bradley C; Foley, Michael A; Hilgendorf, Constanze; Johnston, Stephen E; Lee, Maurice D; Lewis, Richard J; McCarren, Patrick; Muncipinto, Giovanni; Norinder, Ulf; Perry, Matthew W D; Duvall, Jeremy R; Kihlberg, Jan

2016-12-01

Macrocycles are of increasing interest as chemical probes and drugs for intractable targets like protein-protein interactions, but the determinants of their cell permeability and oral absorption are poorly understood. To enable rational design of cell-permeable macrocycles, we generated an extensive data set under consistent experimental conditions for more than 200 non-peptidic, de novo-designed macrocycles from the Broad Institute's diversity-oriented screening collection. This revealed how specific functional groups, substituents and molecular properties impact cell permeability. Analysis of energy-minimized structures for stereo- and regioisomeric sets provided fundamental insight into how dynamic, intramolecular interactions in the 3D conformations of macrocycles may be linked to physicochemical properties and permeability. Combined use of quantitative structure-permeability modeling and the procedure for conformational analysis now, for the first time, provides chemists with a rational approach to design cell-permeable non-peptidic macrocycles with potential for oral absorption.

Prediction of new bioactive molecules using a Bayesian belief network.

PubMed

Abdo, Ammar; Leclère, Valérie; Jacques, Philippe; Salim, Naomie; Pupin, Maude

2014-01-27

Natural products and synthetic compounds are a valuable source of new small molecules leading to novel drugs to cure diseases. However identifying new biologically active small molecules is still a challenge. In this paper, we introduce a new activity prediction approach using Bayesian belief network for classification (BBNC). The roots of the network are the fragments composing a compound. The leaves are, on one side, the activities to predict and, on another side, the unknown compound. The activities are represented by sets of known compounds, and sets of inactive compounds are also used. We calculated a similarity between an unknown compound and each activity class. The more similar activity is assigned to the unknown compound. We applied this new approach on eight well-known data sets extracted from the literature and compared its performance to three classical machine learning algorithms. Experiments showed that BBNC provides interesting prediction rates (from 79% accuracy for high diverse data sets to 99% for low diverse ones) with a short time calculation. Experiments also showed that BBNC is particularly effective for homogeneous data sets but has been found to perform less well with structurally heterogeneous sets. However, it is important to stress that we believe that using several approaches whenever possible for activity prediction can often give a broader understanding of the data than using only one approach alone. Thus, BBNC is a useful addition to the computational chemist's toolbox.
Hybrid detection of lung nodules on CT scan images

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

Lu, Lin; Tan, Yongqiang; Schwartz, Lawrence H.

Purpose: The diversity of lung nodules poses difficulty for the current computer-aided diagnostic (CAD) schemes for lung nodule detection on computed tomography (CT) scan images, especially in large-scale CT screening studies. We proposed a novel CAD scheme based on a hybrid method to address the challenges of detection in diverse lung nodules. Methods: The hybrid method proposed in this paper integrates several existing and widely used algorithms in the field of nodule detection, including morphological operation, dot-enhancement based on Hessian matrix, fuzzy connectedness segmentation, local density maximum algorithm, geodesic distance map, and regression tree classification. All of the adopted algorithmsmore » were organized into tree structures with multi-nodes. Each node in the tree structure aimed to deal with one type of lung nodule. Results: The method has been evaluated on 294 CT scans from the Lung Image Database Consortium (LIDC) dataset. The CT scans were randomly divided into two independent subsets: a training set (196 scans) and a test set (98 scans). In total, the 294 CT scans contained 631 lung nodules, which were annotated by at least two radiologists participating in the LIDC project. The sensitivity and false positive per scan for the training set were 87% and 2.61%. The sensitivity and false positive per scan for the testing set were 85.2% and 3.13%. Conclusions: The proposed hybrid method yielded high performance on the evaluation dataset and exhibits advantages over existing CAD schemes. We believe that the present method would be useful for a wide variety of CT imaging protocols used in both routine diagnosis and screening studies.« less
Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations.

PubMed

Zehdi-Azouzi, Salwa; Cherif, Emira; Moussouni, Souhila; Gros-Balthazard, Muriel; Abbas Naqvi, Summar; Ludeña, Bertha; Castillo, Karina; Chabrillange, Nathalie; Bouguedoura, Nadia; Bennaceur, Malika; Si-Dehbi, Farida; Abdoulkader, Sabira; Daher, Abdourahman; Terral, Jean-Frederic; Santoni, Sylvain; Ballardini, Marco; Mercuri, Antonio; Ben Salah, Mohamed; Kadri, Karim; Othmani, Ahmed; Littardi, Claudio; Salhi-Hannachi, Amel; Pintaud, Jean-Christophe; Aberlenc-Bertossi, Frédérique

2015-07-01

Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species. Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite. Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species. This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Development and characterization of a new set of genomic microsatellite markers in rice bean (Vigna umbellata (Thunb.) Ohwi and Ohashi) and their utilization in genetic diversity analysis of collections from North East India.

PubMed

Iangrai, Banshanlang; Pattanayak, Arunava; Khongwir, D Evanoreen Ann; Pale, Gratify; Gatphoh, Emica Mary; Das, Alpana; Chrungoo, Nikhil Kumar

2017-01-01

Rice bean [Vigna umbellate (Thumb.) Ohwi and Ohashi] is an underutilized crop believed to be domesticated in the Myanmar-Thailand region of Asia. In India, rice bean is mainly cultivated in the North-Eastern Hills, which is a hotspot for biological diversity. A 5' anchored PCR was used to develop microsatellite markers in rice bean. Twenty-eight specific primer pairs were designed and employed to characterize sixty five ricebean accessions collected from North East India. A total of 179 alleles were amplified with an average of 6.393 alleles per locus. The gene diversity was high (mean 0.534) in the accessions collected from Darjeeling, Nagaland and Manipur, which are bordering areas with East Nepal and Myanmar, respectively. Exceptionally high outcrossing rate was observed in the entire population. Population structure analysis identified three distinct clusters in which accessions collected from areas bordering Myanmar and East Nepal grouped separately. Using a combination of STRUCTURE and Principal Coordinate Analysis, relative affinity of the intermediate accessions could be established. However, differences in allelic counts among populations were non-significant. The results showed that there is a high level of genetic diversity within the accessions, with high outcrossing rate.
Microsatellite analysis of Saccharomyces uvarum diversity.

PubMed

Masneuf-Pomarede, Isabelle; Salin, Franck; Börlin, Marine; Coton, Emmanuel; Coton, Monika; Jeune, Christine Le; Legras, Jean-Luc

2016-03-01

Considered as a sister species of Saccharomyces cerevisiae, S. uvarum is, to a lesser extent, an interesting species for fundamental and applied research studies. Despite its potential interest as a new gene pool for fermenting agents, the intraspecific molecular genetic diversity of this species is still poorly investigated. In this study, we report the use of nine microsatellite markers to describe S. uvarum genetic diversity and population structure among 108 isolates from various geographical and substrate origins (wine, cider and natural sources). Our combined microsatellite markers set allowed differentiating 89 genotypes. In contrast to S. cerevisiae genetic diversity, wild and human origin isolates were intertwined. A total of 75% of strains were proven to be homozygotes and estimated heterozygosity suggests a selfing rate above 0.95 for the different population tested here. From this point of view, the S. uvarum life cycle appears to be more closely related to S. paradoxus or S. cerevisiae of natural resources than S. cerevisiae wine isolates. Population structure could not be correlated to distinct geographic or technological origins, suggesting lower differentiation that may result from a large exchange between human and natural populations mediated by insects or human activities. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Evaluation of Genetic Diversity, Population Structure, and Relationship Between Legendary Vechur Cattle and Crossbred Cattle of Kerala State, India.

PubMed

Radhika, G; Aravindakshan, T V; Jinty, S; Ramya, K

2018-01-02

The legendary Vechur cattle of Kerala, described as a very short breed, and the crossbred (CB) Sunandini cattle population exhibited great phenotypic variation; hence, the present study attempted to analyze the genetic diversity existing between them. A set of 14 polymorphic microsatellites were chosen from FAO-ISAG panel and amplified from genomic DNA isolated from blood samples of 30 Vechur and 64 unrelated crossbred cattle, using fluorescent labeled primers. Both populations revealed high genetic diversity as evidenced from high observed number of alleles, Polymorphic Information Content and expected heterozygosity. Observed heterozygosity was lesser (0.699) than expected (0.752) in Vechur population which was further supported by positive F IS value of 0.1149, indicating slight level of inbreeding in Vechur population. Overall, F ST value was 0.065, which means genetic differentiation between crossbred and Vechur population was 6.5%, indicating that the crossbred cattle must have differentiated into a definite population that is different from the indigenous Vechur cows. Structure analysis indicated that the two populations showed distinct differences, with two underlying clusters. The present study supports the separation between Taurine and Zebu cattle and throws light onto the genetic diversity and relationship between native Vechur and crossbred cattle populations in Kerala state.
Geothermal activity helps life survive glacial cycles

PubMed Central

Fraser, Ceridwen I.; Terauds, Aleks; Smellie, John; Convey, Peter; Chown, Steven L.

2014-01-01

Climate change has played a critical role in the evolution and structure of Earth’s biodiversity. Geothermal activity, which can maintain ice-free terrain in glaciated regions, provides a tantalizing solution to the question of how diverse life can survive glaciations. No comprehensive assessment of this “geothermal glacial refugia” hypothesis has yet been undertaken, but Antarctica provides a unique setting for doing so. The continent has experienced repeated glaciations that most models indicate blanketed the continent in ice, yet many Antarctic species appear to have evolved in almost total isolation for millions of years, and hence must have persisted in situ throughout. How could terrestrial species have survived extreme glaciation events on the continent? Under a hypothesis of geothermal glacial refugia and subsequent recolonization of nongeothermal regions, we would expect to find greater contemporary diversity close to geothermal sites than in nongeothermal regions, and significant nestedness by distance of this diversity. We used spatial modeling approaches and the most comprehensive, validated terrestrial biodiversity dataset yet created for Antarctica to assess spatial patterns of diversity on the continent. Models clearly support our hypothesis, indicating that geothermally active regions have played a key role in structuring biodiversity patterns in Antarctica. These results provide critical insights into the evolutionary importance of geothermal refugia and the history of Antarctic species. PMID:24616489
Detecting Below-Ground Processes, Diversity, and Ecosystem Function in a Savanna Ecosystem Using Spectroscopy Across Different Vegetation Layers

NASA Astrophysics Data System (ADS)

Cavender-Bares, J.; Schweiger, A. K.; Madritch, M. D.; Gamon, J. A.; Hobbie, S. E.; Montgomery, R.; Townsend, P. A.

2017-12-01

Above-and below-ground plant traits are important for substrate input to the rhizosphere. The substrate composition of the rhizosphere, in turn, affects the diversity of soil organisms, influences soil biochemistry, and water content, and resource availability for plant growth. This has substantial consequences for ecosystem functions, such as above-ground productivity and stability. Above-ground plant chemical and structural traits can be linked to the characteristics of other plant organs, including roots. Airborne imaging spectroscopy has been successfully used to model and predict chemical and structural traits of the above-ground vegetation. However, remotely sensed images capture, almost exclusively, signals from the top of the canopy, providing limited direct information about understory vegetation. Here, we use a data set collected in a savanna ecosystem consisting of spectral measurements gathered at the leaf, the whole plant, and vegetation canopy level to test for hypothesized linkages between above- and below-ground processes that influence root biomass, soil biochemistry, and the diversity of the soil community. In this environment, consisting of herbaceous vegetation intermixed with shrubs and trees growing at variable densities, we investigate the contribution of different vegetation strata to soil characteristics and test the ability of imaging spectroscopy to detect these in plant communities with contrasting vertical structure.
Network modules and hubs in plant-root fungal biomes

PubMed Central

Toju, Hirokazu; Yamamoto, Satoshi; Tanabe, Akifumi S.; Hayakawa, Takashi; Ishii, Hiroshi S.

2016-01-01

Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/survival in both natural and agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one of the major challenges in ecology and plant science. We here report that diverse root-associated fungi can form highly compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities can be partitioned into semi-discrete types even within a single host plant population. Illumina sequencing of root-associated fungi in a monodominant south beech forest revealed that the network representing symbiont–symbiont co-occurrence patterns was compartmentalized into clear modules, which consisted of diverse functional groups of mycorrhizal and endophytic fungi. Consequently, terminal roots of the plant were colonized by either of the two largest fungal species sets (represented by Oidiodendron or Cenococcum). Thus, species-rich root microbiomes can have alternative community structures, as recently shown in the relationships between human gut microbiome type (i.e. ‘enterotype’) and host individual health. This study also shows an analytical framework for pinpointing network hubs in symbiont–symbiont networks, leading to the working hypothesis that a small number of microbial species organize the overall root–microbiome dynamics. PMID:26962029
Does Staff Diversity Imply Openness to Diversity?

ERIC Educational Resources Information Center

Lauring, Jakob; Selmer, Jan

2013-01-01

Purpose: Post-secondary educational organizations are currently some of the most diverse settings to be found. However, few educational studies have dealt with staff diversity and hardly any has looked outside the USA. The purpose of this paper is to present a study of members of international university departments in Denmark. The authors set out…
DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS ...

EPA Pesticide Factsheets

DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction ModelsAnn M. RichardUS Environmental Protection Agency, Research Triangle Park, NC, USADistributed: Decentralized set of standardized, field-delimited databases, each separatelyauthored and maintained, that are able to accommodate diverse toxicity data content;Structure-Searchable: Standard format (SDF) structure-data files that can be readily imported into available chemical relational databases and structure-searched;Tox: Toxicity data as it exists in widely disparate forms in current public databases, spanning diverse toxicity endpoints, test systems, levels of biological content, degrees of summarization, and information content.INTRODUCTIONThe economic and social pressures to reduce the need for animal testing and to better anticipate the potential for human and eco-toxicity of environmental, industrial, or pharmaceutical chemicals are as pressing today as at any time prior. However, the goal of predicting chemical toxicity in its many manifestations, the `T' in 'ADMET' (adsorption, distribution, metabolism, elimination, toxicity), remains one of the most difficult and largely unmet challenges in a chemical screening paradigm [1]. It is widely acknowledged that the single greatest hurdle to improving structure-activity relationship (SAR) toxicity prediction capabilities, in both the pharmaceutical and environmental regulation arenas, is the lack of suffici
Structural Analysis of the Tobramycin and Gentamicin Clinical Resistome Reveals Limitations for Next-generation Aminoglycoside Design.

PubMed

Bassenden, Angelia V; Rodionov, Dmitry; Shi, Kun; Berghuis, Albert M

2016-05-20

Widespread use and misuse of antibiotics has allowed for the selection of resistant bacteria capable of avoiding the effects of antibiotics. The primary mechanism for resistance to aminoglycosides, a broad-spectrum class of antibiotics, is through covalent enzymatic modification of the drug, waning their bactericidal effect. Tobramycin and gentamicin are two medically important aminoglycosides targeted by several different resistance factors, including aminoglycoside 2″-nucleotidyltransferase [ANT(2″)], the primary cause of aminoglycoside resistance in North America. We describe here two crystal structures of ANT(2″), each in complex with AMPCPP, Mn(2+), and either tobramycin or gentamicin. Together these structures outline ANT(2″)'s specificity for clinically used substrates. Importantly, these structures complete our structural knowledge for the set of enzymes that most frequently confer clinically observed resistance to tobramycin and gentamicin. Comparison of tobramycin and gentamicin binding to enzymes in this resistome, as well as to the intended target, the bacterial ribosome, reveals surprising diversity in observed drug-target interactions. Analysis of the diverse binding modes informs that there are limited opportunities for developing aminoglycoside analogs capable of evading resistance.
An eco-compatible strategy for the diversity-oriented synthesis of macrocycles exploiting carbohydrate-derived building blocks.

PubMed

Maurya, Sushil K; Rana, Rohit

2017-01-01

An efficient, eco-compatible diversity-oriented synthesis (DOS) approach for the generation of library of sugar embedded macrocyclic compounds with various ring size containing 1,2,3-triazole has been developed. This concise strategy involves the iterative use of readily available sugar-derived alkyne/azide-alkene building blocks coupled through copper catalyzed azide-alkyne cycloaddition (CuAAC) reaction followed by pairing of the linear cyclo-adduct using greener reaction conditions. The eco-compatibility, mild reaction conditions, greener solvents, easy purification and avoidance of hazards and toxic solvents are advantages of this protocol to access this important structural class. The diversity of the macrocycles synthesized (in total we have synthesized 13 macrocycles) using a set of standard reaction protocols demonstrate the potential of the new eco-compatible approach for the macrocyclic library generation.
Use of the Monte Carlo Method for OECD Principles-Guided QSAR Modeling of SIRT1 Inhibitors.

PubMed

Kumar, Ashwani; Chauhan, Shilpi

2017-01-01

SIRT1 inhibitors offer therapeutic potential for the treatment of a number of diseases including cancer and human immunodeficiency virus infection. A diverse series of 45 compounds with reported SIRT1 inhibitory activity has been employed for the development of quantitative structure-activity relationship (QSAR) models using the Monte Carlo optimization method. This method makes use of simplified molecular input line entry system notation of the molecular structure. The QSAR models were built up according to OECD principles. Three subsets of three splits were examined and validated by respective external sets. All the three described models have good statistical quality. The best model has the following statistical characteristics: R 2 = 0.8350, Q 2 test = 0.7491 for the test set and R 2 = 0.9655, Q 2 ext = 0.9261 for the validation set. In the mechanistic interpretation, structural attributes responsible for the endpoint increase and decrease are defined. Further, the design of some prospective SIRT1 inhibitors is also presented on the basis of these structural attributes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
A new fun and robust version of an fMRI localizer for the frontotemporal language system.

PubMed

Scott, Terri L; Gallée, Jeanne; Fedorenko, Evelina

2017-07-01

A set of brain regions in the frontal, temporal, and parietal lobes supports high-level linguistic processing. These regions can be reliably identified in individual subjects using fMRI, by contrasting neural responses to meaningful and structured language stimuli vs. stimuli matched for low-level properties but lacking meaning and/or structure. We here present a novel version of a language 'localizer,' which should be suitable for diverse populations including children and/or clinical populations who may have difficulty with reading or cognitively demanding tasks. In particular, we contrast responses to auditorily presented excerpts from engaging interviews or stories, and acoustically degraded versions of these materials. This language localizer is appealing because it uses (a) naturalistic and engaging linguistic materials, (b) auditory presentation, (c) a passive listening task, and can be easily adapted to new stimulus materials enabling comparisons of language activation in children and speakers of diverse languages.
A genomic approach for isolating chloroplast microsatellite markers for Pachyptera kerere (Bignoniaceae)1

PubMed Central

Francisco, Jessica N. C.; Nazareno, Alison G.; Lohmann, Lúcia G.

2016-01-01

Premise of the study: In this study, we developed chloroplast microsatellite markers (cpSSRs) for Pachyptera kerere (Bignoniaceae) to investigate the population structure and genetic diversity of this species. Methods and Results: We used Illumina HiSeq data to reconstruct the chloroplast genome of P. kerere by a combination of de novo and reference-guided assembly. We then used the chloroplast genome to develop a set of cpSSRs from intergenic regions. Overall, 24 primer pairs were designed, 21 of which amplified successfully and were polymorphic, presenting three to nine alleles per locus. The unbiased haploid diversity per locus varied from 0.207 (Pac28) to 0.817 (Pac04). All but one locus amplified for all other taxa of Pachyptera. Conclusions: The markers reported here will serve as a basis for studies to assess the genetic structure and phylogeographic history of Pachyptera. PMID:27672522
Development of ten microsatellite loci in the invasive giant African land snail, Achatina (=Lissachatina) fulica Bowdich, 1822

USGS Publications Warehouse

Morrison, Cheryl L.; Springmann, Marcus J.; Iwanowicz, Deborah D.; Wade, Christopher M.

2015-01-01

A suite of tetra-nucleotide microsatellite loci were developed for the invasive giant African land snail, Achatina (=Lissachatina) fulica Bowdich, 1822, from Ion Torrent next-generation sequencing data. Ten of the 96 primer sets tested amplified consistently in 30 snails from Miami, Florida, plus 12 individuals representative of their native East Africa, Indian and Pacific Ocean regions. The loci displayed moderate levels of allelic diversity (average 5.6 alleles/locus) and heterozygosity (average 42 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and detect phylogeographic structuring among regional samples. The invasive A. fulica can cause extensive damage to important food crops and natural resources, including native flora and fauna. The loci characterized here will be useful for determining the origins and tracking the spread of invasions, detecting fine-scale spatial structuring and estimating demographic parameters.
The poly(C)-binding proteins: a multiplicity of functions and a search for mechanisms.

PubMed Central

Makeyev, Aleksandr V; Liebhaber, Stephen A

2002-01-01

The poly(C) binding proteins (PCBPs) are encoded at five dispersed loci in the mouse and human genomes. These proteins, which can be divided into two groups, hnRNPs K/J and the alphaCPs (alphaCP1-4), are linked by a common evolutionary history, a shared triple KH domain configuration, and by their poly(C) binding specificity. Given these conserved characteristics it is remarkable to find a substantial diversity in PCBP functions. The roles of these proteins in mRNA stabilization, translational activation, and translational silencing suggest a complex and diverse set of post-transcriptional control pathways. Their additional putative functions in transcriptional control and as structural components of important DNA-protein complexes further support their remarkable structural and functional versatility. Clearly the identification of additional binding targets and delineation of corresponding control mechanisms and effector pathways will establish highly informative models for further exploration. PMID:12003487
The poly(C)-binding proteins: a multiplicity of functions and a search for mechanisms.

PubMed

Makeyev, Aleksandr V; Liebhaber, Stephen A

2002-03-01

The poly(C) binding proteins (PCBPs) are encoded at five dispersed loci in the mouse and human genomes. These proteins, which can be divided into two groups, hnRNPs K/J and the alphaCPs (alphaCP1-4), are linked by a common evolutionary history, a shared triple KH domain configuration, and by their poly(C) binding specificity. Given these conserved characteristics it is remarkable to find a substantial diversity in PCBP functions. The roles of these proteins in mRNA stabilization, translational activation, and translational silencing suggest a complex and diverse set of post-transcriptional control pathways. Their additional putative functions in transcriptional control and as structural components of important DNA-protein complexes further support their remarkable structural and functional versatility. Clearly the identification of additional binding targets and delineation of corresponding control mechanisms and effector pathways will establish highly informative models for further exploration.
Longevity extension by phytochemicals.

PubMed

Leonov, Anna; Arlia-Ciommo, Anthony; Piano, Amanda; Svistkova, Veronika; Lutchman, Vicky; Medkour, Younes; Titorenko, Vladimir I

2015-04-13

Phytochemicals are structurally diverse secondary metabolites synthesized by plants and also by non-pathogenic endophytic microorganisms living within plants. Phytochemicals help plants to survive environmental stresses, protect plants from microbial infections and environmental pollutants, provide them with a defense from herbivorous organisms and attract natural predators of such organisms, as well as lure pollinators and other symbiotes of these plants. In addition, many phytochemicals can extend longevity in heterotrophic organisms across phyla via evolutionarily conserved mechanisms. In this review, we discuss such mechanisms. We outline how structurally diverse phytochemicals modulate a complex network of signaling pathways that orchestrate a distinct set of longevity-defining cellular processes. This review also reflects on how the release of phytochemicals by plants into a natural ecosystem may create selective forces that drive the evolution of longevity regulation mechanisms in heterotrophic organisms inhabiting this ecosystem. We outline the most important unanswered questions and directions for future research in this vibrant and rapidly evolving field.

Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs.

PubMed

Laucou, Valérie; Launay, Amandine; Bacilieri, Roberto; Lacombe, Thierry; Adam-Blondon, Anne-Françoise; Bérard, Aurélie; Chauveau, Aurélie; de Andrés, Maria Teresa; Hausmann, Ludger; Ibáñez, Javier; Le Paslier, Marie-Christine; Maghradze, David; Martinez-Zapater, José Miguel; Maul, Erika; Ponnaiah, Maharajah; Töpfer, Reinhard; Péros, Jean-Pierre; Boursiquot, Jean-Michel

2018-01-01

Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26-0.32) and linkage disequilibrium (LD, 28.8-58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine.
Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs

PubMed Central

Launay, Amandine; Bacilieri, Roberto; Lacombe, Thierry; Adam-Blondon, Anne-Françoise; Bérard, Aurélie; Chauveau, Aurélie; de Andrés, Maria Teresa; Maghradze, David; Maul, Erika; Ponnaiah, Maharajah; Töpfer, Reinhard; Péros, Jean-Pierre; Boursiquot, Jean-Michel

2018-01-01

Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26–0.32) and linkage disequilibrium (LD, 28.8–58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine. PMID:29420602
Why evolutionary biologists should get seriously involved in ecological monitoring and applied biodiversity assessment programs

PubMed Central

Brodersen, Jakob; Seehausen, Ole

2014-01-01

While ecological monitoring and biodiversity assessment programs are widely implemented and relatively well developed to survey and monitor the structure and dynamics of populations and communities in many ecosystems, quantitative assessment and monitoring of genetic and phenotypic diversity that is important to understand evolutionary dynamics is only rarely integrated. As a consequence, monitoring programs often fail to detect changes in these key components of biodiversity until after major loss of diversity has occurred. The extensive efforts in ecological monitoring have generated large data sets of unique value to macro-scale and long-term ecological research, but the insights gained from such data sets could be multiplied by the inclusion of evolutionary biological approaches. We argue that the lack of process-based evolutionary thinking in ecological monitoring means a significant loss of opportunity for research and conservation. Assessment of genetic and phenotypic variation within and between species needs to be fully integrated to safeguard biodiversity and the ecological and evolutionary dynamics in natural ecosystems. We illustrate our case with examples from fishes and conclude with examples of ongoing monitoring programs and provide suggestions on how to improve future quantitative diversity surveys. PMID:25553061
QSAR modeling for predicting mutagenic toxicity of diverse chemicals for regulatory purposes.

PubMed

Basant, Nikita; Gupta, Shikha

2017-06-01

The safety assessment process of chemicals requires information on their mutagenic potential. The experimental determination of mutagenicity of a large number of chemicals is tedious and time and cost intensive, thus compelling for alternative methods. We have established local and global QSAR models for discriminating low and high mutagenic compounds and predicting their mutagenic activity in a quantitative manner in Salmonella typhimurium (TA) bacterial strains (TA98 and TA100). The decision treeboost (DTB)-based classification QSAR models discriminated among two categories with accuracies of >96% and the regression QSAR models precisely predicted the mutagenic activity of diverse chemicals yielding high correlations (R 2 ) between the experimental and model-predicted values in the respective training (>0.96) and test (>0.94) sets. The test set root mean squared error (RMSE) and mean absolute error (MAE) values emphasized the usefulness of the developed models for predicting new compounds. Relevant structural features of diverse chemicals that were responsible and influence the mutagenic activity were identified. The applicability domains of the developed models were defined. The developed models can be used as tools for screening new chemicals for their mutagenicity assessment for regulatory purpose.
Engineering the shape and structure of materials by fractal cut.

PubMed

Cho, Yigil; Shin, Joong-Ho; Costa, Avelino; Kim, Tae Ann; Kunin, Valentin; Li, Ju; Lee, Su Yeon; Yang, Shu; Han, Heung Nam; Choi, In-Suk; Srolovitz, David J

2014-12-09

In this paper we discuss the transformation of a sheet of material into a wide range of desired shapes and patterns by introducing a set of simple cuts in a multilevel hierarchy with different motifs. Each choice of hierarchical cut motif and cut level allows the material to expand into a unique structure with a unique set of properties. We can reverse-engineer the desired expanded geometries to find the requisite cut pattern to produce it without changing the physical properties of the initial material. The concept was experimentally realized and applied to create an electrode that expands to >800% the original area with only very minor stretching of the underlying material. The generality of our approach greatly expands the design space for materials so that they can be tuned for diverse applications.
Selection of appropriate training and validation set chemicals for modelling dermal permeability by U-optimal design.

PubMed

Xu, G; Hughes-Oliver, J M; Brooks, J D; Yeatts, J L; Baynes, R E

2013-01-01

Quantitative structure-activity relationship (QSAR) models are being used increasingly in skin permeation studies. The main idea of QSAR modelling is to quantify the relationship between biological activities and chemical properties, and thus to predict the activity of chemical solutes. As a key step, the selection of a representative and structurally diverse training set is critical to the prediction power of a QSAR model. Early QSAR models selected training sets in a subjective way and solutes in the training set were relatively homogenous. More recently, statistical methods such as D-optimal design or space-filling design have been applied but such methods are not always ideal. This paper describes a comprehensive procedure to select training sets from a large candidate set of 4534 solutes. A newly proposed 'Baynes' rule', which is a modification of Lipinski's 'rule of five', was used to screen out solutes that were not qualified for the study. U-optimality was used as the selection criterion. A principal component analysis showed that the selected training set was representative of the chemical space. Gas chromatograph amenability was verified. A model built using the training set was shown to have greater predictive power than a model built using a previous dataset [1].
"Not Everybody Walks around and Thinks 'That's an Example of Othering or Stigmatisation'": Identity, Pedagogic Rights and the Acquisition of Undergraduate Sociology-Based Social Science Knowledge

ERIC Educational Resources Information Center

McLean, Monica; Abbas, Andrea; Ashwin, Paul

2015-01-01

This article places itself in conversation with literature about how the experience and outcomes of university education are structured by intersections between social class, ethnicity, gender, age and type of university attended. It addresses undergraduate students' acquisition of sociological knowledge in four diverse university settings. Basil…
The Diversity Present in 5140 Human Mitochondrial Genomes

PubMed Central

Pereira, Luísa; Freitas, Fernando; Fernandes, Verónica; Pereira, Joana B.; Costa, Marta D.; Costa, Stephanie; Máximo, Valdemar; Macaulay, Vincent; Rocha, Ricardo; Samuels, David C.

2009-01-01

We analyzed the current status (as of the end of August 2008) of human mitochondrial genomes deposited in GenBank, amounting to 5140 complete or coding-region sequences, in order to present an overall picture of the diversity present in the mitochondrial DNA of the global human population. To perform this task, we developed mtDNA-GeneSyn, a computer tool that identifies and exhaustedly classifies the diversity present in large genetic data sets. The diversity observed in the 5140 human mitochondrial genomes was compared with all possible transitions and transversions from the standard human mitochondrial reference genome. This comparison showed that tRNA and rRNA secondary structures have a large effect in limiting the diversity of the human mitochondrial sequences, whereas for the protein-coding genes there is a bias toward less variation at the second codon positions. The analysis of the observed amino acid variations showed a tolerance of variations that convert between the amino acids V, I, A, M, and T. This defines a group of amino acids with similar chemical properties that can interconvert by a single transition. PMID:19426953
De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks.

PubMed

Schneider, G; Lee, M L; Stahl, M; Schneider, P

2000-07-01

An evolutionary algorithm was developed for fragment-based de novo design of molecules (TOPAS, TOPology-Assigning System). This stochastic method aims at generating a novel molecular structure mimicking a template structure. A set of approximately 25,000 fragment structures serves as the building block supply, which were obtained by a straightforward fragmentation procedure applied to 36,000 known drugs. Eleven reaction schemes were implemented for both fragmentation and building block assembly. This combination of drug-derived building blocks and a restricted set of reaction schemes proved to be a key for the automatic development of novel, synthetically tractable structures. In a cyclic optimization process, molecular architectures were generated from a parent structure by virtual synthesis, and the best structure of a generation was selected as the parent for the subsequent TOPAS cycle. Similarity measures were used to define 'fitness', based on 2D-structural similarity or topological pharmacophore distance between the template molecule and the variants. The concept of varying library 'diversity' during a design process was consequently implemented by using adaptive variant distributions. The efficiency of the design algorithm was demonstrated for the de novo construction of potential thrombin inhibitors mimicking peptide and non-peptide template structures.
Diversity of Bats in Contrasting Habitats of Hulu Terengganu Dipterocarp Forest and Setiu Wetland BRIS Forest with a Note on Preliminary Study of Vertical Stratification of Pteropodid Bats

PubMed Central

Pounsin, Grace; Wahab, Nur Syahirah; Roslan, Azuan; Zahidin, Muhamad Aidil; Pesiu, Elizabeth; Tamrin, Nur Aida Md; Abdullah, M T

2018-01-01

A study of the bat diversity was conducted in Hulu Terengganu dipterocarp forest and Setiu Wetland Beach Ridges Interspersed with Swales (BRIS) forest in Terengganu, to study the species diversity, composition and stratification of fruit bats from the understorey to the forest canopy. Mist nets were set up at the understorey, sub-canopy and canopy layer while harp traps were set up at the understorey layer. We recorded 170 individuals from six families’ compromised 21 species from Hulu Terengganu dipterocarp forests and four species from Setiu Wetland BRIS forests throughout the sampling period. Megaerops ecaudatus and Cynopterus brachyotis were the most dominant species in Hulu Terengganu dipterocarp forest and Setiu Wetland BRIS forests. Our study also recorded two species with new distributional records for the east coast of Peninsular Malaysia, namely, Rhinolophus chiewkweeae and Chaerephon johorensis in Hulu Terengganu dipterocarp forests. Potential factors that might influence the results were in terms of the canopy covers, the structural complexity of canopy, food availability and spatial characteristics. This study was able to increase the knowledge on the species diversity and composition of bats in Hulu Terengganu dipterocarp forest and Setiu Wetland BRIS forest, thus, further aid in the effort of bat conservation in both areas. PMID:29644015
A practical implementation for a data dictionary in an environment of diverse data sets

USGS Publications Warehouse

Sprenger, Karla K.; Larsen, Dana M.

1993-01-01

The need for a data dictionary database at the U.S. Geological Survey's EROS Data Center (EDC) was reinforced with the Earth Observing System Data and Information System (EOSDIS) requirement for consistent field definitions of data sets residing at more than one archive center. The EDC requirement addresses the existence of multiple sets with identical field definitions using various naming conventions. The EDC is developing a data dictionary database to accomplish the following foals: to standardize field names for ease in software development; to facilitate querying and updating of the date; and to generate ad hoc reports. The structure of the EDC electronic data dictionary database supports different metadata systems as well as many different data sets. A series of reports is used to keep consistency among data sets and various metadata systems.
Multisector Health Policy Networks in 15 Large US Cities

PubMed Central

Leider, J. P.; Carothers, Bobbi J.; Castrucci, Brian C.; Hearne, Shelley

2016-01-01

Context: Local health departments (LHDs) have historically not prioritized policy development, although it is one of the 3 core areas they address. One strategy that may influence policy in LHD jurisdictions is the formation of partnerships across sectors to work together on local public health policy. Design: We used a network approach to examine LHD local health policy partnerships across 15 large cities from the Big Cities Health Coalition. Setting/Participants: We surveyed the health departments and their partners about their working relationships in 5 policy areas: core local funding, tobacco control, obesity and chronic disease, violence and injury prevention, and infant mortality. Outcome Measures: Drawing on prior literature linking network structures with performance, we examined network density, transitivity, centralization and centrality, member diversity, and assortativity of ties. Results: Networks included an average of 21.8 organizations. Nonprofits and government agencies made up the largest proportions of the networks, with 28.8% and 21.7% of network members, whereas for-profits and foundations made up the smallest proportions in all of the networks, with just 1.2% and 2.4% on average. Mean values of density, transitivity, diversity, assortativity, centralization, and centrality showed similarity across policy areas and most LHDs. The tobacco control and obesity/chronic disease networks were densest and most diverse, whereas the infant mortality policy networks were the most centralized and had the highest assortativity. Core local funding policy networks had lower scores than other policy area networks by most network measures. Conclusion: Urban LHDs partner with organizations from diverse sectors to conduct local public health policy work. Network structures are similar across policy areas jurisdictions. Obesity and chronic disease, tobacco control, and infant mortality networks had structures consistent with higher performing networks, whereas core local funding networks had structures consistent with lower performing networks. PMID:26910868
Fast 3D shape screening of large chemical databases through alignment-recycling

PubMed Central

Fontaine, Fabien; Bolton, Evan; Borodina, Yulia; Bryant, Stephen H

2007-01-01

Background Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes. Results Using a dataset of more than one million PubChem compounds of limited size (< 28 heavy atoms) and flexibility (< 6 rotatable bonds), we obtained a set of a few thousand diverse structures covering entirely the 3D shape space of the conformers of the dataset. Transformation matrices gathered from the overlays between these diverse structures and the 3D conformer dataset allowed us to drastically (100-fold) reduce the CPU time required for shape overlay. The alignment-recycling heuristic produces results consistent with de novo alignment calculation, with better than 80% hit list overlap on average. Conclusion Overlay-based 3D methods are computationally demanding when searching large databases. Alignment-recycling reduces the CPU time to perform shape similarity searches by breaking the alignment problem into three steps: selection of diverse shapes to describe the database shape-space; overlay of the database conformers to the diverse shapes; and non-optimized overlay of query and database conformers using common reference shapes. The precomputation, required by the first two steps, is a significant cost of the method; however, once performed, querying is two orders of magnitude faster. Extensions and variations of this methodology, for example, to handle more flexible and larger small-molecules are discussed. PMID:17880744
Toward automated biochemotype annotation for large compound libraries.

PubMed

Chen, Xian; Liang, Yizeng; Xu, Jun

2006-08-01

Combinatorial chemistry allows scientists to probe large synthetically accessible chemical space. However, identifying the sub-space which is selectively associated with an interested biological target, is crucial to drug discovery and life sciences. This paper describes a process to automatically annotate biochemotypes of compounds in a library and thus to identify bioactivity related chemotypes (biochemotypes) from a large library of compounds. The process consists of two steps: (1) predicting all possible bioactivities for each compound in a library, and (2) deriving possible biochemotypes based on predictions. The Prediction of Activity Spectra for Substances program (PASS) was used in the first step. In second step, structural similarity and scaffold-hopping technologies are employed. These technologies are used to derive biochemotypes from bioactivity predictions and the corresponding annotated biochemotypes from MDL Drug Data Report (MDDR) database. About a one million (982,889) commercially available compound library (CACL) has been tested using this process. This paper demonstrates the feasibility of automatically annotating biochemotypes for large libraries of compounds. Nevertheless, some issues need to be considered in order to improve the process. First, the prediction accuracy of PASS program has no significant correlation with the number of compounds in a training set. Larger training sets do not necessarily increase the maximal error of prediction (MEP), nor do they increase the hit structural diversity. Smaller training sets do not necessarily decrease MEP, nor do they decrease the hit structural diversity. Second, the success of systematic bioactivity prediction relies on modeling, training data, and the definition of bioactivities (biochemotype ontology). Unfortunately, the biochemotype ontology was not well developed in the PASS program. Consequently, "ill-defined" bioactivities can reduce the quality of predictions. This paper suggests the ways in which the systematic bioactivities prediction program should be improved.
Comparison of Thaumarchaeotal populations from four deep sea basins

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

Techtman, Stephen M.; Mahmoudi, Nagissa; Whitt, Kendall T.

The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. Wemore » demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. In conclusion, these findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.« less
Comparison of Thaumarchaeotal populations from four deep sea basins

DOE PAGES

Techtman, Stephen M.; Mahmoudi, Nagissa; Whitt, Kendall T.; ...

2017-10-03

The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. Wemore » demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. In conclusion, these findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.« less
Diversity-based reasoning in children.

PubMed

Heit, E; Hahn, U

2001-12-01

One of the hallmarks of inductive reasoning by adults is the diversity effect, namely that people draw stronger inferences from a diverse set of evidence than from a more homogenous set of evidence. However, past developmental work has not found consistent diversity effects with children age 9 and younger. We report robust sensitivity to diversity in children as young as 5, using everyday stimuli such as pictures of objects with people. Experiment 1 showed the basic diversity effect in 5- to 9-year-olds. Experiment 2 showed that, like adults, children restrict their use of diversity information when making inferences about remote categories. Experiment 3 used other stimulus sets to overcome an alternate explanation in terms of sample size rather than diversity effects. Finally, Experiment 4 showed that children more readily draw on diversity when reasoning about objects and their relations with people than when reasoning about objects' internal, hidden properties, thus partially explaining the negative findings of previous work. Relations to cross-cultural work and models of induction are discussed. Copyright 2001 Academic Press.
Genetic diversity and population structure of an important wild berry crop

PubMed Central

Zoratti, Laura; Palmieri, Luisa; Jaakola, Laura; Häggman, Hely

2015-01-01

The success of plant breeding in the coming years will be associated with access to new sources of variation, which will include landraces and wild relatives of crop species. In order to access the reservoir of favourable alleles within wild germplasm, knowledge about the genetic diversity and the population structure of wild species is needed. Bilberry (Vaccinium myrtillus) is one of the most important wild crops growing in the forests of Northern European countries, noted for its nutritional properties and its beneficial effects on human health. Assessment of the genetic diversity of wild bilberry germplasm is needed for efforts such as in situ conservation, on-farm management and development of plant breeding programmes. However, to date, only a few local (small-scale) genetic studies of this species have been performed. We therefore conducted a study of genetic variability within 32 individual samples collected from different locations in Iceland, Norway, Sweden, Finland and Germany, and analysed genetic diversity among geographic groups. Four selected inter-simple sequence repeat primers allowed the amplification of 127 polymorphic loci which, based on analysis of variance, made it possible to identify 85 % of the genetic diversity within studied bilberry populations, being in agreement with the mixed-mating system of bilberry. Significant correlations were obtained between geographic and genetic distances for the entire set of samples. The analyses also highlighted the presence of a north–south genetic gradient, which is in accordance with recent findings on phenotypic traits of bilberry. PMID:26483325
Mapping uncharted territory in ice from zeolite networks to ice structures.

PubMed

Engel, Edgar A; Anelli, Andrea; Ceriotti, Michele; Pickard, Chris J; Needs, Richard J

2018-06-05

Ice is one of the most extensively studied condensed matter systems. Yet, both experimentally and theoretically several new phases have been discovered over the last years. Here we report a large-scale density-functional-theory study of the configuration space of water ice. We geometry optimise 74,963 ice structures, which are selected and constructed from over five million tetrahedral networks listed in the databases of Treacy, Deem, and the International Zeolite Association. All prior knowledge of ice is set aside and we introduce "generalised convex hulls" to identify configurations stabilised by appropriate thermodynamic constraints. We thereby rediscover all known phases (I-XVII, i, 0 and the quartz phase) except the metastable ice IV. Crucially, we also find promising candidates for ices XVIII through LI. Using the "sketch-map" dimensionality-reduction algorithm we construct an a priori, navigable map of configuration space, which reproduces similarity relations between structures and highlights the novel candidates. By relating the known phases to the tractably small, yet structurally diverse set of synthesisable candidate structures, we provide an excellent starting point for identifying formation pathways.
Signs of universality in the structure of culture

NASA Astrophysics Data System (ADS)

Băbeanu, Alexandru-Ionuţ; Talman, Leandros; Garlaschelli, Diego

2017-11-01

Understanding the dynamics of opinions, preferences and of culture as whole requires more use of empirical data than has been done so far. It is clear that an important role in driving this dynamics is played by social influence, which is the essential ingredient of many quantitative models. Such models require that all traits are fixed when specifying the "initial cultural state". Typically, this initial state is randomly generated, from a uniform distribution over the set of possible combinations of traits. However, recent work has shown that the outcome of social influence dynamics strongly depends on the nature of the initial state. If the latter is sampled from empirical data instead of being generated in a uniformly random way, a higher level of cultural diversity is found after long-term dynamics, for the same level of propensity towards collective behavior in the short-term. Moreover, if the initial state is randomized by shuffling the empirical traits among people, the level of long-term cultural diversity is in-between those obtained for the empirical and uniformly random counterparts. The current study repeats the analysis for multiple empirical data sets, showing that the results are remarkably similar, although the matrix of correlations between cultural variables clearly differs across data sets. This points towards robust structural properties inherent in empirical cultural states, possibly due to universal laws governing the dynamics of culture in the real world. The results also suggest that this dynamics might be characterized by criticality and involve mechanisms beyond social influence.

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level.

PubMed

Urrestarazu, Jorge; Denancé, Caroline; Ravon, Elisa; Guyader, Arnaud; Guisnel, Rémi; Feugey, Laurence; Poncet, Charles; Lateur, Marc; Houben, Patrick; Ordidge, Matthew; Fernandez-Fernandez, Felicidad; Evans, Kate M; Paprstein, Frantisek; Sedlak, Jiri; Nybom, Hilde; Garkava-Gustavsson, Larisa; Miranda, Carlos; Gassmann, Jennifer; Kellerhals, Markus; Suprun, Ivan; Pikunova, Anna V; Krasova, Nina G; Torutaeva, Elnura; Dondini, Luca; Tartarini, Stefano; Laurens, François; Durel, Charles-Eric

2016-06-08

The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.
Cultural factors of visitors' understanding of United States National Park Service natural resource messages

NASA Astrophysics Data System (ADS)

Hilton, Sunita Claire

Current trends in the demographic structure of the US population indicate increasing cultural diversity. Culturally-diverse populations have varying beliefs, views and understandings of natural resource use and management. This study concentrates on understanding how messages pertaining to natural resources concepts and associated management decisions are communicated to and received by culturally-diverse audiences. This is particularly relevant to land managing agencies, such as the US National Park Service (NPS), that rely on a high degree of public contact and support. Failure to consider cultural-diversity has the potential to interfere with this agency's success at communicating its mission and management decisions. The study took place in three US National Parks; Grand Canyon National Park (North Rim), Guadalupe Mountains National Park, and Hawai'i Volcanoes National Park. Visitors were asked to complete an on-site anonymous questionnaire. Data were collected at various locations including trailheads, scenic overlooks, at visitor centers, and after interpretive programs. Total number of participants was 549, Grand Canyon National Park n = 156, Guadalupe Mountains National Park n = 153, and Hawai'i Volcanoes National Park n = 240. Results indicate that visitors were knowledgeable about the resources they were visiting. Visitors to NPS sites have achieved a high level of formal education. Certain aspects of culture, religion/spirituality seem to have a greater role in how visitors identify themselves, as opposed to ethnicity/cultural heritage. However when visitors are in a park they seem display similar cultural characteristics, which may come to the forefront while in the park setting as opposed to home setting. Methodological challenges of studying culture in a national park setting are also discussed.
New multidimensional functional diversity indices for a multifaceted framework in functional ecology.

PubMed

Villéger, Sébastien; Mason, Norman W H; Mouillot, David

2008-08-01

Functional diversity is increasingly identified as an important driver of ecosystem functioning. Various indices have been proposed to measure the functional diversity of a community, but there is still no consensus on which are most suitable. Indeed, none of the existing indices meets all the criteria required for general use. The main criteria are that they must be designed to deal with several traits, take into account abundances, and measure all the facets of functional diversity. Here we propose three indices to quantify each facet of functional diversity for a community with species distributed in a multidimensional functional space: functional richness (volume of the functional space occupied by the community), functional evenness (regularity of the distribution of abundance in this volume), and functional divergence (divergence in the distribution of abundance in this volume). Functional richness is estimated using the existing convex hull volume index. The new functional evenness index is based on the minimum spanning tree which links all the species in the multidimensional functional space. Then this new index quantifies the regularity with which species abundances are distributed along the spanning tree. Functional divergence is measured using a novel index which quantifies how species diverge in their distances (weighted by their abundance) from the center of gravity in the functional space. We show that none of the indices meets all the criteria required for a functional diversity index, but instead we show that the set of three complementary indices meets these criteria. Through simulations of artificial data sets, we demonstrate that functional divergence and functional evenness are independent of species richness and that the three functional diversity indices are independent of each other. Overall, our study suggests that decomposition of functional diversity into its three primary components provides a meaningful framework for its quantification and for the classification of existing functional diversity indices. This decomposition has the potential to shed light on the role of biodiversity on ecosystem functioning and on the influence of biotic and abiotic filters on the structure of species communities. Finally, we propose a general framework for applying these three functional diversity indices.
Pairwise diversity ranking of polychotomous features for ensemble physiological signal classifiers.

PubMed

Gupta, Lalit; Kota, Srinivas; Molfese, Dennis L; Vaidyanathan, Ravi

2013-06-01

It is well known that fusion classifiers for physiological signal classification with diverse components (classifiers or data sets) outperform those with less diverse components. Determining component diversity, therefore, is of the utmost importance in the design of fusion classifiers that are often employed in clinical diagnostic and numerous other pattern recognition problems. In this article, a new pairwise diversity-based ranking strategy is introduced to select a subset of ensemble components, which when combined will be more diverse than any other component subset of the same size. The strategy is unified in the sense that the components can be classifiers or data sets. Moreover, the classifiers and data sets can be polychotomous. Classifier-fusion and data-fusion systems are formulated based on the diversity-based selection strategy, and the application of the two fusion strategies are demonstrated through the classification of multichannel event-related potentials. It is observed that for both classifier and data fusion, the classification accuracy tends to increase/decrease when the diversity of the component ensemble increases/decreases. For the four sets of 14-channel event-related potentials considered, it is shown that data fusion outperforms classifier fusion. Furthermore, it is demonstrated that the combination of data components that yield the best performance, in a relative sense, can be determined through the diversity-based selection strategy.
Conflicting patterns of genetic structure produced by nuclear and mitochondrial markers in the Oregon Slender Salamander (Batrachoseps wrighti): implications for conservation efforts and species management

USGS Publications Warehouse

Miller, Mark; Haig, Susan M.; Wagner, R.S.

2005-01-01

Endemic to Oregon in the northwestern US, the Oregon slender salamander (Batrachoseps wrighti) is a terrestrial plethodontid found associated with late successional mesic forests. Consequently, forest management practices such as timber harvesting may impact their persistence. Therefore, to infer possible future effects of these practices on population structure and differentiation, we used mitochondrial DNA sequences (cytochrome b) and RAPD markers to analyze 22 populations across their range. Phylogenetic analyses of sequence data (774 bp) revealed two historical lineages corresponding to northern and southern-distributed populations. Relationships among haplotypes and haplotype diversity within lineages suggested that the northern region may have more recently been colonized compared to the southern region. In contrast to the mitochondrial data, analyses of 46 RAPD loci suggested an overall pattern of isolation-by-distance in the set of populations examined and no particularly strong clustering of populations based on genetic distances. We propose two non-exclusive hypotheses to account for discrepancies between mitochondrial and nuclear data sets. First, our data may reflect an overall ancestral pattern of isolation-by-distance that has subsequently been influenced by vicariance. Alternately, our analyses may suggest that male-mediated gene flow and female philopatry are important contributors to the pattern of genetic diversity. We discuss the importance of distinguishing between these two hypotheses for the purposes of identifying conservation units and note that, regardless of the relative contribution of each mechanism towards the observed pattern of diversity, protection of habitat will likely prove critical for the long-term persistence of this species.
Presumed fair: ironic effects of organizational diversity structures.

PubMed

Kaiser, Cheryl R; Major, Brenda; Jurcevic, Ines; Dover, Tessa L; Brady, Laura M; Shapiro, Jenessa R

2013-03-01

This research tests the hypothesis that the presence (vs. absence) of organizational diversity structures causes high-status group members (Whites, men) to perceive organizations with diversity structures as procedurally fairer environments for underrepresented groups (racial minorities, women), even when it is clear that underrepresented groups have been unfairly disadvantaged within these organizations. Furthermore, this illusory sense of fairness derived from the mere presence of diversity structures causes high-status group members to legitimize the status quo by becoming less sensitive to discrimination targeted at underrepresented groups and reacting more harshly toward underrepresented group members who claim discrimination. Six experiments support these hypotheses in designs using 4 types of diversity structures (diversity policies, diversity training, diversity awards, idiosyncratically generated diversity structures from participants' own organizations) among 2 high-status groups in tests involving several types of discrimination (discriminatory promotion practices, adverse impact in hiring, wage discrimination). Implications of these experiments for organizational diversity and employment discrimination law are discussed. PsycINFO Database Record (c) 2013 APA, all rights reserved
Diversity surveys and evolutionary relationships of aoxB genes in aerobic arsenite-oxidizing bacteria.

PubMed

Quéméneur, Marianne; Heinrich-Salmeron, Audrey; Muller, Daniel; Lièvremont, Didier; Jauzein, Michel; Bertin, Philippe N; Garrido, Francis; Joulian, Catherine

2008-07-01

A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria-, Betaproteobacteria-, and Gammaproteobacteria-related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers.
Influence of landscape structure on reef fish assemblages

USGS Publications Warehouse

Grober-Dunsmore, R.; Frazer, T.K.; Beets, J.P.; Lindberg, W.J.; Zwick, P.; Funicelli, N.A.

2008-01-01

Management of tropical marine environments calls for interdisciplinary studies and innovative methodologies that consider processes occurring over broad spatial scales. We investigated relationships between landscape structure and reef fish assemblage structure in the US Virgin Islands. Measures of landscape structure were transformed into a reduced set of composite indices using principal component analyses (PCA) to synthesize data on the spatial patterning of the landscape structure of the study reefs. However, composite indices (e.g., habitat diversity) were not particularly informative for predicting reef fish assemblage structure. Rather, relationships were interpreted more easily when functional groups of fishes were related to individual habitat features. In particular, multiple reef fish parameters were strongly associated with reef context. Fishes responded to benthic habitat structure at multiple spatial scales, with various groups of fishes each correlated to a unique suite of variables. Accordingly, future experiments should be designed to test functional relationships based on the ecology of the organisms of interest. Our study demonstrates that landscape-scale habitat features influence reef fish communities, illustrating promise in applying a landscape ecology approach to better understand factors that structure coral reef ecosystems. Furthermore, our findings may prove useful in design of spatially-based conservation approaches such as marine protected areas (MPAs), because landscape-scale metrics may serve as proxies for areas with high species diversity and abundance within the coral reef landscape. ?? 2007 Springer Science+Business Media B.V.
Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase

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

Agarwal R.; Swaminathan S.; Burley, S. K.

2012-01-01

The araBAD operon encodes three different enzymes required for catabolism of L-arabinose, which is one of the most abundant monosaccharides in nature. L-ribulokinase, encoded by the araB gene, catalyzes conversion of L-ribulose to L-ribulose-5-phosphate, the second step in the catabolic pathway. Unlike other kinases, ribulokinase exhibits diversity in substrate selectivity and catalyzes phosphorylation of all four 2-ketopentose sugars with comparable k{sub cat} values. To understand ribulokinase recognition and phosphorylation of a diverse set of substrates, we have determined the X-ray structure of ribulokinase from Bacillus halodurans bound to L-ribulose and investigated its substrate and ATP co-factor binding properties. The polypeptidemore » chain is folded into two domains, one small and the other large, with a deep cleft in between. By analogy with related sugar kinases, we identified {sup 447}{und GG}LPQ{und K}{sup 452} as the ATP-binding motif within the smaller domain. L-ribulose binds in the cleft between the two domains via hydrogen bonds with the side chains of highly conserved Trp126, Lys208, Asp274, and Glu329 and the main chain nitrogen of Ala96. The interaction of L-ribulokinase with L-ribulose reveals versatile structural features that help explain recognition of various 2-ketopentose substrates and competitive inhibition by L-erythrulose. Comparison of our structure to that of the structures of other sugar kinases revealed conformational variations that suggest domain-domain closure movements are responsible for establishing the observed active site environment.« less
Finite Nuclei in the Quark-Meson Coupling Model.

PubMed

Stone, J R; Guichon, P A M; Reinhard, P G; Thomas, A W

2016-03-04

We report the first use of the effective quark-meson coupling (QMC) energy density functional (EDF), derived from a quark model of hadron structure, to study a broad range of ground state properties of even-even nuclei across the periodic table in the nonrelativistic Hartree-Fock+BCS framework. The novelty of the QMC model is that the nuclear medium effects are treated through modification of the internal structure of the nucleon. The density dependence is microscopically derived and the spin-orbit term arises naturally. The QMC EDF depends on a single set of four adjustable parameters having a clear physics basis. When applied to diverse ground state data the QMC EDF already produces, in its present simple form, overall agreement with experiment of a quality comparable to a representative Skyrme EDF. There exist, however, multiple Skyrme parameter sets, frequently tailored to describe selected nuclear phenomena. The QMC EDF set of fewer parameters, derived in this work, is not open to such variation, chosen set being applied, without adjustment, to both the properties of finite nuclei and nuclear matter.
Revealing the global map of protein folding space by large-scale simulations

NASA Astrophysics Data System (ADS)

Sinner, Claude; Lutz, Benjamin; Verma, Abhinav; Schug, Alexander

2015-12-01

The full characterization of protein folding is a remarkable long-standing challenge both for experiment and simulation. Working towards a complete understanding of this process, one needs to cover the full diversity of existing folds and identify the general principles driving the process. Here, we want to understand and quantify the diversity in folding routes for a large and representative set of protein topologies covering the full range from all alpha helical topologies towards beta barrels guided by the key question: Does the majority of the observed routes contribute to the folding process or only a particular route? We identified a set of two-state folders among non-homologous proteins with a sequence length of 40-120 residues. For each of these proteins, we ran native-structure based simulations both with homogeneous and heterogeneous contact potentials. For each protein, we simulated dozens of folding transitions in continuous uninterrupted simulations and constructed a large database of kinetic parameters. We investigate folding routes by tracking the formation of tertiary structure interfaces and discuss whether a single specific route exists for a topology or if all routes are equiprobable. These results permit us to characterize the complete folding space for small proteins in terms of folding barrier ΔG‡, number of routes, and the route specificity RT.
Genetic analysis of Apuleia leiocarpa as revealed by random amplified polymorphic DNA markers: prospects for population genetic studies.

PubMed

Lencina, K H; Konzen, E R; Tsai, S M; Bisognin, D A

2016-12-19

Apuleia leiocarpa (Vogel) J.F. MacBride is a hardwood species native to South America, which is at serious risk of extinction. Therefore, it is of prime importance to examine the genetic diversity of this species, information required for developing conservation, sustainable management, and breeding strategies. Although scarcely used in recent years, random amplified polymorphic DNA markers are useful resources for the analysis of genetic diversity and structure of tree species. This study represents the first genetic analysis based on DNA markers in A. leiocarpa that aimed to investigate the levels of polymorphism and to select markers for the precise characterization of its genetic structure. We adapted the original DNA extraction protocol based on cetyltrimethyl ammonium bromide, and describe a simple procedure that can be used to obtain high-quality samples from leaf tissues of this tree. Eighteen primers were selected, revealing 92 bands, from which 75 were polymorphic and 61 were sufficient to represent the overall genetic structure of the population without compromising the precision of the analysis. Some fragments were conserved among individuals, which can be sequenced and used to analyze nucleotide diversity parameters through a wider set of A. leiocarpa individuals and populations. The individuals were separated into 11 distinct groups with variable levels of genetic diversity, which is important for selecting desirable genotypes and for the development of a conservation and sustainable management program. Our results are of prime importance for further investigations concerning the genetic characterization of this important, but vulnerable species.
Authoritative parenting and cigarette smoking among multiethnic preadolescents: the mediating role of anti-tobacco parenting strategies.

PubMed

Stanton, Cassandra A; Highland, Krista B; Tercyak, Kenneth P; Luta, Gheorghe; Niaura, Raymond S

2014-01-01

Parenting has been shown to affect smoking among children in U.S. majority groups, but less is known about this association among multiethnic urban populations. Our study examines the role of parenting on smoking among a highly diverse sample. Health surveys were collected from eighth graders (N = 459) in 2 low-income urban schools. Structural equation models examined the direct and indirect effects of authoritative parenting on lifetime smoking. A moderated mediation analysis examined whether indirect effects of authoritative parenting vary among racial/ethnic groups. Authoritative controlling parenting, characterized by limit setting, was positively associated with anti-tobacco parenting. Anti-tobacco parenting was inversely associated with smoking, mediating the relationship between controlling parenting and smoking. There was no evidence that mediation was moderated by race/ethnicity. Parent training, which focuses on setting rules and expectations, can be an important and universal element of smoking prevention programs targeted to youth in diverse communities.
Authoritative Parenting and Cigarette Smoking Among Multiethnic Preadolescents: The Mediating Role of Anti-Tobacco Parenting Strategies

PubMed Central

Highland, Krista B.; Tercyak, Kenneth P.; Luta, Gheorghe; Niaura, Raymond S.

2014-01-01

Introduction Parenting has been shown to affect smoking among children in U.S. majority groups, but less is known about this association among multiethnic urban populations. Our study examines the role of parenting on smoking among a highly diverse sample. Methods Health surveys were collected from eighth graders (N =459) in 2 low-income urban schools. Structural equation models examined the direct and indirect effects of authoritative parenting on lifetime smoking. A moderated mediation analysis examined whether indirect effects of authoritative parenting vary among racial/ethnic groups. Results Authoritative controlling parenting, characterized by limit setting, was positively associated with anti-tobacco parenting. Anti-tobacco parenting was inversely associated with smoking, mediating the relationship between controlling parenting and smoking. There was no evidence that mediation was moderated by race/ethnicity. Conclusions Parent training, which focuses on setting rules and expectations, can be an important and universal element of smoking prevention programs targeted to youth in diverse communities. PMID:24306966
Using genomic data to develop chloroplast DNA SSRs for the Neotropical liana Stizophyllum riparium (Bignonieae, Bignoniaceae)1

PubMed Central

Beyer, Maila; Nazareno, Alison G.; Lohmann, Lúcia G.

2017-01-01

Premise of the study: We developed chloroplast microsatellite markers (cpSSRs) to be used to study the patterns of genetic structure and genetic diversity of populations of Stizophyllum riparium (Bignonieae, Bignoniaceae). Methods and Results: We used genomic data obtained through an Illumina HiSeq sequencing platform to develop a set of cpSSRs for S. riparium. A total of 36 primer pairs were developed, of which 28 displayed polymorphisms across 59 individuals from three populations. Two to 12 alleles were recorded, and the unbiased haploid diversity per locus ranged from 0.037 to 0.905. All 28 cpSSRs presented transferability to two closely related species, S. inaequilaterum and S. perforatum. Conclusions: We report a set of 28 cpSSRs for S. riparium. All markers were shown to be variable in S. riparium, indicating that these markers will be valuable for population genetic studies across S. riparium and congeneric species. PMID:29109920
A High-Content Live-Cell Viability Assay and Its Validation on a Diverse 12K Compound Screen.

PubMed

Chiaravalli, Jeanne; Glickman, J Fraser

2017-08-01

We have developed a new high-content cytotoxicity assay using live cells, called "ImageTOX." We used a high-throughput fluorescence microscope system, image segmentation software, and the combination of Hoechst 33342 and SYTO 17 to simultaneously score the relative size and the intensity of the nuclei, the nuclear membrane permeability, and the cell number in a 384-well microplate format. We then performed a screen of 12,668 diverse compounds and compared the results to a standard cytotoxicity assay. The ImageTOX assay identified similar sets of compounds to the standard cytotoxicity assay, while identifying more compounds having adverse effects on cell structure, earlier in treatment time. The ImageTOX assay uses inexpensive commercially available reagents and facilitates the use of live cells in toxicity screens. Furthermore, we show that we can measure the kinetic profile of compound toxicity in a high-content, high-throughput format, following the same set of cells over an extended period of time.
Transcultural comparison of hospital and hospice as caring environments for dying patients.

PubMed

Gates, M F

1991-01-01

Leininger's nursing Theory of Cultural Care Diversity and Universality provided the framework for this comparative study of two environments for persons who are dying; namely a hospital oncology unit and a free-standing hospice unit. Analysis of data from ethnographic and ethnonursing research methods including unstructured interviews, observation-participation, and field journal materials yielded contrasts with two settings. The presence of a caring atmosphere/ambience was apparent in both the hospital and hospice. Universal patterns common to both were: caring beliefs and practices of staff; identification of each setting as "community" or "home"; and multiple symbolic uses of humor and food. Diversities included hierarchical organizational structure and cure orientation in the hospital; interdisciplinary collaboration and care orientation in hospice; more pronounced use of touch as a caring modality; and greater evidence of symbolism and ritual related to death and dying in hospice. Adoption of the cultural care modes of accommodation, repatterning, and maintenance are suggested in promoting a caring atmosphere wherever dying patients are served.
SemanticOrganizer: A Customizable Semantic Repository for Distributed NASA Project Teams

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Berrios, Daniel C.; Carvalho, Robert E.; Hall, David R.; Rich, Stephen J.; Sturken, Ian B.; Swanson, Keith J.; Wolfe, Shawn R.

2004-01-01

SemanticOrganizer is a collaborative knowledge management system designed to support distributed NASA projects, including diverse teams of scientists, engineers, and accident investigators. The system provides a customizable, semantically structured information repository that stores work products relevant to multiple projects of differing types. SemanticOrganizer is one of the earliest and largest semantic web applications deployed at NASA to date, and has been used in diverse contexts ranging from the investigation of Space Shuttle Columbia's accident to the search for life on other planets. Although the underlying repository employs a single unified ontology, access control and ontology customization mechanisms make the repository contents appear different for each project team. This paper describes SemanticOrganizer, its customization facilities, and a sampling of its applications. The paper also summarizes some key lessons learned from building and fielding a successful semantic web application across a wide-ranging set of domains with diverse users.
Ultra-performance liquid chromatography/tandem mass spectrometric quantification of structurally diverse drug mixtures using an ESI-APCI multimode ionization source.

PubMed

Yu, Kate; Di, Li; Kerns, Edward; Li, Susan Q; Alden, Peter; Plumb, Robert S

2007-01-01

We report in this paper an ultra-performance liquid chromatography/tandem mass spectrometric (UPLC(R)/MS/MS) method utilizing an ESI-APCI multimode ionization source to quantify structurally diverse analytes. Eight commercial drugs were used as test compounds. Each LC injection was completed in 1 min using a UPLC system coupled with MS/MS multiple reaction monitoring (MRM) detection. Results from three separate sets of experiments are reported. In the first set of experiments, the eight test compounds were analyzed as a single mixture. The mass spectrometer was switching rapidly among four ionization modes (ESI+, ESI-, APCI-, and APCI+) during an LC run. Approximately 8-10 data points were collected across each LC peak. This was insufficient for a quantitative analysis. In the second set of experiments, four compounds were analyzed as a single mixture. The mass spectrometer was switching rapidly among four ionization modes during an LC run. Approximately 15 data points were obtained for each LC peak. Quantification results were obtained with a limit of detection (LOD) as low as 0.01 ng/mL. For the third set of experiments, the eight test compounds were analyzed as a batch. During each LC injection, a single compound was analyzed. The mass spectrometer was detecting at a particular ionization mode during each LC injection. More than 20 data points were obtained for each LC peak. Quantification results were also obtained. This single-compound analytical method was applied to a microsomal stability test. Compared with a typical HPLC method currently used for the microsomal stability test, the injection-to-injection cycle time was reduced to 1.5 min (UPLC method) from 3.5 min (HPLC method). The microsome stability results were comparable with those obtained by traditional HPLC/MS/MS.
Tackling the conformational sampling of larger flexible compounds and macrocycles in pharmacology and drug discovery.

PubMed

Chen, I-Jen; Foloppe, Nicolas

2013-12-15

Computational conformational sampling underpins much of molecular modeling and design in pharmaceutical work. The sampling of smaller drug-like compounds has been an active area of research. However, few studies have tested in details the sampling of larger more flexible compounds, which are also relevant to drug discovery, including therapeutic peptides, macrocycles, and inhibitors of protein-protein interactions. Here, we investigate extensively mainstream conformational sampling methods on three carefully curated compound sets, namely the 'Drug-like', larger 'Flexible', and 'Macrocycle' compounds. These test molecules are chemically diverse with reliable X-ray protein-bound bioactive structures. The compared sampling methods include Stochastic Search and the recent LowModeMD from MOE, all the low-mode based approaches from MacroModel, and MD/LLMOD recently developed for macrocycles. In addition to default settings, key parameters of the sampling protocols were explored. The performance of the computational protocols was assessed via (i) the reproduction of the X-ray bioactive structures, (ii) the size, coverage and diversity of the output conformational ensembles, (iii) the compactness/extendedness of the conformers, and (iv) the ability to locate the global energy minimum. The influence of the stochastic nature of the searches on the results was also examined. Much better results were obtained by adopting search parameters enhanced over the default settings, while maintaining computational tractability. In MOE, the recent LowModeMD emerged as the method of choice. Mixed torsional/low-mode from MacroModel performed as well as LowModeMD, and MD/LLMOD performed well for macrocycles. The low-mode based approaches yielded very encouraging results with the flexible and macrocycle sets. Thus, one can productively tackle the computational conformational search of larger flexible compounds for drug discovery, including macrocycles. Copyright © 2013 Elsevier Ltd. All rights reserved.

Reporting on the Strategies Needed to Implement Proven Interventions: An Example From a "Real-World" Cross-Setting Implementation Study.

PubMed

Gold, Rachel; Bunce, Arwen E; Cohen, Deborah J; Hollombe, Celine; Nelson, Christine A; Proctor, Enola K; Pope, Jill A; DeVoe, Jennifer E

2016-08-01

The objective of this study was to empirically demonstrate the use of a new framework for describing the strategies used to implement quality improvement interventions and provide an example that others may follow. Implementation strategies are the specific approaches, methods, structures, and resources used to introduce and encourage uptake of a given intervention's components. Such strategies have not been regularly reported in descriptions of interventions' effectiveness, or in assessments of how proven interventions are implemented in new settings. This lack of reporting may hinder efforts to successfully translate effective interventions into "real-world" practice. A recently published framework was designed to standardize reporting on implementation strategies in the implementation science literature. We applied this framework to describe the strategies used to implement a single intervention in its original commercial care setting, and when implemented in community health centers from September 2010 through May 2015. Per this framework, the target (clinic staff) and outcome (prescribing rates) remained the same across settings; the actor, action, temporality, and dose were adapted to fit local context. The framework proved helpful in articulating which of the implementation strategies were kept constant and which were tailored to fit diverse settings, and simplified our reporting of their effects. Researchers should consider consistently reporting this information, which could be crucial to the success or failure of implementing proven interventions effectively across diverse care settings. clinicaltrials.gov Identifier: NCT02299791. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
Betweenness and diversity in journal citation networks as measures of interdisciplinarity-A tribute to Eugene Garfield.

PubMed

Leydesdorff, Loet; Wagner, Caroline S; Bornmann, Lutz

2018-01-01

Journals were central to Eugene Garfield's research interests. Among other things, journals are considered as units of analysis for bibliographic databases such as the Web of Science and Scopus. In addition to providing a basis for disciplinary classifications of journals, journal citation patterns span networks across boundaries to variable extents. Using betweenness centrality (BC) and diversity, we elaborate on the question of how to distinguish and rank journals in terms of interdisciplinarity. Interdisciplinarity, however, is difficult to operationalize in the absence of an operational definition of disciplines; the diversity of a unit of analysis is sample-dependent. BC can be considered as a measure of multi-disciplinarity. Diversity of co-citation in a citing document has been considered as an indicator of knowledge integration, but an author can also generate trans-disciplinary-that is, non-disciplined-variation by citing sources from other disciplines. Diversity in the bibliographic coupling among citing documents can analogously be considered as diffusion or differentiation of knowledge across disciplines. Because the citation networks in the cited direction reflect both structure and variation, diversity in this direction is perhaps the best available measure of interdisciplinarity at the journal level. Furthermore, diversity is based on a summation and can therefore be decomposed; differences among (sub)sets can be tested for statistical significance. In the appendix, a general-purpose routine for measuring diversity in networks is provided.
General Platform for Systematic Quantitative Evaluation of Small-Molecule Permeability in Bacteria

PubMed Central

2015-01-01

The chemical features that impact small-molecule permeability across bacterial membranes are poorly understood, and the resulting lack of tools to predict permeability presents a major obstacle to the discovery and development of novel antibiotics. Antibacterials are known to have vastly different structural and physicochemical properties compared to nonantiinfective drugs, as illustrated herein by principal component analysis (PCA). To understand how these properties influence bacterial permeability, we have developed a systematic approach to evaluate the penetration of diverse compounds into bacteria with distinct cellular envelopes. Intracellular compound accumulation is quantitated using LC-MS/MS, then PCA and Pearson pairwise correlations are used to identify structural and physicochemical parameters that correlate with accumulation. An initial study using 10 sulfonyladenosines in Escherichia coli, Bacillus subtilis, and Mycobacterium smegmatis has identified nonobvious correlations between chemical structure and permeability that differ among the various bacteria. Effects of cotreatment with efflux pump inhibitors were also investigated. This sets the stage for use of this platform in larger prospective analyses of diverse chemotypes to identify global relationships between chemical structure and bacterial permeability that would enable the development of predictive tools to accelerate antibiotic drug discovery. PMID:25198656
Chemometric Analysis of Bacterial Peptidoglycan Reveals Atypical Modifications That Empower the Cell Wall against Predatory Enzymes and Fly Innate Immunity.

PubMed

Espaillat, Akbar; Forsmo, Oskar; El Biari, Khouzaima; Björk, Rafael; Lemaitre, Bruno; Trygg, Johan; Cañada, Francisco Javier; de Pedro, Miguel A; Cava, Felipe

2016-07-27

Peptidoglycan is a fundamental structure for most bacteria. It contributes to the cell morphology and provides cell wall integrity against environmental insults. While several studies have reported a significant degree of variability in the chemical composition and organization of peptidoglycan in the domain Bacteria, the real diversity of this polymer is far from fully explored. This work exploits rapid ultraperformance liquid chromatography and multivariate data analysis to uncover peptidoglycan chemical diversity in the Class Alphaproteobacteria, a group of Gram negative bacteria that are highly heterogeneous in terms of metabolism, morphology and life-styles. Indeed, chemometric analyses revealed novel peptidoglycan structures conserved in Acetobacteria: amidation at the α-(l)-carboxyl of meso-diaminopimelic acid and the presence of muropeptides cross-linked by (1-3) l-Ala-d-(meso)-diaminopimelate cross-links. Both structures are growth-controlled modifications that influence sensitivity to Type VI secretion system peptidoglycan endopeptidases and recognition by the Drosophila innate immune system, suggesting relevant roles in the environmental adaptability of these bacteria. Collectively our findings demonstrate the discriminative power of chemometric tools on large cell wall-chromatographic data sets to discover novel peptidoglycan structural properties in bacteria.
Detecting macroecological patterns in bacterial communities across independent studies of global soils.

PubMed

Ramirez, Kelly S; Knight, Christopher G; de Hollander, Mattias; Brearley, Francis Q; Constantinides, Bede; Cotton, Anne; Creer, Si; Crowther, Thomas W; Davison, John; Delgado-Baquerizo, Manuel; Dorrepaal, Ellen; Elliott, David R; Fox, Graeme; Griffiths, Robert I; Hale, Chris; Hartman, Kyle; Houlden, Ashley; Jones, David L; Krab, Eveline J; Maestre, Fernando T; McGuire, Krista L; Monteux, Sylvain; Orr, Caroline H; van der Putten, Wim H; Roberts, Ian S; Robinson, David A; Rocca, Jennifer D; Rowntree, Jennifer; Schlaeppi, Klaus; Shepherd, Matthew; Singh, Brajesh K; Straathof, Angela L; Bhatnagar, Jennifer M; Thion, Cécile; van der Heijden, Marcel G A; de Vries, Franciska T

2018-02-01

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
Scaling of phloem structure and optimality of sugar transport in conifer needles

NASA Astrophysics Data System (ADS)

Jensen, Kaare H.; Ronellenfitsch, Henrik; Liesche, Johannes; Holbrook, N. Michele; Schulz, Alexander; Katifori, Eleni

2015-11-01

The phloem vascular system facilitates transport of energy-rich sugar and signalling molecules in plants, thus permitting long-range communication within the organism and growth of non-photosynthesizing organs such as roots and fruits. The flow is driven by osmotic pressure, generated by differences in sugar concentration between distal parts of the plant. The phloem is an intricate distribution system, and many questions about its regulation and structural diversity remain unanswered. Here, we investigate the phloem structure in the simplest possible geometry: a linear leaf, found, for example, in the needles of conifer trees. We measure the phloem structure in four tree species representing a diverse set of habitats and needle sizes, from 1 cm (Picea omorika) to 35 cm (Pinus palustris). We show that the phloem shares common traits across these four species and find that the size of its conductive elements obeys a power law. We present a minimal model that accounts for these common traits and takes into account the transport strategy and natural constraints. This minimal model predicts a power law phloem distribution consistent with transport energy minimization, suggesting that energetics are more important than translocation speed at the leaf level.
Identification of Genetic Differentiation between Waxy and Common Maize by SNP Genotyping

PubMed Central

Hao, Derong; Zhang, Zhenliang; Cheng, Yujing; Chen, Guoqing; Lu, Huhua; Mao, Yuxiang; Shi, Mingliang; Huang, Xiaolan; Zhou, Guangfei; Xue, Lin

2015-01-01

Waxy maize (Zea mays L. var. ceratina) is an important vegetable and economic crop that is thought to have originated from cultivated flint maize and most recently underwent divergence from common maize. In this study, a total of 110 waxy and 110 common maize inbred lines were genotyped with 3072 SNPs to evaluate the genetic diversity, population structure, and linkage disequilibrium decay as well as identify putative loci that are under positive selection. The results revealed abundant genetic diversity in the studied panel and that genetic diversity was much higher in common than in waxy maize germplasms. Principal coordinate analysis and neighbor-joining cluster analysis consistently classified the 220 accessions into two major groups and a mixed group with mixed ancestry. Subpopulation structure in both waxy and common maize sets were associated with the germplasm origin and corresponding heterotic groups. The LD decay distance (1500–2000 kb) in waxy maize was lower than that in common maize. Fourteen candidate loci were identified as under positive selection between waxy and common maize at the 99% confidence level. The information from this study can assist waxy maize breeders by enhancing parental line selection and breeding program design. PMID:26566240
Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing

PubMed Central

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-01-01

ABSTRACT Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure. PMID:28277933
Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing.

PubMed

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-10-03

Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure.
The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism.

PubMed

Salm, Maximilian P A; Horswell, Stuart D; Hutchison, Claire E; Speedy, Helen E; Yang, Xia; Liang, Liming; Schadt, Eric E; Cookson, William O; Wierzbicki, Anthony S; Naoumova, Rossi P; Shoulders, Carol C

2012-06-01

Genomic inversions are an increasingly recognized source of genetic variation. However, a lack of reliable high-throughput genotyping assays for these structures has precluded a full understanding of an inversion's phylogenetic, phenotypic, and population genetic properties. We characterize these properties for one of the largest polymorphic inversions in man (the ∼4.5-Mb 8p23.1 inversion), a structure that encompasses numerous signals of natural selection and disease association. We developed and validated a flexible bioinformatics tool that utilizes SNP data to enable accurate, high-throughput genotyping of the 8p23.1 inversion. This tool was applied retrospectively to diverse genome-wide data sets, revealing significant population stratification that largely follows a clinal "serial founder effect" distribution model. Phylogenetic analyses establish the inversion's ancestral origin within the Homo lineage, indicating that 8p23.1 inversion has occurred independently in the Pan lineage. The human inversion breakpoint was localized to an inverted pair of human endogenous retrovirus elements within the large, flanking low-copy repeats; experimental validation of this breakpoint confirmed these elements as the likely intermediary substrates that sponsored inversion formation. In five data sets, mRNA levels of disease-associated genes were robustly associated with inversion genotype. Moreover, a haplotype associated with systemic lupus erythematosus was restricted to the derived inversion state. We conclude that the 8p23.1 inversion is an evolutionarily dynamic structure that can now be accommodated into the understanding of human genetic and phenotypic diversity.
The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism

PubMed Central

Salm, Maximilian P.A.; Horswell, Stuart D.; Hutchison, Claire E.; Speedy, Helen E.; Yang, Xia; Liang, Liming; Schadt, Eric E.; Cookson, William O.; Wierzbicki, Anthony S.; Naoumova, Rossi P.; Shoulders, Carol C.

2012-01-01

Genomic inversions are an increasingly recognized source of genetic variation. However, a lack of reliable high-throughput genotyping assays for these structures has precluded a full understanding of an inversion's phylogenetic, phenotypic, and population genetic properties. We characterize these properties for one of the largest polymorphic inversions in man (the ∼4.5-Mb 8p23.1 inversion), a structure that encompasses numerous signals of natural selection and disease association. We developed and validated a flexible bioinformatics tool that utilizes SNP data to enable accurate, high-throughput genotyping of the 8p23.1 inversion. This tool was applied retrospectively to diverse genome-wide data sets, revealing significant population stratification that largely follows a clinal “serial founder effect” distribution model. Phylogenetic analyses establish the inversion's ancestral origin within the Homo lineage, indicating that 8p23.1 inversion has occurred independently in the Pan lineage. The human inversion breakpoint was localized to an inverted pair of human endogenous retrovirus elements within the large, flanking low-copy repeats; experimental validation of this breakpoint confirmed these elements as the likely intermediary substrates that sponsored inversion formation. In five data sets, mRNA levels of disease-associated genes were robustly associated with inversion genotype. Moreover, a haplotype associated with systemic lupus erythematosus was restricted to the derived inversion state. We conclude that the 8p23.1 inversion is an evolutionarily dynamic structure that can now be accommodated into the understanding of human genetic and phenotypic diversity. PMID:22399572
Prioritization for conservation of northern European cattle breeds based on analysis of microsatellite data.

PubMed

Tapio, I; Värv, S; Bennewitz, J; Maleviciute, J; Fimland, E; Grislis, Z; Meuwissen, T H E; Miceikiene, I; Olsaker, I; Viinalass, H; Vilkki, J; Kantanen, J

2006-12-01

Northern European indigenous cattle breeds are currently endangered and at a risk of becoming extinct. We analyzed variation at 20 microsatellite loci in 23 indigenous, 3 old imported, and 9 modern commercial cattle breeds that are presently distributed in northern Europe. We measured the breeds' allelic richness and heterozygosity, and studied their genetic relationships with a neighbor-joining tree based on the Chord genetic distance matrix. We used the Weitzman approach and the core set diversity measure of Eding et al. (2002) to quantify the contribution of each breed to the maximum amount of genetic diversity and to identify breeds important for the conservation of genetic diversity. We defined 11 breeds as a "safe set" of breeds (not endangered) and estimated a reduction in genetic diversity if all nonsafe (endangered) breeds were lost. We then calculated the increase in genetic diversity by adding one by one each of the nonsafe breeds to the safe set (the safe-set-plus-one approach). The neighbor-joining tree grouped the northern European cattle breeds into Black-and-White type, Baltic Red, and Nordic cattle groups. Väne cattle, Bohus Poll, and Danish Jersey had the highest relative contribution to the maximum amount of genetic diversity when the diversity was quantified by the Weitzman diversity measure. These breeds not only showed phylogenetic distinctiveness but also low within-population variation. When the Eding et al. method was applied, Eastern Finncattle and Lithuanian White Backed cattle contributed most of the genetic variation. If the loss of the nonsafe set of breeds happens, the reduction in genetic diversity would be substantial (72%) based on the Weitzman approach, but relatively small (1.81%) based on the Eding et al. method. The safe set contained only 66% of the observed microsatellite alleles. The safe-set-plus-one approach indicated that Bohus Poll and Väne cattle contributed most to the Weitzman diversity, whereas the Eastern Finncattle contribution was the highest according to the Eding et al. method. Our results indicate that both methods of Weitzman and Eding et al. recognize the importance of local populations as a valuable resource of genetic variation.
Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties

PubMed Central

Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

2015-01-01

Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP marker set will be useful for systematic estimation of admixture structure of citrus germplasm and for diverse genetic studies. PMID:25973611
Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties.

PubMed

Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

2015-01-01

Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP marker set will be useful for systematic estimation of admixture structure of citrus germplasm and for diverse genetic studies.
A Score of the Ability of a Three-Dimensional Protein Model to Retrieve Its Own Sequence as a Quantitative Measure of Its Quality and Appropriateness

PubMed Central

Martínez-Castilla, León P.; Rodríguez-Sotres, Rogelio

2010-01-01

Background Despite the remarkable progress of bioinformatics, how the primary structure of a protein leads to a three-dimensional fold, and in turn determines its function remains an elusive question. Alignments of sequences with known function can be used to identify proteins with the same or similar function with high success. However, identification of function-related and structure-related amino acid positions is only possible after a detailed study of every protein. Folding pattern diversity seems to be much narrower than sequence diversity, and the amino acid sequences of natural proteins have evolved under a selective pressure comprising structural and functional requirements acting in parallel. Principal Findings The approach described in this work begins by generating a large number of amino acid sequences using ROSETTA [Dantas G et al. (2003) J Mol Biol 332:449–460], a program with notable robustness in the assignment of amino acids to a known three-dimensional structure. The resulting sequence-sets showed no conservation of amino acids at active sites, or protein-protein interfaces. Hidden Markov models built from the resulting sequence sets were used to search sequence databases. Surprisingly, the models retrieved from the database sequences belonged to proteins with the same or a very similar function. Given an appropriate cutoff, the rate of false positives was zero. According to our results, this protocol, here referred to as Rd.HMM, detects fine structural details on the folding patterns, that seem to be tightly linked to the fitness of a structural framework for a specific biological function. Conclusion Because the sequence of the native protein used to create the Rd.HMM model was always amongst the top hits, the procedure is a reliable tool to score, very accurately, the quality and appropriateness of computer-modeled 3D-structures, without the need for spectroscopy data. However, Rd.HMM is very sensitive to the conformational features of the models' backbone. PMID:20830209
A novel complexity-to-diversity strategy for the diversity-oriented synthesis of structurally diverse and complex macrocycles from quinine.

PubMed

Ciardiello, J J; Stewart, H L; Sore, H F; Galloway, W R J D; Spring, D R

2017-06-01

Recent years have witnessed a global decline in the productivity and advancement of the pharmaceutical industry. A major contributing factor to this is the downturn in drug discovery successes. This can be attributed to the lack of structural (particularly scaffold) diversity and structural complexity exhibited by current small molecule screening collections. Macrocycles have been shown to exhibit a diverse range of biological properties, with over 100 natural product-derived examples currently marketed as FDA-approved drugs. Despite this, synthetic macrocycles are widely considered to be a poorly explored structural class within drug discovery, which can be attributed to their synthetic intractability. Herein we describe a novel complexity-to-diversity strategy for the diversity-oriented synthesis of novel, structurally complex and diverse macrocyclic scaffolds from natural product starting materials. This approach exploits the inherent structural (including functional) and stereochemical complexity of natural products in order to rapidly generate diversity and complexity. Readily-accessible natural product-derived intermediates serve as structural templates which can be divergently functionalized with different building blocks to generate a diverse range of acyclic precursors. Subsequent macrocyclisation then furnishes compounds that are each based around a distinct molecular scaffold. Thus, high levels of library scaffold diversity can be rapidly achieved. In this proof-of-concept study, the natural product quinine was used as the foundation for library synthesis, and six novel structurally diverse, highly complex and functionalized macrocycles were generated. Copyright © 2017 Elsevier Ltd. All rights reserved.
Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil.

PubMed

Santos, Elisa S L; Cerqueira-Silva, Carlos Bernard M; Mori, Gustavo M; Ahnert, Dário; Mello, Durval L N; Pires, José Luis; Corrêa, Ronan X; de Souza, Anete P

2015-01-01

Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called 'Bahian cacao' or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide.
Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil

PubMed Central

Santos, Elisa S. L.; Cerqueira-Silva, Carlos Bernard M.; Mori, Gustavo M.; Ahnert, Dário; Mello, Durval L. N.; Pires, José Luis; Corrêa, Ronan X.; de Souza, Anete P.

2015-01-01

Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called ‘Bahian cacao’ or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide. PMID:26675449
Modeling backbone flexibility to achieve sequence diversity: The design of novel alpha-helical ligands for Bcl-xL

PubMed Central

Fu, Xiaoran; Apgar, James R.; Keating, Amy E.

2007-01-01

Computational protein design can be used to select sequences that are compatible with a fixed-backbone template. This strategy has been used in numerous instances to engineer novel proteins. However, the fixed-backbone assumption severely restricts the sequence space that is accessible via design. For challenging problems, such as the design of functional proteins, this may not be acceptable. In this paper, we present a method for introducing backbone flexibility into protein design calculations and apply it to the design of diverse helical BH3 ligands that bind to the anti-apoptotic protein Bcl-xL, a member of the Bcl-2 protein family. We demonstrate how normal mode analysis can be used to sample different BH3 backbones, and show that this leads to a larger and more diverse set of low-energy solutions than can be achieved using a native high-resolution Bcl-xL complex crystal structure as a template. We tested several of the designed solutions experimentally and found that this approach worked well when normal mode calculations were used to deform a native BH3 helix structure, but less well when they were used to deform an idealized helix. A subsequent round of design and testing identified a likely source of the problem as inadequate sampling of the helix pitch. In all, we tested seventeen designed BH3 peptide sequences, including several point mutants. Of these, eight bound well to Bcl-xL and four others showed weak but detectable binding. The successful designs showed a diversity of sequences that would have been difficult or impossible to achieve using only a fixed backbone. Thus, introducing backbone flexibility via normal mode analysis effectively broadened the set of sequences identified by computational design, and provided insight into positions important for binding Bcl-xL. PMID:17597151
Perspectives on the energy landscape of Au-Cl binary systems from the structural phase diagram of AuxCly (x + y = 20).

PubMed

Tian, Zhimei; Cheng, Longjiu

2015-05-28

Ligand-protected gold (Au-L) nanoclusters have attracted much attention, where the reported electronic and geometric structures show great diversity. To give a direct and overall view of the energy landscape of Au-L binary systems, the AuxCly (x + y = 20) system is taken as a test case. By intensive global search of the potential energy surface at the level of density functional theory, a diverse set of global minima and low-lying isomers are found at each composition, and the structural phase diagram is obtained. The unbiased global search is carried out using the method combining the genetic algorithm with the TPSS functional. At x = 10 with the stoichiometric ratio of Au and Cl (1 : 1), the cluster presents a catenane structure. When x is in the range of 11-20, the clusters are Au-rich, and the Au-Cl system can be viewed as Cl-protected gold nanoclusters, where the gold cores consist of superatoms, superatom networks, or superatomic molecules in electronic structures. At x = 11-15, the gold cores consist of Au3, Au4 and Au5 2e-superatoms protected by staple motifs. At x = 16-20, the clusters are pyramidal superatomic molecules with one Au16 superatom core bonding with the four vertical atoms (Au or Cl). When x is in the scope of 9-5, the clusters are Cl-rich, and the 5d electrons of Au participate in bonding, resulting in high multiplicities. The Au-Cl binary system shows great diversity and flexibility in electronic and geometric structures, and there are corresponding structures to most of the experimentally produced Au-L nanoclusters in our structural phase diagram. We believe that the structural phase diagram gives an overall perspective on the universe of Au-L nanoclusters.

Biogeography and Biodiversity in Sulfide Structures of Active and Inactive Vents at Deep-Sea Hydrothermal Fields of the Southern Mariana Trough▿ †

PubMed Central

Kato, Shingo; Takano, Yoshinori; Kakegawa, Takeshi; Oba, Hironori; Inoue, Kazuhiko; Kobayashi, Chiyori; Utsumi, Motoo; Marumo, Katsumi; Kobayashi, Kensei; Ito, Yuki; Ishibashi, Jun-ichiro; Yamagishi, Akihiko

2010-01-01

The abundance, diversity, activity, and composition of microbial communities in sulfide structures both of active and inactive vents were investigated by culture-independent methods. These sulfide structures were collected at four hydrothermal fields, both on- and off-axis of the back-arc spreading center of the Southern Mariana Trough. The microbial abundance and activity in the samples were determined by analyzing total organic content, enzymatic activity, and copy number of the 16S rRNA gene. To assess the diversity and composition of the microbial communities, 16S rRNA gene clone libraries including bacterial and archaeal phylotypes were constructed from the sulfide structures. Despite the differences in the geological settings among the sampling points, phylotypes related to the Epsilonproteobacteria and cultured hyperthermophilic archaea were abundant in the libraries from the samples of active vents. In contrast, the relative abundance of these phylotypes was extremely low in the libraries from the samples of inactive vents. These results suggest that the composition of microbial communities within sulfide structures dramatically changes depending on the degree of hydrothermal activity, which was supported by statistical analyses. Comparative analyses suggest that the abundance, activity and diversity of microbial communities within sulfide structures of inactive vents are likely to be comparable to or higher than those in active vent structures, even though the microbial community composition is different between these two types of vents. The microbial community compositions in the sulfide structures of inactive vents were similar to those in seafloor basaltic rocks rather than those in marine sediments or the sulfide structures of active vents, suggesting that the microbial community compositions on the seafloor may be constrained by the available energy sources. Our findings provide helpful information for understanding the biogeography, biodiversity and microbial ecosystems in marine environments. PMID:20228114
Effects of Short-Term Set-Aside Management Practices on Soil Microorganism and Enzyme Activity in China.

PubMed

Li, Guangyu; Wu, Cifang

2017-08-14

Set-aside farmland can effectively improve the self-rehabilitation of arable soil. Long-term set-asides however cannot satisfy provisionment, therefore the use of short-term set-asides to restore cultivated soil is a better option. Few studies have compared short-term set-aside patterns, and the effects of set-asides on soil microbial community and enzyme enzymes. We analyzed the bacterial structure, microbial biomass carbon/nitrogen and enzyme activity of farmland soil under different set-aside regimes in the Yellow River Delta of China. Bacterial alpha diversity was relatively lower under only irrigation, and farmyard manure applications showed clear advantages. Set-asides should consider their influence on soil organic carbon and nitrogen, which were correlated with microbial community structure. Nitrospira (0.47-1.67%), Acidobacteria Gp6 (8.26-15.91%) and unclassified Burkholderiales (1.50-2.81%) were significantly altered ( p < 0.01). Based on functions of these genera, some set-aside patterns led to a relative balance in nitrogen and carbon turnover. Partial treatments showed a deficiency in organic matter. In addition, farmyard manure may lead to the increased consumption of organic matter, with the exception of native plants set-asides. Conventional farming (control group) displayed a significant enzyme activity advantage. Set-aside management practices guided soil microbial communities to different states. Integrated soil microbiota and the content of carbon and nitrogen, native plants with farmyard manure showed an equilibrium state relatively, which would be helpful to improve land quality in the short-term.
Sharing of Diverse Mycorrhizal and Root-Endophytic Fungi among Plant Species in an Oak-Dominated Cool–Temperate Forest

PubMed Central

Toju, Hirokazu; Yamamoto, Satoshi; Sato, Hirotoshi; Tanabe, Akifumi S.

2013-01-01

Most terrestrial plants interact with diverse clades of mycorrhizal and root-endophytic fungi in their roots. Through belowground plant–fungal interactions, dominant plants can benefit by interacting with host-specific mutualistic fungi and proliferate in a community based on positive plant–mutualistic fungal feedback. On the other hand, subordinate plant species may persist in the community by sharing other sets (functional groups) of fungal symbionts with each other. Therefore, revealing how diverse clades of root-associated fungi are differentially hosted by dominant and subordinate plant species is essential for understanding plant community structure and dynamics. Based on 454-pyrosequencing, we determined the community composition of root-associated fungi on 36 co-occurring plant species in an oak-dominated forest in northern Japan and statistically evaluated the host preference phenotypes of diverse mycorrhizal and root-endophytic fungi. An analysis of 278 fungal taxa indicated that an ectomycorrhizal basidiomycete fungus in the genus Lactarius and a possibly endophytic ascomycete fungus in the order Helotiales significantly favored the dominant oak (Quercus) species. In contrast, arbuscular mycorrhizal fungi were generally shared among subordinate plant species. Although fungi with host preferences contributed to the compartmentalization of belowground plant–fungal associations, diverse clades of ectomycorrhizal fungi and possible root endophytes were associated not only with the dominant Quercus but also with the remaining plant species. Our findings suggest that dominant-ectomycorrhizal and subordinate plant species can host different subsets of root-associated fungi, and diverse clades of generalist fungi can counterbalance the compartmentalization of plant–fungal associations. Such insights into the overall structure of belowground plant–fungal associations will help us understand the mechanisms that facilitate the coexistence of plant species in natural communities. PMID:24250752
Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity

PubMed Central

Messier, Christian; Kembel, Steven W.

2017-01-01

ABSTRACT Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria. Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. PMID:29238751
Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity.

PubMed

Laforest-Lapointe, Isabelle; Messier, Christian; Kembel, Steven W

2017-01-01

Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria . Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.
Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean.

PubMed

Shi, Xiao Li; Lepère, Cécile; Scanlan, David J; Vaulot, Daniel

2011-04-28

The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of the plastid 16S rRNA gene were constructed on picoeukaryote populations sorted by flow cytometry, using two different primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards plastids of marine algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker. The first 16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other reasons, such as DNA accessibility or gene copy numbers, may be also critical. Based on plastid 16S rRNA gene sequences, the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX), which seems to be restricted to hyper-oligotrophic stations. Our data suggest that a single gene marker, even as widely used as 18S rRNA, provides a biased view of eukaryotic communities and that the use of several markers is necessary to obtain a complete image.
Virtual High-Throughput Screening for Matrix Metalloproteinase Inhibitors.

PubMed

Choi, Jun Yong; Fuerst, Rita

2017-01-01

Structure-based virtual screening (SBVS) is a common method for the fast identification of hit structures at the beginning of a medicinal chemistry program in drug discovery. The SBVS, described in this manuscript, is focused on finding small molecule hits that can be further utilized as a starting point for the development of inhibitors of matrix metalloproteinase 13 (MMP-13) via structure-based molecular design. We intended to identify a set of structurally diverse hits, which occupy all subsites (S1'-S3', S2, and S3) centering the zinc containing binding site of MMP-13, by the virtual screening of a chemical library comprising more than ten million commercially available compounds. In total, 23 compounds were found as potential MMP-13 inhibitors using Glide docking followed by the analysis of the structural interaction fingerprints (SIFt) of the docked structures.
Language-concordant automated telephone queries to assess medication adherence in a diverse population: a cross-sectional analysis of convergent validity with pharmacy claims.

PubMed

Ratanawongsa, Neda; Quan, Judy; Handley, Margaret A; Sarkar, Urmimala; Schillinger, Dean

2018-04-06

Clinicians have difficulty accurately assessing medication non-adherence within chronic disease care settings. Health information technology (HIT) could offer novel tools to assess medication adherence in diverse populations outside of usual health care settings. In a multilingual urban safety net population, we examined the validity of assessing adherence using automated telephone self-management (ATSM) queries, when compared with non-adherence using continuous medication gap (CMG) on pharmacy claims. We hypothesized that patients reporting greater days of missed pills to ATSM queries would have higher rates of non-adherence as measured by CMG, and that ATSM adherence assessments would perform as well as structured interview assessments. As part of an ATSM-facilitated diabetes self-management program, low-income health plan members typed numeric responses to rotating weekly ATSM queries: "In the last 7 days, how many days did you MISS taking your …" diabetes, blood pressure, or cholesterol pill. Research assistants asked similar questions in computer-assisted structured telephone interviews. We measured continuous medication gap (CMG) by claims over 12 preceding months. To evaluate convergent validity, we compared rates of optimal adherence (CMG ≤ 20%) across respondents reporting 0, 1, and ≥ 2 missed pill days on ATSM and on structured interview. Among 210 participants, 46% had limited health literacy, 57% spoke Cantonese, and 19% Spanish. ATSM respondents reported ≥1 missed day for diabetes (33%), blood pressure (19%), and cholesterol (36%) pills. Interview respondents reported ≥1 missed day for diabetes (28%), blood pressure (21%), and cholesterol (26%) pills. Optimal adherence rates by CMG were lower among ATSM respondents reporting more missed days for blood pressure (p = 0.02) and cholesterol (p < 0.01); by interview, differences were significant for cholesterol (p = 0.01). Language-concordant ATSM demonstrated modest potential for assessing adherence. Studies should evaluate HIT assessments of medication beliefs and concerns in diverse populations. NCT00683020 , registered May 21, 2008.
Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity.

PubMed

Rodriguez-R, Luis M; Gunturu, Santosh; Tiedje, James M; Cole, James R; Konstantinidis, Konstantinos T

2018-01-01

Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Here, we extend Nonpareil, a database-independent tool for the estimation of coverage in metagenomic data sets, to a high-performance computing implementation that scales up to hundreds of cores and includes, in addition, a k -mer-based estimation as sensitive as the original alignment-based version but about three hundred times as fast. Further, we propose a metric of sequence diversity ( N d ) derived directly from Nonpareil curves that correlates well with alpha diversity assessed by traditional metrics. We use this metric in different experiments demonstrating the correlation with the Shannon index estimated on 16S rRNA gene profiles and show that N d additionally reveals seasonal patterns in marine samples that are not captured by the Shannon index and more precise rankings of the magnitude of diversity of microbial communities in different habitats. Therefore, the new version of Nonpareil, called Nonpareil 3, advances the toolbox for metagenomic analyses of microbiomes. IMPORTANCE Estimation of the coverage provided by a metagenomic data set, i.e., what fraction of the microbial community was sampled by DNA sequencing, represents an essential first step of every culture-independent genomic study that aims to robustly assess the sequence diversity present in a sample. However, estimation of coverage remains elusive because of several technical limitations associated with high computational requirements and limiting statistical approaches to quantify diversity. Here we described Nonpareil 3, a new bioinformatics algorithm that circumvents several of these limitations and thus can facilitate culture-independent studies in clinical or environmental settings, independent of the sequencing platform employed. In addition, we present a new metric of sequence diversity based on rarefied coverage and demonstrate its use in communities from diverse ecosystems.
A thorough experimental study of CH/π interactions in water: quantitative structure-stability relationships for carbohydrate/aromatic complexes.

PubMed

Jiménez-Moreno, Ester; Jiménez-Osés, Gonzalo; Gómez, Ana M; Santana, Andrés G; Corzana, Francisco; Bastida, Agatha; Jiménez-Barbero, Jesus; Asensio, Juan Luis

2015-11-13

CH/π interactions play a key role in a large variety of molecular recognition processes of biological relevance. However, their origins and structural determinants in water remain poorly understood. In order to improve our comprehension of these important interaction modes, we have performed a quantitative experimental analysis of a large data set comprising 117 chemically diverse carbohydrate/aromatic stacking complexes, prepared through a dynamic combinatorial approach recently developed by our group. The obtained free energies provide a detailed picture of the structure-stability relationships that govern the association process, opening the door to the rational design of improved carbohydrate-based ligands or carbohydrate receptors. Moreover, this experimental data set, supported by quantum mechanical calculations, has contributed to the understanding of the main driving forces that promote complex formation, underlining the key role played by coulombic and solvophobic forces on the stabilization of these complexes. This represents the most quantitative and extensive experimental study reported so far for CH/π complexes in water.
RE-AIM in Clinical, Community, and Corporate Settings: Perspectives, Strategies, and Recommendations to Enhance Public Health Impact

PubMed Central

Harden, Samantha M.; Smith, Matthew Lee; Ory, Marcia G.; Smith-Ray, Renae L.; Estabrooks, Paul A.; Glasgow, Russell E.

2018-01-01

The RE-AIM Framework is a planning and evaluation model that has been used in a variety of settings to address various programmatic, environmental, and policy innovations for improving population health. In addition to the broad application and diverse use of the framework, there are lessons learned and recommendations for the future use of the framework across clinical, community, and corporate settings. The purposes of this article are to: (A) provide a brief overview of the RE-AIM Framework and its pragmatic use for planning and evaluation; (B) offer recommendations to facilitate the application of RE-AIM in clinical, community, and corporate settings; and (C) share perspectives and lessons learned about employing RE-AIM dimensions in the planning, implementation, and evaluation phases within these different settings. In this article, we demonstrate how the RE-AIM concepts and elements within each dimension can be applied by researchers and practitioners in diverse settings, among diverse populations and for diverse health topics. PMID:29623270
10 CFR 960.3-1-1 - Diversity of geohydrologic settings.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false Diversity of geohydrologic settings. 960.3-1-1 Section 960.3-1-1 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-1 Diversity of geohydrologic...
10 CFR 960.3-1-1 - Diversity of geohydrologic settings.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false Diversity of geohydrologic settings. 960.3-1-1 Section 960.3-1-1 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-1 Diversity of geohydrologic...
10 CFR 960.3-1-1 - Diversity of geohydrologic settings.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Diversity of geohydrologic settings. 960.3-1-1 Section 960.3-1-1 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-1 Diversity of geohydrologic...
10 CFR 960.3-1-1 - Diversity of geohydrologic settings.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false Diversity of geohydrologic settings. 960.3-1-1 Section 960.3-1-1 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-1 Diversity of geohydrologic...
Improvement of Predictive Ability by Uniform Coverage of the Target Genetic Space

PubMed Central

Bustos-Korts, Daniela; Malosetti, Marcos; Chapman, Scott; Biddulph, Ben; van Eeuwijk, Fred

2016-01-01

Genome-enabled prediction provides breeders with the means to increase the number of genotypes that can be evaluated for selection. One of the major challenges in genome-enabled prediction is how to construct a training set of genotypes from a calibration set that represents the target population of genotypes, where the calibration set is composed of a training and validation set. A random sampling protocol of genotypes from the calibration set will lead to low quality coverage of the total genetic space by the training set when the calibration set contains population structure. As a consequence, predictive ability will be affected negatively, because some parts of the genotypic diversity in the target population will be under-represented in the training set, whereas other parts will be over-represented. Therefore, we propose a training set construction method that uniformly samples the genetic space spanned by the target population of genotypes, thereby increasing predictive ability. To evaluate our method, we constructed training sets alongside with the identification of corresponding genomic prediction models for four genotype panels that differed in the amount of population structure they contained (maize Flint, maize Dent, wheat, and rice). Training sets were constructed using uniform sampling, stratified-uniform sampling, stratified sampling and random sampling. We compared these methods with a method that maximizes the generalized coefficient of determination (CD). Several training set sizes were considered. We investigated four genomic prediction models: multi-locus QTL models, GBLUP models, combinations of QTL and GBLUPs, and Reproducing Kernel Hilbert Space (RKHS) models. For the maize and wheat panels, construction of the training set under uniform sampling led to a larger predictive ability than under stratified and random sampling. The results of our methods were similar to those of the CD method. For the rice panel, all training set construction methods led to similar predictive ability, a reflection of the very strong population structure in this panel. PMID:27672112
Conformational diversity analysis reveals three functional mechanisms in proteins

PubMed Central

Fornasari, María Silvina

2017-01-01

Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein. This procedure allowed us to describe the RMSD distribution in terms of three main protein classes sharing given properties. The largest of these protein subsets (~60%), which we call “rigid” (average RMSD = 0.83 Å), has no disordered regions, shows low conformational diversity, the largest tunnels and smaller and buried cavities. The two additional subsets contain disordered regions, but with differential sequence composition and behaviour. Partially disordered proteins have on average 67% of their conformers with disordered regions, average RMSD = 1.1 Å, the highest number of hinges and the longest disordered regions. In contrast, malleable proteins have on average only 25% of disordered conformers and average RMSD = 1.3 Å, flexible cavities affected in size by the presence of disordered regions and show the highest diversity of cognate ligands. Proteins in each set are mostly non-homologous to each other, share no given fold class, nor functional similarity but do share features derived from their conformer population. These shared features could represent conformational mechanisms related with biological functions. PMID:28192432
Prediction in Ungauged Basins (PUB) for estimating water availability during water scarcity conditions: rainfall-runoff modelling of the ungauged diversion inflows to the Ridracoli water supply reservoir

NASA Astrophysics Data System (ADS)

Toth, Elena

2013-04-01

The Ridracoli reservoir is the main drinking water supply reservoir serving the whole Romagna region, in Northern Italy. Such water supply system has a crucial role in an area where the different characteristics of the communities to be served, their size, the mass tourism and the presence of food industries highlight strong differences in drinking water needs. Its operation allows high quality drinking water supply to a million resident customers, plus a few millions of tourists during the summer of people and it reduces the need for water pumping from underground sources, and this is particularly important since the coastal area is subject also to subsidence and saline ingression into aquifers. The system experienced water shortage conditions thrice in the last decade, in 2002, in 2007 and in autumn-winter 2011-2012, when the reservoir water storage fell below the attention and the pre-emergency thresholds, thus prompting the implementation of a set of mitigation measures, including limitations to the population's water consumption. The reservoir receives water not only from the headwater catchment, closed at the dam, but also from four diversion watersheds, linked to the reservoir through an underground water channel. Such withdrawals are currently undersized, abstracting only a part of the streamflow exceeding the established minimum flows, due to the design of the water intake structures; it is therefore crucial understanding how the reservoir water availability might be increased through a fuller exploitation of the existing diversion catchment area. Since one of the four diversion catchment is currently ungauged (at least at the fine temporal scale needed for keeping into account the minimum flow requirements downstream of the intakes), the study first presents the set up and parameterisation of a continuous rainfall-runoff model at hourly time-step for the three gauged diversion watersheds and for the headwater catchment: a regional parameterisation approach is then applied for modelling the streamflow originated in the fourth, ungauged, diversion watershed. Finally, the potential reservoir water availability is estimated, hypothesising to take from the diversion catchments all the streamflow exceeding the minimum flow requirements. The results indicate that modifying the water intake structures might allow a consistent increase in the storage volumes in the reservoir during the water scarcity periods: the water available to the reservoir would in fact - on average - increase of around the 13% of the abstracted annual volume.
Admixture in Latin America.

PubMed

Adhikari, Kaustubh; Mendoza-Revilla, Javier; Chacón-Duque, Juan Camilo; Fuentes-Guajardo, Macarena; Ruiz-Linares, Andrés

2016-12-01

Latin Americans arguably represent the largest recently admixed populations in the world. This reflects a history of massive settlement by immigrants (mostly Europeans and Africans) and their variable admixture with Natives, starting in 1492. This process resulted in the population of Latin America showing an extensive genetic and phenotypic diversity. Here we review how genetic analyses are being applied to examine the demographic history of this population, including patterns of mating, population structure and ancestry. The admixture history of Latin America, and the resulting extensive diversity of the region, represents a natural experiment offering an advantageous setting for genetic association studies. We review how recent analyses in Latin Americans are contributing to elucidating the genetic architecture of human complex traits. Copyright © 2016 Elsevier Ltd. All rights reserved.
BRIEF-REPORT New set of microsatellites for Chinese tallow tree, Triadica sebifera.

PubMed

Zhuang, Y F; Wang, Z F; Wu, L F

2017-04-05

Chinese tallow (Triadica sebifera) is an important crop and ornamental tree. After it was introduced into the USA, it gradually became a noxious invasive tree in south-eastern America since the middle of the 1900s. Because only six microsatellites were reported previously in T. sebifera, to better understand the genetic diversity and population dynamics of such species, we reported here 28 new microsatellite markers. For these 28 microsatellites, the number of alleles per locus ranged from 2-16. The expected heterozygosity and the expected heterozygosity corrected for sample size varied from 0.0796 to 0.9081 and from 0.0805 to 0.9176, respectively. These microsatellites will provide additional choice to investigate the genetic diversity and structure in T. sebifera.

Aging and Family Life: A Decade Review

PubMed Central

Silverstein, Merril; Giarrusso, Roseann

2010-01-01

In this review, we summarize and critically evaluate the major empirical, conceptual, and theoretical directions that studies of aging families have taken during the first decade of the 21st century. The field has benefited from an expanded perspective based on four overarching themes: (a) complexity in emotional relations, (b) diversity in family structures and households, (c) interdependence of family roles and functions, and (d) patterns and outcomes of caregiving. Although research on aging families has advanced theory and applied innovative statistical techniques, the literature has fallen short in fully representing diverse populations and in applying the broadest set of methodological tools available. We discuss these and other frontier areas of scholarship in light of the aging of baby boomers and their families. PMID:22930600
Diversity Surveys and Evolutionary Relationships of aoxB Genes in Aerobic Arsenite-Oxidizing Bacteria▿ †

PubMed Central

Quéméneur, Marianne; Heinrich-Salmeron, Audrey; Muller, Daniel; Lièvremont, Didier; Jauzein, Michel; Bertin, Philippe N.; Garrido, Francis; Joulian, Catherine

2008-01-01

A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria-, Betaproteobacteria-, and Gammaproteobacteria-related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers. PMID:18502920
Computational modeling-based discovery of novel classes of anti-inflammatory drugs that target lanthionine synthetase C-like protein 2.

PubMed

Lu, Pinyi; Hontecillas, Raquel; Horne, William T; Carbo, Adria; Viladomiu, Monica; Pedragosa, Mireia; Bevan, David R; Lewis, Stephanie N; Bassaganya-Riera, Josep

2012-01-01

Lanthionine synthetase component C-like protein 2 (LANCL2) is a member of the eukaryotic lanthionine synthetase component C-Like protein family involved in signal transduction and insulin sensitization. Recently, LANCL2 is a target for the binding and signaling of abscisic acid (ABA), a plant hormone with anti-diabetic and anti-inflammatory effects. The goal of this study was to determine the role of LANCL2 as a potential therapeutic target for developing novel drugs and nutraceuticals against inflammatory diseases. Previously, we performed homology modeling to construct a three-dimensional structure of LANCL2 using the crystal structure of lanthionine synthetase component C-like protein 1 (LANCL1) as a template. Using this model, structure-based virtual screening was performed using compounds from NCI (National Cancer Institute) Diversity Set II, ChemBridge, ZINC natural products, and FDA-approved drugs databases. Several potential ligands were identified using molecular docking. In order to validate the anti-inflammatory efficacy of the top ranked compound (NSC61610) in the NCI Diversity Set II, a series of in vitro and pre-clinical efficacy studies were performed using a mouse model of dextran sodium sulfate (DSS)-induced colitis. Our findings showed that the lead compound, NSC61610, activated peroxisome proliferator-activated receptor gamma in a LANCL2- and adenylate cyclase/cAMP dependent manner in vitro and ameliorated experimental colitis by down-modulating colonic inflammatory gene expression and favoring regulatory T cell responses. LANCL2 is a novel therapeutic target for inflammatory diseases. High-throughput, structure-based virtual screening is an effective computational-based drug design method for discovering anti-inflammatory LANCL2-based drug candidates.
Computational Modeling-Based Discovery of Novel Classes of Anti-Inflammatory Drugs That Target Lanthionine Synthetase C-Like Protein 2

PubMed Central

Lu, Pinyi; Hontecillas, Raquel; Horne, William T.; Carbo, Adria; Viladomiu, Monica; Pedragosa, Mireia; Bevan, David R.; Lewis, Stephanie N.; Bassaganya-Riera, Josep

2012-01-01

Background Lanthionine synthetase component C-like protein 2 (LANCL2) is a member of the eukaryotic lanthionine synthetase component C-Like protein family involved in signal transduction and insulin sensitization. Recently, LANCL2 is a target for the binding and signaling of abscisic acid (ABA), a plant hormone with anti-diabetic and anti-inflammatory effects. Methodology/Principal Findings The goal of this study was to determine the role of LANCL2 as a potential therapeutic target for developing novel drugs and nutraceuticals against inflammatory diseases. Previously, we performed homology modeling to construct a three-dimensional structure of LANCL2 using the crystal structure of lanthionine synthetase component C-like protein 1 (LANCL1) as a template. Using this model, structure-based virtual screening was performed using compounds from NCI (National Cancer Institute) Diversity Set II, ChemBridge, ZINC natural products, and FDA-approved drugs databases. Several potential ligands were identified using molecular docking. In order to validate the anti-inflammatory efficacy of the top ranked compound (NSC61610) in the NCI Diversity Set II, a series of in vitro and pre-clinical efficacy studies were performed using a mouse model of dextran sodium sulfate (DSS)-induced colitis. Our findings showed that the lead compound, NSC61610, activated peroxisome proliferator-activated receptor gamma in a LANCL2- and adenylate cyclase/cAMP dependent manner in vitro and ameliorated experimental colitis by down-modulating colonic inflammatory gene expression and favoring regulatory T cell responses. Conclusions/Significance LANCL2 is a novel therapeutic target for inflammatory diseases. High-throughput, structure-based virtual screening is an effective computational-based drug design method for discovering anti-inflammatory LANCL2-based drug candidates. PMID:22509338
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

PubMed

Honsa, Erin; Fricke, Thomas; Stephens, Alex J; Ko, Danny; Kong, Fanrong; Gilbert, Gwendolyn L; Huygens, Flavia; Giffard, Philip M

2008-08-19

Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, particularly of newborns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP) based method for assigning GBS isolates to multilocus sequence typing (MLST)-defined clonal complexes. It was found that a SNP set derived from the MLST database on the basis of maximization of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinically significant clonal complex 17 to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates. A five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required.
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms

PubMed Central

Honsa, Erin; Fricke, Thomas; Stephens, Alex J; Ko, Danny; Kong, Fanrong; Gilbert, Gwendolyn L; Huygens, Flavia; Giffard, Philip M

2008-01-01

Background Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, particularly of newborns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP) based method for assigning GBS isolates to multilocus sequence typing (MLST)-defined clonal complexes. Results It was found that a SNP set derived from the MLST database on the basis of maximisation of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinically significant clonal complex 17 to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates. Conclusion A five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required. PMID:18710585
Unity and diversity in human language

PubMed Central

Fitch, W. Tecumseh

2011-01-01

Human language is both highly diverse—different languages have different ways of achieving the same functional goals—and easily learnable. Any language allows its users to express virtually any thought they can conceptualize. These traits render human language unique in the biological world. Understanding the biological basis of language is thus both extremely challenging and fundamentally interesting. I review the literature on linguistic diversity and language universals, suggesting that an adequate notion of ‘formal universals’ provides a promising way to understand the facts of language acquisition, offering order in the face of the diversity of human languages. Formal universals are cross-linguistic generalizations, often of an abstract or implicational nature. They derive from cognitive capacities to perceive and process particular types of structures and biological constraints upon integration of the multiple systems involved in language. Such formal universals can be understood on the model of a general solution to a set of differential equations; each language is one particular solution. An explicit formal conception of human language that embraces both considerable diversity and underlying biological unity is possible, and fully compatible with modern evolutionary theory. PMID:21199842
Enabling Large-Scale Design, Synthesis and Validation of Small Molecule Protein-Protein Antagonists

PubMed Central

Koes, David; Khoury, Kareem; Huang, Yijun; Wang, Wei; Bista, Michal; Popowicz, Grzegorz M.; Wolf, Siglinde; Holak, Tad A.; Dömling, Alexander; Camacho, Carlos J.

2012-01-01

Although there is no shortage of potential drug targets, there are only a handful known low-molecular-weight inhibitors of protein-protein interactions (PPIs). One problem is that current efforts are dominated by low-yield high-throughput screening, whose rigid framework is not suitable for the diverse chemotypes present in PPIs. Here, we developed a novel pharmacophore-based interactive screening technology that builds on the role anchor residues, or deeply buried hot spots, have in PPIs, and redesigns these entry points with anchor-biased virtual multicomponent reactions, delivering tens of millions of readily synthesizable novel compounds. Application of this approach to the MDM2/p53 cancer target led to high hit rates, resulting in a large and diverse set of confirmed inhibitors, and co-crystal structures validate the designed compounds. Our unique open-access technology promises to expand chemical space and the exploration of the human interactome by leveraging in-house small-scale assays and user-friendly chemistry to rationally design ligands for PPIs with known structure. PMID:22427896
Assessing Patient Activation among High-Need, High-Cost Patients in Urban Safety Net Care Settings.

PubMed

Napoles, Tessa M; Burke, Nancy J; Shim, Janet K; Davis, Elizabeth; Moskowitz, David; Yen, Irene H

2017-12-01

We sought to examine the literature using the Patient Activation Measure (PAM) or the Patient Enablement Instrument (PEI) with high-need, high-cost (HNHC) patients receiving care in urban safety net settings. Urban safety net care management programs serve low-income, racially/ethnically diverse patients living with multiple chronic conditions. Although many care management programs track patient progress with the PAM or the PEI, it is not clear whether the PAM or the PEI is an effective and appropriate tool for HNHC patients receiving care in urban safety net settings in the United States. We searched PubMed, EMBASE, Web of Science, and PsycINFO for articles published between 2004 and 2015 that used the PAM and between 1998 and 2015 that used the PEI. The search was limited to English-language articles conducted in the United States and published in peer-reviewed journals. To assess the utility of the PAM and the PEI in urban safety net care settings, we defined a HNHC patient sample as racially/ethnically diverse, low socioeconomic status (SES), and multimorbid. One hundred fourteen articles used the PAM. All articles using the PEI were conducted outside the U.S. and therefore were excluded. Nine PAM studies (8%) included participants similar to those receiving care in urban safety net settings, three of which were longitudinal. Two of the three longitudinal studies reported positive changes following interventions. Our results indicate that research on patient activation is not commonly conducted on racially and ethnically diverse, low SES, and multimorbid patients; therefore, there are few opportunities to assess the appropriateness of the PAM in such populations. Investigators expressed concerns with the potential unreliability and inappropriate nature of the PAM on multimorbid, older, and low-literacy patients. Thus, the PAM may not be able to accurately assess patient progress among HNHC patients receiving care in urban safety net settings. Assessing progress in the urban safety net care setting requires measures that account for the social and structural challenges and competing demands of HNHC patients.
Ultra-Structure database design methodology for managing systems biology data and analyses

PubMed Central

Maier, Christopher W; Long, Jeffrey G; Hemminger, Bradley M; Giddings, Morgan C

2009-01-01

Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping). Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find Ultra-Structure offers substantial benefits for biological information systems, the largest being the integration of diverse information sources into a common framework. This facilitates systems biology research by integrating data from disparate high-throughput techniques. It also enables us to readily incorporate new data types, sources, and domain knowledge with no change to the database structure or associated computer code. Ultra-Structure may be a significant step towards solving the hard problem of data management and integration in the systems biology era. PMID:19691849
Post-Glacial Expansion and Population Genetic Divergence of Mangrove Species Avicennia germinans (L.) Stearn and Rhizophora mangle L. along the Mexican Coast

PubMed Central

Sandoval-Castro, Eduardo; Dodd, Richard S.; Riosmena-Rodríguez, Rafael; Enríquez-Paredes, Luis Manuel; Tovilla-Hernández, Cristian; López-Vivas, Juan Manuel; Aguilar-May, Bily; Muñiz-Salazar, Raquel

2014-01-01

Mangrove forests in the Gulf of California, Mexico represent the northernmost populations along the Pacific coast and thus they are likely to be source populations for colonization at higher latitudes as climate becomes more favorable. Today, these populations are relatively small and fragmented and prior research has indicated that they are poor in genetic diversity. Here we set out to investigate whether the low diversity in this region was a result of recent colonization, or fragmentation and genetic drift of once more extensive mangroves due to climatic changes in the recent past. By sampling the two major mangrove species, Rhizophora mangle and Avicennia germinans, along the Pacific and Atlantic coasts of Mexico, we set out to test whether concordant genetic signals could elucidate recent evolution of the ecosystem. Genetic diversity of both mangrove species showed a decreasing trend toward northern latitudes along the Pacific coast. The lowest levels of genetic diversity were found at the range limits around the Gulf of California and the outer Baja California peninsula. Lack of a strong spatial genetic structure in this area and recent northern gene flow in A. germinans suggest recent colonization by this species. On the other hand, lack of a signal of recent northern dispersal in R. mangle, despite the higher dispersal capability of this species, indicates a longer presence of populations, at least in the southern Gulf of California. We suggest that the longer history, together with higher genetic diversity of R. mangle at the range limits, likely provides a gene pool better able to colonize northwards under climate change than A. germinans. PMID:24699389
Systematic evaluation and optimization of modification reactions of oligonucleotides with amines and carboxylic acids for the synthesis of DNA-encoded chemical libraries.

PubMed

Franzini, Raphael M; Samain, Florent; Abd Elrahman, Maaly; Mikutis, Gediminas; Nauer, Angela; Zimmermann, Mauro; Scheuermann, Jörg; Hall, Jonathan; Neri, Dario

2014-08-20

DNA-encoded chemical libraries are collections of small molecules, attached to DNA fragments serving as identification barcodes, which can be screened against multiple protein targets, thus facilitating the drug discovery process. The preparation of large DNA-encoded chemical libraries crucially depends on the availability of robust synthetic methods, which enable the efficient conjugation to oligonucleotides of structurally diverse building blocks, sharing a common reactive group. Reactions of DNA derivatives with amines and/or carboxylic acids are particularly attractive for the synthesis of encoded libraries, in view of the very large number of building blocks that are commercially available. However, systematic studies on these reactions in the presence of DNA have not been reported so far. We first investigated conditions for the coupling of primary amines to oligonucleotides, using either a nucleophilic attack on chloroacetamide derivatives or a reductive amination on aldehyde-modified DNA. While both methods could be used for the production of secondary amines, the reductive amination approach was generally associated with higher yields and better purity. In a second endeavor, we optimized conditions for the coupling of a diverse set of 501 carboxylic acids to DNA derivatives, carrying primary and secondary amine functions. The coupling efficiency was generally higher for primary amines, compared to secondary amine substituents, but varied considerably depending on the structure of the acids and on the synthetic methods used. Optimal reaction conditions could be found for certain sets of compounds (with conversions >80%), but multiple reaction schemes are needed when assembling large libraries with highly diverse building blocks. The reactions and experimental conditions presented in this article should facilitate the synthesis of future DNA-encoded chemical libraries, while outlining the synthetic challenges that remain to be overcome.
Celebrating Diversity in Early Care and Education Settings: Moving beyond the Margins

ERIC Educational Resources Information Center

Durand, Tina M.

2010-01-01

As the USA continues to live up to its historical reputation as a nation of immigrants, early childhood professionals are increasingly faced with the challenge of supporting children and families from diverse cultural milieu. However, to truly celebrate diversity in early childhood settings, early childhood teachers and caregivers must engage in a…
Tolerance: Woven into the Fabric of the School, or Not?

ERIC Educational Resources Information Center

Pumpian, Ian

2013-01-01

Tolerance must be conceptualized based on the diversity that exists in our world, our communities, and our schools. The author posits that dealing with diversity is a 21st-century skill set and that tolerance of difference is a rudimentary element of that set. The diversity of experiences and situations that confront middle school students and…
Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies

PubMed Central

Edwards, Hannah; Abeln, Sanne; Deane, Charlotte M.

2013-01-01

The evolution of proteins is one of the fundamental processes that has delivered the diversity and complexity of life we see around ourselves today. While we tend to define protein evolution in terms of sequence level mutations, insertions and deletions, it is hard to translate these processes to a more complete picture incorporating a polypeptide's structure and function. By considering how protein structures change over time we can gain an entirely new appreciation of their long-term evolutionary dynamics. In this work we seek to identify how populations of proteins at different stages of evolution explore their possible structure space. We use an annotation of superfamily age to this space and explore the relationship between these ages and a diverse set of properties pertaining to a superfamily's sequence, structure and function. We note several marked differences between the populations of newly evolved and ancient structures, such as in their length distributions, secondary structure content and tertiary packing arrangements. In particular, many of these differences suggest a less elaborate structure for newly evolved superfamilies when compared with their ancient counterparts. We show that the structural preferences we report are not a residual effect of a more fundamental relationship with function. Furthermore, we demonstrate the robustness of our results, using significant variation in the algorithm used to estimate the ages. We present these age estimates as a useful tool to analyse protein populations. In particularly, we apply this in a comparison of domains containing greek key or jelly roll motifs. PMID:24244135
Diverse microbially induced sedimentary structures from 1 Ga lakes of the Diabaig Formation, Torridon Group, northwest Scotland

NASA Astrophysics Data System (ADS)

Callow, Richard H. T.; Battison, Leila; Brasier, Martin D.

2011-08-01

The siliciclastic lacustrine rocks of the ~ 1000 Ma Diabaig Formation, northwest Scotland, contain a remarkable diversity of macroscopic structures on bedding planes that can be compared with various kinds of microbially induced sedimentary structures (MISS). Field sedimentological investigations, combined with laboratory analysis of bedding planes and petrographic study of thin sections have allowed us to characterise a range of depositional environments and document the spectrum of biological structures. MISS are reported from frequently subaerial environments, through commonly submerged facies, and down to permanently sub-wavebase settings. Palaeoenvironmental conditions (water depth, exposure, hydrodynamic energy) control the distribution of MISS within these facies. This demonstrates that mat-forming microbial communities were arguably well adapted to low light levels or periodic exposure. Some MISS from the Diabaig Formation are typical of Precambrian microbial mats, including reticulate fabrics and 'old elephant skin' textures. In addition to these, a number of new and unusual fabrics of putative microbial origin are described, including linear arrays of ridges and grooves (cf. 'Arumberia') and discoidal structures that are comparable with younger Ediacaran fossils such as Beltanelliformis. These observations indicate that benthic microbial ecosystems were thriving in freshwater lake systems ~ 1000 Ma, and indicate how microbially induced sedimentary structures may be applied as facies indicators for Proterozoic lacustrine environments. The discovery of structures closely resembling Ediacaran fossils (cf. Beltanelliformis) also serves to highlight the difficulty of interpreting simple discoidal bedding plane structures as metazoan fossils.
In silico prediction of nematic transition temperature for liquid crystals using quantitative structure-property relationship approaches.

PubMed

Fatemi, Mohammad Hossein; Ghorbanzad'e, Mehdi

2009-11-01

Quantitative structure-property relationship models for the prediction of the nematic transition temperature (T (N)) were developed by using multilinear regression analysis and a feedforward artificial neural network (ANN). A collection of 42 thermotropic liquid crystals was chosen as the data set. The data set was divided into three sets: for training, and an internal and external test set. Training and internal test sets were used for ANN model development, and the external test set was used for evaluation of the predictive power of the model. In order to build the models, a set of six descriptors were selected by the best multilinear regression procedure of the CODESSA program. These descriptors were: atomic charge weighted partial negatively charged surface area, relative negative charged surface area, polarity parameter/square distance, minimum most negative atomic partial charge, molecular volume, and the A component of moment of inertia, which encode geometrical and electronic characteristics of molecules. These descriptors were used as inputs to ANN. The optimized ANN model had 6:6:1 topology. The standard errors in the calculation of T (N) for the training, internal, and external test sets using the ANN model were 1.012, 4.910, and 4.070, respectively. To further evaluate the ANN model, a crossvalidation test was performed, which produced the statistic Q (2) = 0.9796 and standard deviation of 2.67 based on predicted residual sum of square. Also, the diversity test was performed to ensure the model's stability and prove its predictive capability. The obtained results reveal the suitability of ANN for the prediction of T (N) for liquid crystals using molecular structural descriptors.
Structured populations of Sulfolobus acidocaldarius with susceptibility to mobile genetic elements

USGS Publications Warehouse

Anderson, Rika E.; Kouris, Angela; Seward, Christopher H.; Campbell, Kate M.; Whitaker, Rachel J.

2017-01-01

The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S. acidocaldarius apart from its sister Sulfolobus species. To test this hypothesis, we conducted a comparative analysis of 47 genomes of S. acidocaldarius from spatial and temporal sampling of two hot springs in Yellowstone National Park. While we confirm the low diversity in the core genome, we observe differentiation among S. acidocaldarius populations, likely resulting from low migration among hot spring “islands” in Yellowstone National Park. Patterns of genomic variation indicate that differing geological contexts result in the elimination or preservation of diversity among differentiated populations. We observe multiple deletions associated with a large genomic island rich in glycosyltransferases, differential integrations of the Sulfolobus turreted icosahedral virus, as well as two different plasmid elements. These data demonstrate that neither rapid dispersal nor lack of mobile genetic elements result in low diversity in the S. acidocaldariusgenomes. We suggest instead that significant differences in the recent evolutionary history, or the intrinsic evolutionary rates, of sister Sulfolobusspecies result in the relatively low diversity of the S. acidocaldarius genome.
Genome-Scale Multilocus Microsatellite Typing of Trypanosoma cruzi Discrete Typing Unit I Reveals Phylogeographic Structure and Specific Genotypes Linked to Human Infection

PubMed Central

Llewellyn, Martin S.; Miles, Michael A.; Carrasco, Hernan J.; Lewis, Michael D.; Yeo, Matthew; Vargas, Jorge; Torrico, Faustino; Diosque, Patricio; Valente, Vera; Valente, Sebastiao A.; Gaunt, Michael W.

2009-01-01

Trypanosoma cruzi is the most important parasitic infection in Latin America and is also genetically highly diverse, with at least six discrete typing units (DTUs) reported: Tc I, IIa, IIb, IIc, IId, and IIe. However, the current six-genotype classification is likely to be a poor reflection of the total genetic diversity present in this undeniably ancient parasite. To determine whether epidemiologically important information is “hidden” at the sub-DTU level, we developed a 48-marker panel of polymorphic microsatellite loci to investigate population structure among 135 samples from across the geographic distribution of TcI. This DTU is the major cause of resurgent human disease in northern South America but also occurs in silvatic triatomine vectors and mammalian reservoir hosts throughout the continent. Based on a total dataset of 12,329 alleles, we demonstrate that silvatic TcI populations are extraordinarily genetically diverse, show spatial structuring on a continental scale, and have undergone recent biogeographic expansion into the southern United States of America. Conversely, the majority of human strains sampled are restricted to two distinct groups characterised by a considerable reduction in genetic diversity with respect to isolates from silvatic sources. In Venezuela, most human isolates showed little identity with known local silvatic strains, despite frequent invasion of the domestic setting by infected adult vectors. Multilocus linkage indices indicate predominantly clonal parasite propagation among all populations. However, excess homozygosity among silvatic strains and raised heterozygosity among domestic populations suggest that some level of genetic recombination cannot be ruled out. The epidemiological significance of these findings is discussed. PMID:19412340
Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple (Malus × domestica Borkh.) during development.

PubMed

Schaeffer, Scott M; Christian, Ryan; Castro-Velasquez, Nohely; Hyden, Brennan; Lynch-Holm, Valerie; Dhingra, Amit

2017-10-01

Comparative ultrastructural developmental time-course analysis has identified discrete stages at which the fruit plastids undergo structural and consequently functional transitions to facilitate subsequent development-guided understanding of the complex plastid biology. Plastids are the defining organelle for a plant cell and are critical for myriad metabolic functions. The role of leaf plastid, chloroplast, is extensively documented; however, fruit plastids-chromoplasts-are poorly understood, especially in the context of the diverse metabolic processes operating in these diverse plant organs. Recently, in a comparative study of the predicted plastid-targeted proteomes across seven plant species, we reported that each plant species is predicted to harbor a unique set of plastid-targeted proteins. However, the temporal and developmental context of these processes remains unknown. In this study, an ultrastructural analysis approach was used to characterize fruit plastids in the epidermal and collenchymal cell layers at 11 developmental timepoints in three genotypes of apple (Malus × domestica Borkh.): chlorophyll-predominant 'Granny Smith', carotenoid-predominant 'Golden Delicious', and anthocyanin-predominant 'Top Red Delicious'. Plastids transitioned from a proplastid-like plastid to a chromoplast-like plastid in epidermis cells, while in the collenchyma cells, they transitioned from a chloroplast-like plastid to a chloro-chromo-amyloplast plastid. Plastids in the collenchyma cells of the three genotypes demonstrated a diverse array of structures and features. This study enabled the identification of discrete developmental stages during which specific functions are most likely being performed by the plastids as indicated by accumulation of plastoglobuli, starch granules, and other sub-organeller structures. Information regarding the metabolically active developmental stages is expected to facilitate biologically relevant omics studies to unravel the complex biochemistry of plastids in perennial non-model systems.

[Species, functional, structural diversity of typical plant communities and their responses to environmental factors in Miao Archipelago, China.

PubMed

Zheng, Li Ting; Su, Tian; Liu, Xiang Yu; Yin, Fang; Guo, Chao; Tuo, Bin; Yan, En Rong

2018-02-01

Island vegetation plays an important role in biodiversity research across the world. The study of plant diversity in island is helpful for understanding the mechanism of plant diversity maintenance under land-sea interaction. Here, four typical plant communities (Quercus acutissima community, Robinia pseudoacacia community, Pinus thunbergii community and Vitex negundo community) in Miao Archipelago were selected to examine the species, functional and structural diversities and their responses to environmental factors at the community scale by using species diversity indices, functional diversity indices, as well as structural diversity indices. The results showed that the species richness and Rao index of P. thunbergii community was higher than that of Q. acutissima community and R. pseudoacacia community, but the structural diversity was lower. The species diversity and structural diversity of V. Negundo shrub were lower than that of forest community, but the functional diversity was higher than some forest communities. The relationship between the diversity of typical plant communities in island area illustrated a significant positive correlation between species richness with Rao index and tree height diversity, however the correlation with functional evenness was significantly negative. The structural diversity and functional evenness were determined by slope with negative and positive relationships, respectively. Functional heterogeneity, functional divergence and species diversity were affected largely by soil physical and chemical properties, displaying the positive relationship with soil bulk density and soil total carbon content, and a negative relationship with soil water content. In conclusion, diversity pattern of plant community in Miao Archipelago reflected not only the characteristics in mainland vegetation but also the special nature of the sea island.
Iterative Refinement of a Binding Pocket Model: Active Computational Steering of Lead Optimization

PubMed Central

2012-01-01

Computational approaches for binding affinity prediction are most frequently demonstrated through cross-validation within a series of molecules or through performance shown on a blinded test set. Here, we show how such a system performs in an iterative, temporal lead optimization exercise. A series of gyrase inhibitors with known synthetic order formed the set of molecules that could be selected for “synthesis.” Beginning with a small number of molecules, based only on structures and activities, a model was constructed. Compound selection was done computationally, each time making five selections based on confident predictions of high activity and five selections based on a quantitative measure of three-dimensional structural novelty. Compound selection was followed by model refinement using the new data. Iterative computational candidate selection produced rapid improvements in selected compound activity, and incorporation of explicitly novel compounds uncovered much more diverse active inhibitors than strategies lacking active novelty selection. PMID:23046104
Interconnected microbiomes and resistomes in low-income human habitats

PubMed Central

Pehrsson, Erica C.; Tsukayama, Pablo; Patel, Sanket; Mejía-Bautista, Melissa; Sosa-Soto, Giordano; Navarrete, Karla M.; Calderon, Maritza; Cabrera, Lilia; Hoyos-Arango, William; Bertoli, M. Teresita; Berg, Douglas E.; Gilman, Robert H.; Dantas, Gautam

2016-01-01

Summary Antibiotic-resistant infections annually claim hundreds of thousands of lives worldwide. This problem is exacerbated by resistance gene exchange between pathogens and benign microbes from diverse habitats. Mapping resistance gene dissemination between humans and their environment is a public health priority. We characterized the bacterial community structure and resistance exchange networks of hundreds of interconnected human fecal and environmental samples from two low-income Latin American communities. We found that resistomes across habitats are generally structured by bacterial phylogeny along ecological gradients, but identified key resistance genes that cross habitat boundaries and determined their association with mobile genetic elements. We also assessed the effectiveness of widely-used excreta management strategies in reducing fecal bacteria and resistance genes in these settings representative of low- and middle-income countries. Our results lay the foundation for quantitative risk assessment and surveillance of resistance dissemination across interconnected habitats in settings representing over two-thirds of the world’s population. PMID:27172044
Higher agrobiodiversity is associated with improved dietary diversity, but not child anthropometric status, of Mayan Achí people of Guatemala.

PubMed

Luna-González, Diana V; Sørensen, Marten

2018-04-03

Child undernutrition remains one of the greatest challenges for public health nutrition in rural areas in developing countries. Interventions aiming to increase and conserve agrobiodiversity seem to be promising alternatives to improve child nutrition. However, the existing literature on these interventions is not conclusive about their effectiveness in combating child undernutrition. We tested the hypothesis that 'higher agrobiodiversity is associated with greater dietary diversity and better anthropometric status' in rural Guatemala.Design/Setting/SubjectsIn the summer of 2016, we conducted a cross-sectional study with a sample of 154 children (6-60 months). We conducted dietary recalls and structured interviews, measured children's weight and height, and visited food production systems (Milpas, home gardens, coffee plantations). Crop species richness, nutritional functional diversity, dietary diversity scores and anthropometric status were calculated. Higher food self-sufficiency, nutritional functional diversity and dietary diversity scores were positively correlated with higher crop and animal species richness. Contrarily, remoteness to the local market was negatively correlated with dietary diversity scores. However, higher dietary diversity scores were not correlated with better child anthropometric status. Better child anthropometric status was positively correlated with improved sanitary conditions and maternal education; and negatively correlated with large household size and frequent child morbidity. Agricultural diversification could diversify diets, increase nutrient availability and improve child anthropometry. However, these interventions need to be accompanied by sanitation improvements, family planning, nutritional education and women's empowerment to strengthen their positive effect on diet and nutrition.
Phylogenetic diversity and biodiversity indices on phylogenetic networks.

PubMed

Wicke, Kristina; Fischer, Mareike

2018-04-01

In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species according to their contribution to overall phylogenetic diversity. However, in many cases evolution is not treelike and thus, phylogenetic networks have been developed as a generalization of phylogenetic trees, allowing for the representation of non-treelike evolutionary events, such as hybridization. Here, we extend the concepts of phylogenetic diversity and phylogenetic diversity indices from phylogenetic trees to phylogenetic networks. On the one hand, we consider the treelike content of a phylogenetic network, e.g. the (multi)set of phylogenetic trees displayed by a network and the so-called lowest stable ancestor tree associated with it. On the other hand, we derive the phylogenetic diversity of subsets of taxa and biodiversity indices directly from the internal structure of the network. We consider both approaches that are independent of so-called inheritance probabilities as well as approaches that explicitly incorporate these probabilities. Furthermore, we introduce our software package NetDiversity, which is implemented in Perl and allows for the calculation of all generalized measures of phylogenetic diversity and generalized phylogenetic diversity indices established in this note that are independent of inheritance probabilities. We apply our methods to a phylogenetic network representing the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by widespread hybridization. Copyright © 2018 Elsevier Inc. All rights reserved.
Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data

PubMed Central

Laidò, Giovanni; Mangini, Giacomo; Taranto, Francesca; Gadaleta, Agata; Blanco, Antonio; Cattivelli, Luigi; Marone, Daniela; Mastrangelo, Anna M.; Papa, Roberto; De Vita, Pasquale

2013-01-01

Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K = 2), both of the sets of molecular markers distinguished the durum wheat cultivars from the other tetraploid subspecies, and two distinct subgroups were detected within the durum wheat subspecies, which is in agreement with their origin and year of release. The genetic diversity of morphological traits and seed storage proteins was always lower in the improved durum cultivars registered after 1990, than in the intermediate and older ones. This marked effect on diversity was not observed for molecular markers, where there was only a weak reduction. At K >2, the SSR markers showed a greater degree of resolution than for DArT, with their identification of a greater number of groups within each subspecies. Analysis of DArT marker differentiation between the wheat subspecies indicated outlier loci that are potentially linked to genes controlling some important agronomic traits. Among the 211 loci identified under selection, 109 markers were recently mapped, and some of these markers were clustered into specific regions on chromosome arms 2BL, 3BS and 4AL, where several genes/quantitative trait loci (QTLs) are involved in the domestication of tetraploid wheats, such as the tenacious glumes (Tg) and brittle rachis (Br) characteristics. On the basis of these results, it can be assumed that the population structure of the tetraploid wheat collection partially reflects the evolutionary history of Triticum turgidum L. subspecies and the genetic potential of landraces and wild accessions for the detection of unexplored alleles. PMID:23826256
AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set.

PubMed

Sorkheh, Karim; Masaeli, Mohammad; Chaleshtori, Maryam Hosseini; Adugna, Asfaw; Ercisli, Sezai

2016-04-01

Analysis of the genetic diversity and population structure of crops is very important for use in breeding programs and for genetic resources conservation. We analyzed the genetic diversity and population structure of 47 rice genotypes from diverse origins using amplified fragment length polymorphism (AFLP) markers and morphological characters. The 47 genotypes, which were composed of four populations: Iranian native varieties, Iranian improved varieties, International Rice Research Institute (IRRI) rice varieties, and world rice collections, were analyzed using ten primer combinations. A total of 221 scorable bands were produced with an average of 22.1 alleles per pair of primers, of which 120 (54.30%) were polymorphic. The polymorphism information content (PIC) values varied from 0.32 to 0.41 with an average of 0.35. The high percentage of polymorphic bands (%PB) was found to be 64.71 and the resolving power (R p) collections were 63.36. UPGMA clustering based on numerical data from AFLP patterns clustered all 47 genotypes into three large groups. The genetic similarity between individuals ranged from 0.54 to 0.94 with an average of 0.74. Population genetic tree showed that Iranian native cultivars formed far distant cluster from the other populations, which may indicate that these varieties had minimal genetic change over time. Analysis of molecular variance (AMOVA) revealed that the largest proportion of the variation (84%) to be within populations showing the inbreeding nature of rice. Therefore, Iranian native varieties (landraces) may have unique genes, which can be used for future breeding programs and there is a need to conserve this unique diversity. Furthermore, crossing of Iranian genotypes with the genetically distant genotypes in the other three populations may result in useful combinations, which can be used as varieties and/or lines for future rice breeding programs.
Variations in the structural and functional diversity of zooplankton over vertical and horizontal environmental gradients en route to the Arctic Ocean through the Fram Strait.

PubMed

Gluchowska, Marta; Trudnowska, Emilia; Goszczko, Ilona; Kubiszyn, Anna Maria; Blachowiak-Samolyk, Katarzyna; Walczowski, Waldemar; Kwasniewski, Slawomir

2017-01-01

A multi-scale approach was used to evaluate which spatial gradient of environmental variability is the most important in structuring zooplankton diversity in the West Spitsbergen Current (WSC). The WSC is the main conveyor of warm and biologically rich Atlantic water to the Arctic Ocean through the Fram Strait. The data set included 85 stratified vertical zooplankton samples (obtained from depths up to 1000 metres) covering two latitudinal sections (76°30'N and 79°N) located across the multi-path WSC system. The results indicate that the most important environmental variables shaping the zooplankton structural and functional diversity and standing stock variability are those associated with depth, whereas variables acting in the horizontal dimension are of lesser importance. Multivariate analysis of the zooplankton assemblages, together with different univariate descriptors of zooplankton diversity, clearly illustrated the segregation of zooplankton taxa in the vertical plane. The epipelagic zone (upper 200 m) hosted plentiful, Oithona similis-dominated assemblages with a high proportion of filter-feeding zooplankton. Although total zooplankton abundance declined in the mesopelagic zone (200-1000 m), zooplankton assemblages in that zone were more diverse and more evenly distributed, with high contributions from both herbivorous and carnivorous taxa. The vertical distribution of integrated biomass (mg DW m-2) indicated that the total zooplankton biomass in the epipelagic and mesopelagic zones was comparable. Environmental gradients acting in the horizontal plane, such as the ones associated with different ice cover and timing of the spring bloom, were reflected in the latitudinal variability in protist community structure and probably caused differences in succession in the zooplankton community. High abundances of Calanus finmarchicus in the WSC core branch suggest the existence of mechanisms advantageous for higher productivity or/and responsible for physical concentration of zooplankton. Our results indicate that regional hydrography plays a primary role in shaping zooplankton variability in the WSC on the way to the Arctic Ocean, with additional effects caused by biological factors related to seasonality in pelagic ecosystem development, resulting in regional differences in food availability or biological production between the continental slope and the deep ocean regions.
Global genetic diversity of the Plasmodium vivax transmission-blocking vaccine candidate Pvs48/45.

PubMed

Vallejo, Andres F; Martinez, Nora L; Tobon, Alejandra; Alger, Jackeline; Lacerda, Marcus V; Kajava, Andrey V; Arévalo-Herrera, Myriam; Herrera, Sócrates

2016-04-12

Plasmodium vivax 48/45 protein is expressed on the surface of gametocytes/gametes and plays a key role in gamete fusion during fertilization. This protein was recently expressed in Escherichia coli host as a recombinant product that was highly immunogenic in mice and monkeys and induced antibodies with high transmission-blocking activity, suggesting its potential as a P. vivax transmission-blocking vaccine candidate. To determine sequence polymorphism of natural parasite isolates and its potential influence on the protein structure, all pvs48/45 sequences reported in databases from around the world as well as those from low-transmission settings of Latin America were compared. Plasmodium vivax parasite isolates from malaria-endemic regions of Colombia, Brazil and Honduras (n = 60) were used to sequence the Pvs48/45 gene, and compared to those previously reported to GenBank and PlasmoDB (n = 222). Pvs48/45 gene haplotypes were analysed to determine the functional significance of genetic variation in protein structure and vaccine potential. Nine non-synonymous substitutions (E35K, Y196H, H211N, K250N, D335Y, E353Q, A376T, K390T, K418R) and three synonymous substitutions (I73, T149, C156) that define seven different haplotypes were found among the 282 isolates from nine countries when compared with the Sal I reference sequence. Nucleotide diversity (π) was 0.00173 for worldwide samples (range 0.00033-0.00216), resulting in relatively high diversity in Myanmar and Colombia, and low diversity in Mexico, Peru and South Korea. The two most frequent substitutions (E353Q: 41.9 %, K250N: 39.5 %) were predicted to be located in antigenic regions without affecting putative B cell epitopes or the tertiary protein structure. There is limited sequence polymorphism in pvs48/45 with noted geographical clustering among Asian and American isolates. The low genetic diversity of the protein does not influence the predicted antigenicity or protein structure and, therefore, supports its further development as transmission-blocking vaccine candidate.
Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources.

PubMed

Matheus Carnevali, Paula B; Herbold, Craig W; Hand, Kevin P; Priscu, John C; Murray, Alison E

2018-01-01

Developing a microbial ecological understanding of Arctic thermokarst lake sediments in a geochemical context is an essential first step toward comprehending the contributions of these systems to greenhouse gas emissions, and understanding how they may shift as a result of long term changes in climate. In light of this, we set out to study microbial diversity and structure in sediments from four shallow thermokarst lakes in the Arctic Coastal Plain of Alaska. Sediments from one of these lakes (Sukok) emit methane (CH 4 ) of thermogenic origin, as expected for an area with natural gas reserves. However, sediments from a lake 10 km to the North West (Siqlukaq) produce CH 4 of biogenic origin. Sukok and Siqlukaq were chosen among the four lakes surveyed to test the hypothesis that active CH 4 -producing organisms (methanogens) would reflect the distribution of CH 4 gas levels in the sediments. We first examined the structure of the little known microbial community inhabiting the thaw bulb of arctic thermokarst lakes near Barrow, AK. Molecular approaches (PCR-DGGE and iTag sequencing) targeting the SSU rRNA gene and rRNA molecule were used to profile diversity, assemblage structure, and identify potentially active members of the microbial assemblages. Overall, the potentially active (rRNA dominant) fraction included taxa that have also been detected in other permafrost environments (e.g., Bacteroidetes, Actinobacteria, Nitrospirae, Chloroflexi, and others). In addition, Siqlukaq sediments were unique compared to the other sites, in that they harbored CH 4 -cycling organisms (i.e., methanogenic Archaea and methanotrophic Bacteria), as well as bacteria potentially involved in N cycling (e.g., Nitrospirae) whereas Sukok sediments were dominated by taxa typically involved in photosynthesis and biogeochemical sulfur (S) transformations. This study revealed a high degree of archaeal phylogenetic diversity in addition to CH 4 -producing archaea, which spanned nearly the phylogenetic extent of currently recognized Archaea phyla (e.g., Euryarchaeota, Bathyarchaeota, Thaumarchaeota, Woesearchaeota, Pacearchaeota, and others). Together these results shed light on expansive bacterial and archaeal diversity in Arctic thermokarst lakes and suggest important differences in biogeochemical potential in contrasting Arctic thermokarst lake sediment ecosystems.
We Are Family: Using Diverse Family Structure Literature with Children

ERIC Educational Resources Information Center

Gilmore, Deanna Peterschick; Bell, Kari

2006-01-01

The structure of the American family has changed over the years. Although the traditional father, mother, child structure still dominates, other family patterns are emerging. In this article the authors present: (1) current statistics relating to diverse family structures; (2) reasons for using diverse family structure literature with children;…
Rogue taxa phenomenon: a biological companion to simulation analysis

PubMed Central

Westover, Kristi M.; Rusinko, Joseph P.; Hoin, Jon; Neal, Matthew

2013-01-01

To provide a baseline biological comparison to simulation study predictions about the frequency of rogue taxa effects, we evaluated the frequency of a rogue taxa effect using viral data sets which differed in diversity. Using a quartet-tree framework, we measured the frequency of a rogue taxa effect in three data sets of increasing genetic variability (within viral serotype, between viral serotype, and between viral family) to test whether the rogue taxa was correlated with the mean sequence diversity of the respective data sets. We found a slight increase in the percentage of rogues as nucleotide diversity increased. Even though the number of rogues increased with diversity, the distribution of the types of rogues (friendly, crazy, or evil) did not depend on the diversity and in the case of the order-level data set the net rogue effect was slightly positive. This study, assessing frequency of the rogue taxa effect using biological data, indicated that simulation studies may over-predict the prevalence of the rogue taxa effect. Further investigations are necessary to understand which types of data sets are susceptible to a negative rogue effect and thus merit the removal of taxa from large phylogenetic reconstructions. PMID:23707704
Rogue taxa phenomenon: a biological companion to simulation analysis.

PubMed

Westover, Kristi M; Rusinko, Joseph P; Hoin, Jon; Neal, Matthew

2013-10-01

To provide a baseline biological comparison to simulation study predictions about the frequency of rogue taxa effects, we evaluated the frequency of a rogue taxa effect using viral data sets which differed in diversity. Using a quartet-tree framework, we measured the frequency of a rogue taxa effect in three data sets of increasing genetic variability (within viral serotype, between viral serotype, and between viral family) to test whether the rogue taxa was correlated with the mean sequence diversity of the respective data sets. We found a slight increase in the percentage of rogues as nucleotide diversity increased. Even though the number of rogues increased with diversity, the distribution of the types of rogues (friendly, crazy, or evil) did not depend on the diversity and in the case of the order-level data set the net rogue effect was slightly positive. This study, assessing frequency of the rogue taxa effect using biological data, indicated that simulation studies may over-predict the prevalence of the rogue taxa effect. Further investigations are necessary to understand which types of data sets are susceptible to a negative rogue effect and thus merit the removal of taxa from large phylogenetic reconstructions. Copyright © 2013 Elsevier Inc. All rights reserved.
DD-PREF: a language for expressing preferences over sets

NASA Technical Reports Server (NTRS)

Wagstaff, Kiri; desJardins, Marie

2005-01-01

We present a representation language, DD-PREF (for Diversity and Depth PREFrences), for specifying the desired diversity and depth of sets of objects where each object is represented as a vector of feature values.
Beyond Serial Founder Effects: The Impact of Admixture and Localized Gene Flow on Patterns of Regional Genetic Diversity.

PubMed

Hunley, Keith L; Cabana, Graciela S

2016-07-01

Geneticists have argued that the linear decay in within-population genetic diversity with increasing geographic distance from East Africa is best explained by a phylogenetic process of repeated founder effects, growth, and isolation. However, this serial founder effect (SFE) process has not yet been adequately vetted against other evolutionary processes that may also affect geospatial patterns of diversity. Additionally, studies of the SFE process have been largely based on a limited 52-population sample. Here, we assess the effects of founder effect, admixture, and localized gene flow processes on patterns of global and regional diversity using a published data set of 645 autosomal microsatellite genotypes from 5,415 individuals in 248 widespread populations. We used a formal tree-fitting approach to explore the role of founder effects. The approach involved fitting global and regional population trees to extant patterns of gene diversity and then systematically examining the deviations in fit. We also informally tested the SFE process using linear models of gene diversity versus waypoint geographic distances from Africa. We tested the role of localized gene flow using partial Mantel correlograms of gene diversity versus geographic distance controlling for the confounding effects of treelike genetic structure. We corroborate previous findings that global patterns of diversity, both within and between populations, are the product of an out-of-Africa SFE process. Within regions, however, diversity within populations is uncorrelated with geographic distance from Africa. Here, patterns of diversity have been largely shaped by recent interregional admixture and secondary range expansions. Our detailed analyses of the pattern of diversity within and between populations reveal that the signatures of different evolutionary processes dominate at different geographic scales. These findings have important implications for recent publications on the biology of race.
Structure and Function of Ephemeral Streams in the Arid and Semiarid Southwest: Implications for Conservation and Management

DTIC Science & Technology

2015-07-24

stream flow, trade-offs were apparent between riparian plant biomass (high at wetter sites) and plant species diversity (high at dry sites with...iv) between wet and dry seasons? Technical Approach. A space-for-time substitution approach was followed in which changes across spatial water...For arthropods, pitfall traps were set during dry and wet seasons in channel, riparian and upland locations in canyon and piedmont reaches to
Bayesian model aggregation for ensemble-based estimates of protein pKa values

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

Gosink, Luke J.; Hogan, Emilie A.; Pulsipher, Trenton C.

2014-03-01

This paper investigates an ensemble-based technique called Bayesian Model Averaging (BMA) to improve the performance of protein amino acid pmore » $$K_a$$ predictions. Structure-based p$$K_a$$ calculations play an important role in the mechanistic interpretation of protein structure and are also used to determine a wide range of protein properties. A diverse set of methods currently exist for p$$K_a$$ prediction, ranging from empirical statistical models to {\\it ab initio} quantum mechanical approaches. However, each of these methods are based on a set of assumptions that have inherent bias and sensitivities that can effect a model's accuracy and generalizability for p$$K_a$$ prediction in complicated biomolecular systems. We use BMA to combine eleven diverse prediction methods that each estimate pKa values of amino acids in staphylococcal nuclease. These methods are based on work conducted for the pKa Cooperative and the pKa measurements are based on experimental work conducted by the Garc{\\'i}a-Moreno lab. Our study demonstrates that the aggregated estimate obtained from BMA outperforms all individual prediction methods in our cross-validation study with improvements from 40-70\\% over other method classes. This work illustrates a new possible mechanism for improving the accuracy of p$$K_a$$ prediction and lays the foundation for future work on aggregate models that balance computational cost with prediction accuracy.« less
Extending systems thinking in planning and evaluation using group concept mapping and system dynamics to tackle complex problems.

PubMed

Hassmiller Lich, Kristen; Urban, Jennifer Brown; Frerichs, Leah; Dave, Gaurav

2017-02-01

Group concept mapping (GCM) has been successfully employed in program planning and evaluation for over 25 years. The broader set of systems thinking methodologies (of which GCM is one), have only recently found their way into the field. We present an overview of systems thinking emerging from a system dynamics (SD) perspective, and illustrate the potential synergy between GCM and SD. As with GCM, participatory processes are frequently employed when building SD models; however, it can be challenging to engage a large and diverse group of stakeholders in the iterative cycles of divergent thinking and consensus building required, while maintaining a broad perspective on the issue being studied. GCM provides a compelling resource for overcoming this challenge, by richly engaging a diverse set of stakeholders in broad exploration, structuring, and prioritization. SD provides an opportunity to extend GCM findings by embedding constructs in a testable hypothesis (SD model) describing how system structure and changes in constructs affect outcomes over time. SD can be used to simulate the hypothesized dynamics inherent in GCM concept maps. We illustrate the potential of the marriage of these methodologies in a case study of BECOMING, a federally-funded program aimed at strengthening the cross-sector system of care for youth with severe emotional disturbances. Copyright Â© 2016 Elsevier Ltd. All rights reserved.
Assembly of Robust Bacterial Microcompartment Shells Using Building Blocks from an Organelle of Unknown Function

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

Lassila, JK; Bernstein, SL; Kinney, JN

Bacterial microconnpartnnents (BMCs) sequester enzymes from the cytoplasmic environment by encapsulation inside a selectively permeable protein shell. Bioinformatic analyses indicate that many bacteria encode BMC clusters of unknown function and with diverse combinations of shell proteins. The genome of the halophilic myxobacterium Haliangium ochraceum encodes one of the most atypical sets of shell proteins in terms of composition and primary structure. We found that microconnpartnnent shells could be purified in high yield when all seven H. ochraceum BMC shell genes were expressed from a synthetic operon in Escherichia coll. These shells differ substantially from previously isolated shell systems in thatmore » they are considerably smaller and more homogeneous, with measured diameters of 39 2 nm. The size and nearly uniform geometry allowed the development of a structural model for the shells composed of 260 hexagonal units and 13 hexagons per icosahedral face. We found that new proteins could be recruited to the shells by fusion to a predicted targeting peptide sequence, setting the stage for the use of these remarkably homogeneous shells for applications such as three-dimensional scaffolding and the construction of synthetic BMCs. Our results demonstrate the value of selecting from the diversity of BMC shell building blocks found in genomic sequence data for the construction of novel compartments. (C) 2014 Elsevier Ltd. All rights reserved.« less
Annotated bibliography of structural equation modelling: technical work.

PubMed

Austin, J T; Wolfle, L M

1991-05-01

Researchers must be familiar with a variety of source literature to facilitate the informed use of structural equation modelling. Knowledge can be acquired through the study of an expanding literature found in a diverse set of publishing forums. We propose that structural equation modelling publications can be roughly classified into two groups: (a) technical and (b) substantive applications. Technical materials focus on the procedures rather than substantive conclusions derived from applications. The focus of this article is the former category; included are foundational/major contributions, minor contributions, critical and evaluative reviews, integrations, simulations and computer applications, precursor and historical material, and pedagogical textbooks. After a brief introduction, we annotate 294 articles in the technical category dating back to Sewall Wright (1921).

Effects of Short-Term Set-Aside Management Practices on Soil Microorganism and Enzyme Activity in China

PubMed Central

Wu, Cifang

2017-01-01

Set-aside farmland can effectively improve the self-rehabilitation of arable soil. Long-term set-asides however cannot satisfy provisionment, therefore the use of short-term set-asides to restore cultivated soil is a better option. Few studies have compared short-term set-aside patterns, and the effects of set-asides on soil microbial community and enzyme enzymes. We analyzed the bacterial structure, microbial biomass carbon/nitrogen and enzyme activity of farmland soil under different set-aside regimes in the Yellow River Delta of China. Bacterial alpha diversity was relatively lower under only irrigation, and farmyard manure applications showed clear advantages. Set-asides should consider their influence on soil organic carbon and nitrogen, which were correlated with microbial community structure. Nitrospira (0.47–1.67%), Acidobacteria Gp6 (8.26–15.91%) and unclassified Burkholderiales (1.50–2.81%) were significantly altered (p < 0.01). Based on functions of these genera, some set-aside patterns led to a relative balance in nitrogen and carbon turnover. Partial treatments showed a deficiency in organic matter. In addition, farmyard manure may lead to the increased consumption of organic matter, with the exception of native plants set-asides. Conventional farming (control group) displayed a significant enzyme activity advantage. Set-aside management practices guided soil microbial communities to different states. Integrated soil microbiota and the content of carbon and nitrogen, native plants with farmyard manure showed an equilibrium state relatively, which would be helpful to improve land quality in the short-term. PMID:28805737
Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families.

PubMed

Reinharz, Vladimir; Soulé, Antoine; Westhof, Eric; Waldispühl, Jérôme; Denise, Alain

2018-05-04

The wealth of the combinatorics of nucleotide base pairs enables RNA molecules to assemble into sophisticated interaction networks, which are used to create complex 3D substructures. These interaction networks are essential to shape the 3D architecture of the molecule, and also to provide the key elements to carry molecular functions such as protein or ligand binding. They are made of organised sets of long-range tertiary interactions which connect distinct secondary structure elements in 3D structures. Here, we present a de novo data-driven approach to extract automatically from large data sets of full RNA 3D structures the recurrent interaction networks (RINs). Our methodology enables us for the first time to detect the interaction networks connecting distinct components of the RNA structure, highlighting their diversity and conservation through non-related functional RNAs. We use a graphical model to perform pairwise comparisons of all RNA structures available and to extract RINs and modules. Our analysis yields a complete catalog of RNA 3D structures available in the Protein Data Bank and reveals the intricate hierarchical organization of the RNA interaction networks and modules. We assembled our results in an online database (http://carnaval.lri.fr) which will be regularly updated. Within the site, a tool allows users with a novel RNA structure to detect automatically whether the novel structure contains previously observed RINs.
Bitter or not? BitterPredict, a tool for predicting taste from chemical structure.

PubMed

Dagan-Wiener, Ayana; Nissim, Ido; Ben Abu, Natalie; Borgonovo, Gigliola; Bassoli, Angela; Niv, Masha Y

2017-09-21

Bitter taste is an innately aversive taste modality that is considered to protect animals from consuming toxic compounds. Yet, bitterness is not always noxious and some bitter compounds have beneficial effects on health. Hundreds of bitter compounds were reported (and are accessible via the BitterDB http://bitterdb.agri.huji.ac.il/dbbitter.php ), but numerous additional bitter molecules are still unknown. The dramatic chemical diversity of bitterants makes bitterness prediction a difficult task. Here we present a machine learning classifier, BitterPredict, which predicts whether a compound is bitter or not, based on its chemical structure. BitterDB was used as the positive set, and non-bitter molecules were gathered from literature to create the negative set. Adaptive Boosting (AdaBoost), based on decision trees machine-learning algorithm was applied to molecules that were represented using physicochemical and ADME/Tox descriptors. BitterPredict correctly classifies over 80% of the compounds in the hold-out test set, and 70-90% of the compounds in three independent external sets and in sensory test validation, providing a quick and reliable tool for classifying large sets of compounds into bitter and non-bitter groups. BitterPredict suggests that about 40% of random molecules, and a large portion (66%) of clinical and experimental drugs, and of natural products (77%) are bitter.
Comparison of macroinvertebrate community structure between two riffle-based sampling protocols in Wyoming, Colorado, and Montana, 2000-2001

USGS Publications Warehouse

Peterson, David A.; Zumberge, Jeremy R.

2006-01-01

Samples of benthic macroinvertebrates were collected side-by-side from riffles at 12 stream sites in Wyoming, Colorado, and Montana during 2000-2001, following protocols established by the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program and the U.S. Environmental Protection Agency Environmental Monitoring and Assessment Program (EMAP). Samples from riffles were collected following NAWQA protocols, using a sampler with 425-micron net mesh-opening size from a total area of 1.25 m2 per sample in multiple riffles. Samples also were collected following EMAP protocols, using a sampler with 500-micron net mesh-opening size from a total area of 0.72 m2 per sample in multiple riffles. The taxonomic identification and enumeration of the samples followed procedures established for each program. Benthic macroinvertebrate community structure was compared between the data sets using individual metrics, a multimetric index, and multivariate analysis. Comparisons between the macroinvertebrate community structures were made after sequentially adjusting both data sets for: (1) ambiguous taxa, (2) taxonomic inconsistencies, and (3) differences in laboratory subsampling. After removal of ambiguous taxa, pair-wise differences in total taxa richness and Ephemeroptera taxa richness were statistically significant (p < 0.05). Differences between the data sets generally were not significant for richness of other taxa, tolerant taxa, semi-voltine taxa, functional feeding groups, diversity, and dominance. Sample scores calculated using the Wyoming Stream Integrity Index were not significantly different between the two data sets. After reconciling both data sets for taxonomic inconsistencies, total taxa richness and Ephemeroptera taxa richness remained significantly different between the data sets. After adjusting the data for differences in laboratory subsampling, the differences in taxa richness were no longer significant. Bray-Curtis similarity coefficients and non-metric multi-dimensional scaling were used to examine macroinvertebrate community structure. Similarity in community structure between sites was affected to a greater extent by taxa reconciliation than by adjustment for subsampling.
Ancient diversity and geographical sub-structuring in African buffalo Theileria parva populations revealed through metagenetic analysis of antigen-encoding loci.

PubMed

Hemmink, Johanneke D; Sitt, Tatjana; Pelle, Roger; de Klerk-Lorist, Lin-Mari; Shiels, Brian; Toye, Philip G; Morrison, W Ivan; Weir, William

2018-03-01

An infection and treatment protocol involving infection with a mixture of three parasite isolates and simultaneous treatment with oxytetracycline is currently used to vaccinate cattle against Theileria parva. While vaccination results in high levels of protection in some regions, little or no protection is observed in areas where animals are challenged predominantly by parasites of buffalo origin. A previous study involving sequencing of two antigen-encoding genes from a series of parasite isolates indicated that this is associated with greater antigenic diversity in buffalo-derived T. parva. The current study set out to extend these analyses by applying high-throughput sequencing to ex vivo samples from naturally infected buffalo to determine the extent of diversity in a set of antigen-encoding genes. Samples from two populations of buffalo, one in Kenya and the other in South Africa, were examined to investigate the effect of geographical distance on the nature of sequence diversity. The results revealed a number of significant findings. First, there was a variable degree of nucleotide sequence diversity in all gene segments examined, with the percentage of polymorphic nucleotides ranging from 10% to 69%. Second, large numbers of allelic variants of each gene were found in individual animals, indicating multiple infection events. Third, despite the observed diversity in nucleotide sequences, several of the gene products had highly conserved amino acid sequences, and thus represent potential candidates for vaccine development. Fourth, although compelling evidence for population differentiation between the Kenyan and South African T. parva parasites was identified, analysis of molecular variance for each gene revealed that the majority of the underlying nucleotide sequence polymorphism was common to both areas, indicating that much of this aspect of genetic variation in the parasite population arose prior to geographic separation. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.
Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota

PubMed Central

Ellegaard, Kirsten M.; Engel, Philipp

2016-01-01

Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities. PMID:27708630
Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota.

PubMed

Ellegaard, Kirsten M; Engel, Philipp

2016-01-01

Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities.
Scaling of phloem structure and optimality of photoassimilate transport in conifer needles.

PubMed

Ronellenfitsch, Henrik; Liesche, Johannes; Jensen, Kaare H; Holbrook, N Michele; Schulz, Alexander; Katifori, Eleni

2015-02-22

The phloem vascular system facilitates transport of energy-rich sugar and signalling molecules in plants, thus permitting long-range communication within the organism and growth of non-photosynthesizing organs such as roots and fruits. The flow is driven by osmotic pressure, generated by differences in sugar concentration between distal parts of the plant. The phloem is an intricate distribution system, and many questions about its regulation and structural diversity remain unanswered. Here, we investigate the phloem structure in the simplest possible geometry: a linear leaf, found, for example, in the needles of conifer trees. We measure the phloem structure in four tree species representing a diverse set of habitats and needle sizes, from 1 (Picea omorika) to 35 cm (Pinus palustris). We show that the phloem shares common traits across these four species and find that the size of its conductive elements obeys a power law. We present a minimal model that accounts for these common traits and takes into account the transport strategy and natural constraints. This minimal model predicts a power law phloem distribution consistent with transport energy minimization, suggesting that energetics are more important than translocation speed at the leaf level. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
Structural diversity requires individual optimization of ethanol concentration in polysaccharide precipitation.

PubMed

Xu, Jun; Yue, Rui-Qi; Liu, Jing; Ho, Hing-Man; Yi, Tao; Chen, Hu-Biao; Han, Quan-Bin

2014-06-01

Ethanol precipitation is one of the most widely used methods for preparing natural polysaccharides, in which ethanol concentration significantly affects the precipitate yield, however, is usually set at 70-80%. Whether the standardization of ethanol concentration is appropriate has not been investigated. In the present study, the precipitation yields produced in varied ethanol concentrations (10-90%) were qualitatively and quantitatively evaluated by HPGPC (high-performance gel-permeation chromatography), using two series of standard glucans, namely dextrans and pullulans, as reference samples, and then eight natural samples. The results indicated that the response of a polysaccharide's chemical structure, with diversity in structural features and molecular sizes, to ethanol concentration is the decisive factor in precipitation of these glucans. Polysaccharides with different structural features, even though they have similar molecular weights, exhibit significantly different precipitation behaviors. For a specific glucan, the lower its molecular size, the higher the ethanol concentration needed for complete precipitation. The precipitate yield varied from 10% to 100% in 80% ethanol as the molecular size increased from 1kDa to 270kDa. This paper aims to draw scientists' attention to the fact that, in extracting natural polysaccharides by ethanol precipitation, the ethanol concentration must be individually optimized for each type of material. Copyright © 2014 Elsevier B.V. All rights reserved.
Evolutionary Strategies for Protein Folding

NASA Astrophysics Data System (ADS)

Murthy Gopal, Srinivasa; Wenzel, Wolfgang

2006-03-01

The free energy approach for predicting the protein tertiary structure describes the native state of a protein as the global minimum of an appropriate free-energy forcefield. The low-energy region of the free-energy landscape of a protein is extremely rugged. Efficient optimization methods must therefore speed up the search for the global optimum by avoiding high energy transition states, adapt large scale moves or accept unphysical intermediates. Here we investigate an evolutionary strategies(ES) for optimizing a protein conformation in our all-atom free-energy force field([1],[2]). A set of random conformations is evolved using an ES to get a diverse population containing low energy structure. The ES is shown to balance energy improvement and yet maintain diversity in structures. The ES is implemented as a master-client model for distributed computing. Starting from random structures and by using this optimization technique, we were able to fold a 20 amino-acid helical protein and 16 amino-acid beta hairpin[3]. We compare ES to basin hopping method. [1]T. Herges and W. Wenzel,Biophys.J. 87,3100(2004) [2] A. Verma and W. Wenzel Stabilization and folding of beta-sheet and alpha-helical proteins in an all-atom free energy model(submitted)(2005) [3] S. M. Gopal and W. Wenzel Evolutionary Strategies for Protein Folding (in preparation)
Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure.

PubMed

Keskin, O; Bahar, I; Jernigan, R L; Beutler, J A; Shoemaker, R H; Sausville, E A; Covell, D G

2000-04-01

An analysis of the growth inhibitory potency of 122 anticancer agents available from the National Cancer Institute anticancer drug screen is presented. Methods of singular value decomposition (SVD) were applied to determine the matrix of distances between all compounds. These SVD-derived dissimilarity distances were used to cluster compounds that exhibit similar tumor growth inhibitory activity patterns against 60 human cancer cell lines. Cluster analysis divides the 122 standard agents into 25 statistically distinct groups. The first eight groups include structurally diverse compounds with reactive functionalities that act as DNA-damaging agents while the remaining 17 groups include compounds that inhibit nucleic acid biosynthesis and mitosis. Examination of the average activity patterns across the 60 tumor cell lines reveals unique 'fingerprints' associated with each group. A diverse set of structural features are observed for compounds within these groups, with frequent occurrences of strong within-group structural similarities. Clustering of cell types by their response to the 122 anticancer agents divides the 60 cell types into 21 groups. The strongest within-panel groupings were found for the renal, leukemia and ovarian cell panels. These results contribute to the basis for comparisons between log(GI(50)) screening patterns of the 122 anticancer agents and additional tested compounds.
New gSSR and EST-SSR markers reveal high genetic diversity in the invasive plant Ambrosia artemisiifolia L. and can be transferred to other invasive Ambrosia species.

PubMed

Meyer, Lucie; Causse, Romain; Pernin, Fanny; Scalone, Romain; Bailly, Géraldine; Chauvel, Bruno; Délye, Christophe; Le Corre, Valérie

2017-01-01

Ambrosia artemisiifolia L., (common ragweed), is an annual invasive and highly troublesome plant species originating from North America that has become widespread across Europe. New sets of genomic and expressed sequence tag (EST) based simple sequence repeats (SSRs) markers were developed in this species using three approaches. After validation, 13 genomic SSRs and 13 EST-SSRs were retained and used to characterize the genetic diversity and population genetic structure of Ambrosia artemisiifolia populations from the native (North America) and invasive (Europe) ranges of the species. Analysing the mating system based on maternal families did not reveal any departure from complete allogamy and excess homozygosity was mostly due the presence of null alleles. High genetic diversity and patterns of genetic structure in Europe suggest two main introduction events followed by secondary colonization events. Cross-species transferability of the newly developed markers to other invasive species of the Ambrosia genus was assessed. Sixty-five percent and 75% of markers, respectively, were transferable from A. artemisiifolia to Ambrosia psilostachya and Ambrosia tenuifolia. 40% were transferable to Ambrosia trifida, this latter species being seemingly more phylogenetically distantly related to A. artemisiifolia than the former two.
Population Genetics of Plasmodium vivax in Four High Malaria Endemic Areas in Thailand.

PubMed

Congpuong, Kanungnit; Ubalee, Ratawan

2017-10-01

Recent trends of malaria in Thailand illustrate an increasing proportion of Plasmodium vivax, indicating the importance of P. vivax as a major causative agent of malaria. P. vivax malaria is usually considered a benign disease so the knowledge of this parasite has been limited, especially the genetic diversity and genetic structure of isolates from different endemic areas. The aim of this study was to examine the population genetics and structure of P. vivax isolates from 4 provinces with different malaria endemic settings in Thailand using 6 microsatellite markers. Total 234 blood samples from P. vivax mono-infected patients were collected. Strong genetic diversity was observed across all study sites; the expected heterozygosity values ranged from 0.5871 to 0.9033. Genetic variability in this study divided P. vivax population into 3 clusters; first was P. vivax isolates from Mae Hong Son and Kanchanaburi Provinces located on the western part of Thailand; second, Yala isolates from the south; and third, Chanthaburi isolates from the east. P. vivax isolates from patients having parasite clearance time (PCT) longer than 24 hr after the first dose of chloroquine treatment had higher diversity when compared with those having PCT within 24 hr. This study revealed a clear evidence of different population structure of P. vivax from different malaria endemic areas of Thailand. The findings provide beneficial information to malaria control programme as it is a useful tool to track the source of infections and current malaria control efforts.
Predictive modeling: Solubility of C60 and C70 fullerenes in diverse solvents.

PubMed

Gupta, Shikha; Basant, Nikita

2018-06-01

Solubility of fullerenes imposes a major limitation to further advanced research and technological development using these novel materials. There have been continued efforts to discover better solvents and their properties that influence the solubility of fullerenes. Here, we have developed QSPR (quantitative structure-property relationship) models based on structural features of diverse solvents and large experimental data for predicting the solubility of C 60 and C 70 fullerenes. The developed models identified most relevant features of the solvents that encode the polarizability, polarity and lipophilicity properties which largely influence the solubilizing potential of the solvent for the fullerenes. We also established Inter-moieties solubility correlations (IMSC) based quantitative property-property relationship (QPPR) models for predicting solubility of C 60 and C 70 fullerenes. The QSPR and QPPR models were internally and externally validated deriving the most stringent statistical criteria and predicted C 60 and C 70 solubility values in different solvents were in close agreement with the experimental values. In test sets, the QSPR models yielded high correlations (R 2  > 0.964) and low root mean squared error of prediction errors (RMSEP< 0.25). Results of comparison with other studies indicated that the proposed models could effectively improve the accuracy and ability for predicting solubility of C 60 and C 70 fullerenes in solvents with diverse structures and would be useful in development of more effective solvents. Copyright © 2018 Elsevier Ltd. All rights reserved.
Discovery and characterization of natural products that act as pheromones in fish.

PubMed

Li, Ke; Buchinger, Tyler J; Li, Weiming

2018-06-20

Covering: up to 2018 Fish use a diverse collection of molecules to communicate with conspecifics. Since Karlson and Lüscher termed these molecules 'pheromones', chemists and biologists have joined efforts to characterize their structures and functions. In particular, the understanding of insect pheromones developed at a rapid pace, set, in part, by the use of bioassay-guided fractionation and natural product chemistry. Research on vertebrate pheromones, however, has progressed more slowly. Initially, biologists characterized fish pheromones by screening commercially available compounds suspected to act as pheromones based upon their physiological function. Such biology-driven screening has proven a productive approach to studying pheromones in fish. However, the many functions of fish pheromones and diverse metabolites that fish release make predicting pheromone identity difficult and necessitate approaches led by chemistry. Indeed, the few cases in which pheromone identification was led by natural product chemistry indicated novel or otherwise unpredicted compounds act as pheromones. Here, we provide a brief review of the approaches to identifying pheromones, placing particular emphasis on the promise of using natural product chemistry together with assays of biological activity. Several case studies illustrate bioassay-guided fractionation as an approach to pheromone identification in fish and the unexpected diversity of pheromone structures discovered by natural product chemistry. With recent advances in natural product chemistry, bioassay-guided fractionation is likely to unveil an even broader collection of pheromone structures and enable research that spans across disciplines.
Social network analysis of the genetic structure of Pacific islanders.

PubMed

Terrell, John Edward

2010-05-01

Social network analysis (SNA) is a body of theory and a set of relatively new computer-aided techniques used in the analysis and study of relational data. Recent studies of autosomal markers from over 40 human populations in the south-western Pacific have further documented the remarkable degree of genetic diversity in this part of the world. I report additional analysis using SNA methods contributing new controlled observations on the structuring of genetic diversity among these islanders. These SNA mappings are then compared with model-based network expectations derived from the geographic distances among the same populations. Previous studies found that genetic divergence among island Melanesian populations is organised by island, island size/topography, and position (coastal vs. inland), and that similarities observed correlate only weakly with an isolation-by-distance model. Using SNA methods, however, improves the resolution of among population comparison, and suggests that isolation by distance constrained by social networks together with position (coastal/inland) accounts for much of the population structuring observed. The multilocus data now available is also in accord with current thinking on the impact of major biogeographical transformations on prehistoric colonisation and post-settlement human interaction in Oceania.
Identifying functionally informative evolutionary sequence profiles.

PubMed

Gil, Nelson; Fiser, Andras

2018-04-15

Multiple sequence alignments (MSAs) can provide essential input to many bioinformatics applications, including protein structure prediction and functional annotation. However, the optimal selection of sequences to obtain biologically informative MSAs for such purposes is poorly explored, and has traditionally been performed manually. We present Selection of Alignment by Maximal Mutual Information (SAMMI), an automated, sequence-based approach to objectively select an optimal MSA from a large set of alternatives sampled from a general sequence database search. The hypothesis of this approach is that the mutual information among MSA columns will be maximal for those MSAs that contain the most diverse set possible of the most structurally and functionally homogeneous protein sequences. SAMMI was tested to select MSAs for functional site residue prediction by analysis of conservation patterns on a set of 435 proteins obtained from protein-ligand (peptides, nucleic acids and small substrates) and protein-protein interaction databases. Availability and implementation: A freely accessible program, including source code, implementing SAMMI is available at https://github.com/nelsongil92/SAMMI.git. andras.fiser@einstein.yu.edu. Supplementary data are available at Bioinformatics online.
A projection-free method for representing plane-wave DFT results in an atom-centered basis

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

Dunnington, Benjamin D.; Schmidt, J. R., E-mail: schmidt@chem.wisc.edu

2015-09-14

Plane wave density functional theory (DFT) is a powerful tool for gaining accurate, atomic level insight into bulk and surface structures. Yet, the delocalized nature of the plane wave basis set hinders the application of many powerful post-computation analysis approaches, many of which rely on localized atom-centered basis sets. Traditionally, this gap has been bridged via projection-based techniques from a plane wave to atom-centered basis. We instead propose an alternative projection-free approach utilizing direct calculation of matrix elements of the converged plane wave DFT Hamiltonian in an atom-centered basis. This projection-free approach yields a number of compelling advantages, including strictmore » orthonormality of the resulting bands without artificial band mixing and access to the Hamiltonian matrix elements, while faithfully preserving the underlying DFT band structure. The resulting atomic orbital representation of the Kohn-Sham wavefunction and Hamiltonian provides a gateway to a wide variety of analysis approaches. We demonstrate the utility of the approach for a diverse set of chemical systems and example analysis approaches.« less
Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

PubMed Central

de Oliveira Francisco, Flávio; Santiago, Leandro Rodrigues; Arias, Maria Cristina

2013-01-01

Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings. PMID:23569417
Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study.

PubMed

de Oliveira Francisco, Flávio; Santiago, Leandro Rodrigues; Arias, Maria Cristina

2013-03-01

Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.

Demographic faultlines: a meta-analysis of the literature.

PubMed

Thatcher, Sherry M B; Patel, Pankaj C

2011-11-01

We propose and test a theoretical model focusing on antecedents and consequences of demographic faultlines. We also posit contingencies that affect overall team dynamics in the context of demographic faultlines, such as the study setting and performance measurement. Using meta-analysis structural equation modeling with a final data set consisting of 311 data points (i.e., k [predictor-criterion relationships]), from 39 studies that were obtained from 36 papers with a total sample size of 24,388 individuals in 4,366 teams, we found that sex and racial diversity increased demographic faultline strength more than did diversity on the attributes of functional background, educational background, age, and tenure. Demographic faultline strength was found to increase task and relationship conflict as well as decrease team cohesion. Furthermore, although demographic faultline strength decreased both team satisfaction and team performance, there was a stronger decrease in team performance than in team satisfaction. The strength of these relationships increased when the study was conducted in the lab rather than in the field. We describe the theoretical and practical implications of these findings for advancing the study of faultlines. (c) 2011 APA, all rights reserved.
Human dignity in religion-embedded cross-cultural nursing.

PubMed

Cheraghi, Mohammad A; Manookian, Arpi; Nasrabadi, Alireza N

2014-12-01

Although human dignity is an unconditional value of every human being, it can be shattered by extrinsic factors. It is necessary to discover the authentic meaning of patients' dignity preservation from different religious perspectives to provide professional cross-cultural care in a diverse setting. This article identifies common experiences of Iranian Muslim and Armenian Christian patients regarding dignified care at the bedside. This is a qualitative study of participants' experiences of dignified care elicited by individual in-depth semi-structured interviews. A purposeful sample of 10 participants (five Iranian Muslims and five Iranian Armenians) from various private and governmental hospital settings was chosen. This study was approved by the ethics committee of Tehran University of Medical Sciences. All the participants were provided with information about the purpose and the nature of the study, the voluntary condition of their participation in this study, and the anonymous reporting of recorded interviews. The common experiences of Christian and Muslim patients regarding dignity preservation emerged as "exigency of respecting human nobility" and "providing person-centered care." It is essential to recognize the humanness and individuality of each patient to preserve and promote human dignity in diverse cross-cultural settings. The findings support and expand current understanding about the objective and subjective nature of dignity preservation in cross-cultural nursing. © The Author(s) 2014.
A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

PubMed Central

Purps, Josephine; Siegert, Sabine; Willuweit, Sascha; Nagy, Marion; Alves, Cíntia; Salazar, Renato; Angustia, Sheila M.T.; Santos, Lorna H.; Anslinger, Katja; Bayer, Birgit; Ayub, Qasim; Wei, Wei; Xue, Yali; Tyler-Smith, Chris; Bafalluy, Miriam Baeta; Martínez-Jarreta, Begoña; Egyed, Balazs; Balitzki, Beate; Tschumi, Sibylle; Ballard, David; Court, Denise Syndercombe; Barrantes, Xinia; Bäßler, Gerhard; Wiest, Tina; Berger, Burkhard; Niederstätter, Harald; Parson, Walther; Davis, Carey; Budowle, Bruce; Burri, Helen; Borer, Urs; Koller, Christoph; Carvalho, Elizeu F.; Domingues, Patricia M.; Chamoun, Wafaa Takash; Coble, Michael D.; Hill, Carolyn R.; Corach, Daniel; Caputo, Mariela; D’Amato, Maria E.; Davison, Sean; Decorte, Ronny; Larmuseau, Maarten H.D.; Ottoni, Claudio; Rickards, Olga; Lu, Di; Jiang, Chengtao; Dobosz, Tadeusz; Jonkisz, Anna; Frank, William E.; Furac, Ivana; Gehrig, Christian; Castella, Vincent; Grskovic, Branka; Haas, Cordula; Wobst, Jana; Hadzic, Gavrilo; Drobnic, Katja; Honda, Katsuya; Hou, Yiping; Zhou, Di; Li, Yan; Hu, Shengping; Chen, Shenglan; Immel, Uta-Dorothee; Lessig, Rüdiger; Jakovski, Zlatko; Ilievska, Tanja; Klann, Anja E.; García, Cristina Cano; de Knijff, Peter; Kraaijenbrink, Thirsa; Kondili, Aikaterini; Miniati, Penelope; Vouropoulou, Maria; Kovacevic, Lejla; Marjanovic, Damir; Lindner, Iris; Mansour, Issam; Al-Azem, Mouayyad; Andari, Ansar El; Marino, Miguel; Furfuro, Sandra; Locarno, Laura; Martín, Pablo; Luque, Gracia M.; Alonso, Antonio; Miranda, Luís Souto; Moreira, Helena; Mizuno, Natsuko; Iwashima, Yasuki; Neto, Rodrigo S. Moura; Nogueira, Tatiana L.S.; Silva, Rosane; Nastainczyk-Wulf, Marina; Edelmann, Jeanett; Kohl, Michael; Nie, Shengjie; Wang, Xianping; Cheng, Baowen; Núñez, Carolina; Pancorbo, Marian Martínez de; Olofsson, Jill K.; Morling, Niels; Onofri, Valerio; Tagliabracci, Adriano; Pamjav, Horolma; Volgyi, Antonia; Barany, Gusztav; Pawlowski, Ryszard; Maciejewska, Agnieszka; Pelotti, Susi; Pepinski, Witold; Abreu-Glowacka, Monica; Phillips, Christopher; Cárdenas, Jorge; Rey-Gonzalez, Danel; Salas, Antonio; Brisighelli, Francesca; Capelli, Cristian; Toscanini, Ulises; Piccinini, Andrea; Piglionica, Marilidia; Baldassarra, Stefania L.; Ploski, Rafal; Konarzewska, Magdalena; Jastrzebska, Emila; Robino, Carlo; Sajantila, Antti; Palo, Jukka U.; Guevara, Evelyn; Salvador, Jazelyn; Ungria, Maria Corazon De; Rodriguez, Jae Joseph Russell; Schmidt, Ulrike; Schlauderer, Nicola; Saukko, Pekka; Schneider, Peter M.; Sirker, Miriam; Shin, Kyoung-Jin; Oh, Yu Na; Skitsa, Iulia; Ampati, Alexandra; Smith, Tobi-Gail; Calvit, Lina Solis de; Stenzl, Vlastimil; Capal, Thomas; Tillmar, Andreas; Nilsson, Helena; Turrina, Stefania; De Leo, Domenico; Verzeletti, Andrea; Cortellini, Venusia; Wetton, Jon H.; Gwynne, Gareth M.; Jobling, Mark A.; Whittle, Martin R.; Sumita, Denilce R.; Wolańska-Nowak, Paulina; Yong, Rita Y.Y.; Krawczak, Michael; Nothnagel, Michael; Roewer, Lutz

2014-01-01

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent. PMID:24854874
The Genetic Diversity and Structure of Linkage Disequilibrium of the MTHFR Gene in Populations of Northern Eurasia.

PubMed

Trifonova, E A; Eremina, E R; Urnov, F D; Stepanov, V A

2012-01-01

The structure of the haplotypes and linkage disequilibrium (LD) of the methylenetetrahydrofolate reductase gene (MTHFR) in 9 population groups from Northern Eurasia and populations of the international HapMap project was investigated in the present study. The data suggest that the architecture of LD in the human genome is largely determined by the evolutionary history of populations; however, the results of phylogenetic and haplotype analyses seems to suggest that in fact there may be a common "old" mechanism for the formation of certain patterns of LD. Variability in the structure of LD and the level of diversity of MTHFRhaplotypes cause a certain set of tagSNPs with an established prognostic significance for each population. In our opinion, the results obtained in the present study are of considerable interest for understanding multiple genetic phenomena: namely, the association of interpopulation differences in the patterns of LD with structures possessing a genetic susceptibility to complex diseases, and the functional significance of the pleiotropicMTHFR gene effect. Summarizing the results of this study, a conclusion can be made that the genetic variability analysis with emphasis on the structure of LD in human populations is a powerful tool that can make a significant contribution to such areas of biomedical science as human evolutionary biology, functional genomics, genetics of complex diseases, and pharmacogenomics.
Fast, clash-free RNA conformational morphing using molecular junctions

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

Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus

Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less
Fast, clash-free RNA conformational morphing using molecular junctions

DOE PAGES

Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus; ...

2017-03-13

Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less
Current perspectives of CASA applications in diverse mammalian spermatozoa.

PubMed

van der Horst, Gerhard; Maree, Liana; du Plessis, Stefan S

2018-03-26

Since the advent of computer-aided sperm analysis (CASA) some four decades ago, advances in computer technology and software algorithms have helped establish it as a research and diagnostic instrument for the analysis of spermatozoa. Despite mammalian spermatozoa being the most diverse cell type known, CASA is a great tool that has the capacity to provide rapid, reliable and objective quantitative assessment of sperm quality. This paper provides contemporary research findings illustrating the scientific and commercial applications of CASA and its ability to evaluate diverse mammalian spermatozoa (human, primates, rodents, domestic mammals, wildlife species) at both structural and functional levels. The potential of CASA to quantitatively measure essential aspects related to sperm subpopulations, hyperactivation, morphology and morphometry is also demonstrated. Furthermore, applications of CASA are provided for improved mammalian sperm quality assessment, evaluation of sperm functionality and the effect of different chemical substances or pathologies on sperm fertilising ability. It is clear that CASA has evolved significantly and is currently superior to many manual techniques in the research and clinical setting.
Deep neural nets as a method for quantitative structure-activity relationships.

PubMed

Ma, Junshui; Sheridan, Robert P; Liaw, Andy; Dahl, George E; Svetnik, Vladimir

2015-02-23

Neural networks were widely used for quantitative structure-activity relationships (QSAR) in the 1990s. Because of various practical issues (e.g., slow on large problems, difficult to train, prone to overfitting, etc.), they were superseded by more robust methods like support vector machine (SVM) and random forest (RF), which arose in the early 2000s. The last 10 years has witnessed a revival of neural networks in the machine learning community thanks to new methods for preventing overfitting, more efficient training algorithms, and advancements in computer hardware. In particular, deep neural nets (DNNs), i.e. neural nets with more than one hidden layer, have found great successes in many applications, such as computer vision and natural language processing. Here we show that DNNs can routinely make better prospective predictions than RF on a set of large diverse QSAR data sets that are taken from Merck's drug discovery effort. The number of adjustable parameters needed for DNNs is fairly large, but our results show that it is not necessary to optimize them for individual data sets, and a single set of recommended parameters can achieve better performance than RF for most of the data sets we studied. The usefulness of the parameters is demonstrated on additional data sets not used in the calibration. Although training DNNs is still computationally intensive, using graphical processing units (GPUs) can make this issue manageable.
Temporal and geographic variation in fish communities of lower Cook Inlet, Alaska

USGS Publications Warehouse

Robards, Martin D.; Piatt, John F.; Kettle, Arthur B.; Abookire, Alisa A.

1999-01-01

Nearshore and shelf fish communities were studied in three areas of lower Cook Inlet, Alaska: the Barren Islands (oceanic and well-mixed waters), Kachemak Bay (mixed oceanic waters with significant freshwater runoff), and Chisik Island (estuarine waters). Fish were sampled with beach seines (n=413 sets) and midwater trawls (n=39 sets). We found that lower Cook Inlet supported a diverse nearshore fish community of at least 52 species. Fifty of these species were caught in Kachemak Bay, 24 at Chisik Island, and 12 at the Barren Islands. Pacific sand lance dominated Barren Islands and Kachemak Bay nearshore habitats, comprising 99% and 71% of total individuals, respectively. The nearshore Chisik Island fish community was not dominated by any one species; instead it exhibited higher diversity. These spatial differences appeared linked to local oceanographic regimes and sediment influx. Analysis of historical data revealed that the nearshore Kachemak Bay fish community changed significantly between 1976 and 1996, showing increased diversity and abundance in several taxa, notably gadids, salmonids, pleuronectids, and sculpins. Decadal differences appeared to be related to large-scale climate changes in the North Pacific. Catches of most taxa peaked in May-August, and were low during other months of the year. Several species were present for only part of the summer. Species composition of seine catches differed significantly between consecutive high and low tides, but not between consecutive sets or years. Midwater trawls took 26 species, 14 of which were present in Kachemak Bay, 19 near Chisik Island, and 7 at the Barren Islands. Community structures in shelf and nearshore waters were similar: diversity was high and abundance low at Chisik Island, whereas a few abundant species dominated at both Kachemak Bay and the Barren Islands. In addition, the low fish abundance near Chisik Island appeared to be related to declining seabird numbers at this colony.
Comparison of genetic diversity between Canadian adapted genotypes and exotic germplasm of soybean.

PubMed

Iquira, Elmer; Gagnon, Eric; Belzile, François

2010-05-01

Soybean (Glycine max (L.) Merr.) was domesticated in China and the greatest genetic diversity for this species is found in Asia. In contrast, in North America, soybean cultivars trace back to a small number of plant introductions from Asia and genetic diversity is typically quite limited. The purpose of this work was to measure and compare the genetic diversity in two sets of soybean lines. The first set (termed "local") was composed of 100 lines used in a private breeding program in Quebec. The second set (termed "exotic") was composed of 200 lines from elsewhere in the world (but mostly from Asia) and included a few lines of Glycine soja, the wild progenitor of cultivated soybean. Almost all the genotypes belonged to maturity groups between 000 and II. A total of 39 microsatellites (SSRs) were used to genotype the two collections. The number of alleles per locus was almost twice as great in the exotic set compared with the local set. Also, the number of "unique" alleles, i.e., those uniquely present in one set and absent in the other, was almost fivefold greater (191 vs. 37) in a subset of 108 exotic lines with good adaptation than among the local set. A genetic distance matrix, a UPGMA cluster analysis, and a principal coordinate analysis were conducted based on the SSR data. These analyses all indicated that the exotic set was much more diverse and formed a clearly distinct group from the local set. Interestingly, some of the lines showing the best adaptation to local conditions were quite distinctive in terms of their genotype and could potentially contribute useful novel genetic variation within the breeding program.
The complex roles of space and environment in structuring functional, taxonomic and phylogenetic beta diversity of frogs in the Atlantic Forest

PubMed Central

Luiz, Amom Mendes; Sawaya, Ricardo J.

2018-01-01

Ecological communities are complex entities that can be maintained and structured by niche-based processes such as environmental conditions, and spatial processes such as dispersal. Thus, diversity patterns may be shaped simultaneously at different spatial scales by very distinct processes. Herein we assess whether and how functional, taxonomic, and phylogenetic beta diversities of frog tadpoles are explained by environmental and/or spatial predictors. We implemented a distance–based redundancy analysis to explore variation in components of beta diversity explained by pure environmental and pure spatial predictors, as well as their interactions, at both fine and broad spatial scales. Our results indicated important but complex roles of spatial and environmental predictors in structuring phylogenetic, taxonomic and functional beta diversities. The pure fine-scales spatial fraction was more important in structuring all beta diversity components, especially to functional and taxonomical spatial turnover. Environmental variables such as canopy cover and vegetation structure were important predictors of all components, but especially to functional and taxonomic beta diversity. We emphasize that distinct factors related to environment and space are affecting distinct components of beta diversity in different ways. Although weaker, phylogenetic beta diversity, which is structured more on biogeographical scales, and thus can be represented by spatially structured processes, was more related to broad spatial processes than other components. However, selected fine-scale spatial predictors denoted negative autocorrelation, which may be revealing the existence of differences in unmeasured habitat variables among samples. Although overall important, local environmental-based processes explained better functional and taxonomic beta diversity, as these diversity components carry an important ecological value. We highlight the importance of assessing different components of diversity patterns at different scales by spatially explicit models in order to improve our understanding of community structure and help to unravel the complex nature of biodiversity. PMID:29672575
Genetic Diversity in Lens Species Revealed by EST and Genomic Simple Sequence Repeat Analysis

PubMed Central

Dikshit, Harsh Kumar; Singh, Akanksha; Singh, Dharmendra; Aski, Muraleedhar Sidaram; Prakash, Prapti; Jain, Neelu; Meena, Suresh; Kumar, Shiv; Sarker, Ashutosh

2015-01-01

Low productivity of pilosae type lentils grown in South Asia is attributed to narrow genetic base of the released cultivars which results in susceptibility to biotic and abiotic stresses. For enhancement of productivity and production, broadening of genetic base is essentially required. The genetic base of released cultivars can be broadened by using diverse types including bold seeded and early maturing lentils from Mediterranean region and related wild species. Genetic diversity in eighty six accessions of three species of genus Lens was assessed based on twelve genomic and thirty one EST-SSR markers. The evaluated set of genotypes included diverse lentil varieties and advanced breeding lines from Indian programme, two early maturing ICARDA lines and five related wild subspecies/species endemic to the Mediterranean region. Genomic SSRs exhibited higher polymorphism in comparison to EST SSRs. GLLC 598 produced 5 alleles with highest gene diversity value of 0.80. Among the studied subspecies/species 43 SSRs detected maximum number of alleles in L. orientalis. Based on Nei’s genetic distance cultivated lentil L. culinaris subsp. culinaris was found to be close to its wild progenitor L. culinaris subsp. orientalis. The Prichard’s structure of 86 genotypes distinguished different subspecies/species. Higher variability was recorded among individuals within population than among populations. PMID:26381889
Inferring influenza global transmission networks without complete phylogenetic information

PubMed Central

Aris-Brosou, Stéphane

2014-01-01

Influenza is one of the most severe respiratory infections affecting humans throughout the world, yet the dynamics of its global transmission network are still contentious. Here, I describe a novel combination of phylogenetics, time series, and graph theory to analyze 14.25 years of data stratified in space and in time, focusing on the main target of the human immune response, the hemagglutinin gene. While bypassing the complete phylogenetic inference of huge data sets, the method still extracts information suggesting that waves of genetic or of nucleotide diversity circulate continuously around the globe for subtypes that undergo sustained transmission over several seasons, such as H3N2 and pandemic H1N1/09, while diversity of prepandemic H1N1 viruses had until 2009 a noncontinuous transmission pattern consistent with a source/sink model. Irrespective of the shift in the structure of H1N1 diversity circulation with the emergence of the pandemic H1N1/09 strain, US prevalence peaks during the winter months when genetic diversity is at its lowest. This suggests that a dominant strain is generally responsible for epidemics and that monitoring genetic and/or nucleotide diversity in real time could provide public health agencies with an indirect estimate of prevalence. PMID:24665342
Genetic diversity and population structure of a protected species: Polygala tenuifolia Willd.

PubMed

Peng, Yan Qun; Fan, Ling Ling; Mao, Fu Ying; Zhao, Yun Sheng; Xu, Rui; Yin, Yu Jie; Chen, Xin; Wan, De Guang; Zhang, Xin Hui

2018-03-01

Polygala tenuifolia Willd. is an important protected species used in traditional Chinese medicine. In the present study, amplified fragment length polymorphism (AFLP) markers were employed to characterize the genetic diversity in wild and cultivated P. tenuifolia populations. Twelve primer combinations of AFLP produced 310 unambiguous and repetitious bands. Among these bands, 261 (84.2%) were polymorphic. The genetic diversity was high at the species level: percentage of polymorphic loci (PPL)=84.2%, Nei's gene diversity (h)=0.3296 and Shannon's information index (I)=0.4822. Between the two populations, the genetic differentiation of 0.1250 was low and the gene flow was relatively high, at 3.4989. The wild population (PPL=81.9%, h=0.3154, I=0.4635) showed a higher genetic diversity level than the cultivated population (PPL=63.9%, h=0.2507, I=0.3688). The results suggest that the major factors threatening the persistence of P. tenuifolia resources are ecological and human factors rather than genetic. These results will assist with the design of conservation and management programs, such as in natural habitat conservation, setting the excavation time interval for resource regeneration and the substitution of cultivated for wild plants. Copyright © 2018 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.
Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity.

PubMed

Guillot, Elsa G; Hazelton, Martin L; Karafet, Tatiana M; Lansing, J Stephen; Sudoyo, Herawati; Cox, Murray P

2015-09-01

Marriage rules, the community prescriptions that dictate who an individual can or cannot marry, are extremely diverse and universally present in traditional societies. A major focus of research in the early decades of modern anthropology, marriage rules impose social and economic forces that help structure societies and forge connections between them. However, in those early anthropological studies, the biological benefits or disadvantages of marriage rules could not be determined. We revisit this question by applying a novel simulation framework and genome-wide data to explore the effects of Asymmetric Prescriptive Alliance, an elaborate set of marriage rules that has been a focus of research for many anthropologists. Simulations show that strict adherence to these marriage rules reduces genetic diversity on the autosomes, X chromosome and mitochondrial DNA, but relaxed compliance produces genetic diversity similar to random mating. Genome-wide data from the Indonesian community of Rindi, one of the early study populations for Asymmetric Prescriptive Alliance, are more consistent with relaxed compliance than strict adherence. We therefore suggest that, in practice, marriage rules are treated with sufficient flexibility to allow social connectivity without significant degradation of biological diversity. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Evaluation of genetic diversity of Panicum turgidum Forssk from Saudi Arabia.

PubMed

Assaeed, Abdulaziz M; Al-Faifi, Sulieman A; Migdadi, Hussein M; El-Bana, Magdy I; Al Qarawi, Abdulaziz A; Khan, Mohammad Altaf

2018-01-01

The genetic diversity of 177 accessions of Panicum turgidum Forssk, representing ten populations collected from four geographical regions in Saudi Arabia, was analyzed using amplified fragment length polymorphism (AFLP) markers. A set of four primer-pairs with two/three selective nucleotides scored 836 AFLP amplified fragments (putative loci/genome landmarks), all of which were polymorphic. Populations collected from the southern region of the country showed the highest genetic diversity parameters, whereas those collected from the central regions showed the lowest values. Analysis of molecular variance (AMOVA) revealed that 78% of the genetic variability was attributable to differences within populations. Pairwise values for population differentiation and genetic structure were statistically significant for all variances. The UPGMA dendrogram, validated by principal coordinate analysis-grouped accessions, corresponded to the geographical origin of the accessions. Mantel's test showed that there was a significant correlation between the genetic and geographical distances ( r = 0.35, P < 0.04). In summary, the AFLP assay demonstrated the existence of substantial genetic variation in P. turgidum . The relationship between the genetic diversity and geographical source of P. turgidum populations of Saudi Arabia, as revealed through this comprehensive study, will enable effective resource management and restoration of new areas without compromising adaptation and genetic diversity.
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.
Functional roles affect diversity-succession relationships for boreal beetles.

PubMed

Gibb, Heloise; Johansson, Therese; Stenbacka, Fredrik; Hjältén, Joakim

2013-01-01

Species diversity commonly increases with succession and this relationship is an important justification for conserving large areas of old-growth habitats. However, species with different ecological roles respond differently to succession. We examined the relationship between a range of diversity measures and time since disturbance for boreal forest beetles collected over a 285 year forest chronosequence. We compared responses of "functional" groups related to threat status, dependence on dead wood habitats, diet and the type of trap in which they were collected (indicative of the breadth of ecologies of species). We examined fits of commonly used rank-abundance models for each age class and traditional and derived diversity indices. Rank abundance distributions were closest to the Zipf-Mandelbrot distribution, suggesting little role for competition in structuring most assemblages. Diversity measures for most functional groups increased with succession, but differences in slopes were common. Evenness declined with succession; more so for red-listed species than common species. Saproxylic species increased in diversity with succession while non-saproxylic species did not. Slopes for fungivores were steeper than other diet groups, while detritivores were not strongly affected by succession. Species trapped using emergence traps (log specialists) responded more weakly to succession than those trapped using flight intercept traps (representing a broader set of ecologies). Species associated with microhabitats that accumulate with succession (fungi and dead wood) thus showed the strongest diversity responses to succession. These clear differences between functional group responses to forest succession should be considered in planning landscapes for optimum conservation value, particularly functional resilience.
Relational Autonomy in Assisted Living: A Focus on Diverse Care Settings for Older Adults

PubMed Central

Perkins, Molly M.; Ball, Mary M.; Whittington, Frank J.; Hollingsworth, Carole

2012-01-01

Consistent with Western cultural values, the traditional liberal theory of autonomy, which places emphasis on self-determination, liberty of choice, and freedom from interference by others, has been a leading principle in health care discourse for several decades. In context to aging, chronic illness, disability, and long-term care, increasingly there has been a call for a relational conception of autonomy that acknowledges issues of dependency, interdependence, and care relationships. Although autonomy is a core philosophy of assisted living (AL) and a growing number of studies focus on this issue, theory development in this area is lagging and little research has considered race, class, or cultural differences, despite the growing diversity of AL. We present a conceptual model of autonomy in AL based on over a decade of research conducted in diverse facility settings. This relational model provides an important conceptual lens for understanding the dynamic linkages between varieties of factors at multiple levels of social structure that shape residents' ability to maintain a sense of autonomy in this often socially challenging care environment. Social and institutional change, which is ongoing, as well as the multiple and ever-changing cultural contexts within which residents are embedded, are important factors that shape residents' experiences over time and impact resident-facility fit and residents' ability to age in place. PMID:22707852
Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities.

PubMed

Bradley, Ian M; Pinto, Ameet J; Guest, Jeremy S

2016-10-01

The use of high-throughput sequencing technologies with the 16S rRNA gene for characterization of bacterial and archaeal communities has become routine. However, the adoption of sequencing methods for eukaryotes has been slow, despite their significance to natural and engineered systems. There are large variations among the target genes used for amplicon sequencing, and for the 18S rRNA gene, there is no consensus on which hypervariable region provides the most suitable representation of diversity. Additionally, it is unclear how much PCR/sequencing bias affects the depiction of community structure using current primers. The present study amplified the V4 and V8-V9 regions from seven microalgal mock communities as well as eukaryotic communities from freshwater, coastal, and wastewater samples to examine the effect of PCR/sequencing bias on community structure and membership. We found that degeneracies on the 3' end of the current V4-specific primers impact read length and mean relative abundance. Furthermore, the PCR/sequencing error is markedly higher for GC-rich members than for communities with balanced GC content. Importantly, the V4 region failed to reliably capture 2 of the 12 mock community members, and the V8-V9 hypervariable region more accurately represents mean relative abundance and alpha and beta diversity. Overall, the V4 and V8-V9 regions show similar community representations over freshwater, coastal, and wastewater environments, but specific samples show markedly different communities. These results indicate that multiple primer sets may be advantageous for gaining a more complete understanding of community structure and highlight the importance of including mock communities composed of species of interest. The quantification of error associated with community representation by amplicon sequencing is a critical challenge that is often ignored. When target genes are amplified using currently available primers, differential amplification efficiencies result in inaccurate estimates of community structure. The extent to which amplification bias affects community representation and the accuracy with which different gene targets represent community structure are not known. As a result, there is no consensus on which region provides the most suitable representation of diversity for eukaryotes. This study determined the accuracy with which commonly used 18S rRNA gene primer sets represent community structure and identified particular biases related to PCR amplification and Illumina MiSeq sequencing in order to more accurately study eukaryotic microbial communities. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.

PubMed

Erickson, Jon A; Jalaie, Mehran; Robertson, Daniel H; Lewis, Richard A; Vieth, Michal

2004-01-01

The key to success for computational tools used in structure-based drug design is the ability to accurately place or "dock" a ligand in the binding pocket of the target of interest. In this report we examine the effect of several factors on docking accuracy, including ligand and protein flexibility. To examine ligand flexibility in an unbiased fashion, a test set of 41 ligand-protein cocomplex X-ray structures were assembled that represent a diversity of size, flexibility, and polarity with respect to the ligands. Four docking algorithms, DOCK, FlexX, GOLD, and CDOCKER, were applied to the test set, and the results were examined in terms of the ability to reproduce X-ray ligand positions within 2.0A heavy atom root-mean-square deviation. Overall, each method performed well (>50% accuracy) but for all methods it was found that docking accuracy decreased substantially for ligands with eight or more rotatable bonds. Only CDOCKER was able to accurately dock most of those ligands with eight or more rotatable bonds (71% accuracy rate). A second test set of structures was gathered to examine how protein flexibility influences docking accuracy. CDOCKER was applied to X-ray structures of trypsin, thrombin, and HIV-1-protease, using protein structures bound to several ligands and also the unbound (apo) form. Docking experiments of each ligand to one "average" structure and to the apo form were carried out, and the results were compared to docking each ligand back to its originating structure. The results show that docking accuracy falls off dramatically if one uses an average or apo structure. In fact, it is shown that the drop in docking accuracy mirrors the degree to which the protein moves upon ligand binding.
Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement.

PubMed

Cuevas, Hugo E; Rosa-Valentin, Giseiry; Hayes, Chad M; Rooney, William L; Hoffmann, Leo

2017-01-26

The USDA Agriculture Research Service National Plant Germplasm System (NPGS) preserves the largest sorghum germplasm collection in the world, which includes 7,217 accessions from the center of diversity in Ethiopia. The characterization of this exotic germplasm at a genome-wide scale will improve conservation efforts and its utilization in research and breeding programs. Therefore, we phenotyped a representative core set of 374 Ethiopian accessions at two locations for agronomic traits and characterized the genomes. Using genotyping-by-sequencing, we identified 148,476 single-nucleotide polymorphism (SNP) markers distributed across the entire genome. Over half of the alleles were rare (frequency < 0.05). The genetic profile of each accession was unique (i.e., no duplicates), and the average genetic distance among accessions was 0.70. Based on population structure and cluster analyses, we separated the collection into 11 populations with pairwise F ST values ranging from 0.11 to 0.47. In total, 198 accessions (53%) were assigned to one of these populations with an ancestry membership coefficient of larger than 0.60; these covered 90% of the total genomic variation. We characterized these populations based on agronomic and seed compositional traits. We performed a cluster analysis with the sorghum association panel based on 26,026 SNPs and determined that nine of the Ethiopian populations expanded the genetic diversity in the panel. Genome-wide association analysis demonstrated that these low-coverage data and the observed population structure could be employed for the genomic dissection of important phenotypes in this core set of Ethiopian sorghum germplasm. The NPGS Ethiopian sorghum germplasm is a genetically and phenotypically diverse collection comprising 11 populations with high levels of admixture. Genetic associations with agronomic traits can be used to improve the screening of exotic germplasm for selection of specific populations. We detected many rare alleles, suggesting that this germplasm contains potentially useful undiscovered alleles, but their discovery and characterization will require extensive effort. The genotypic data available for these accessions provide a valuable resource for sorghum breeders and geneticists to effectively improve crops.
The Population Structure and Diversity of Eggplant from Asia and the Mediterranean Basin

PubMed Central

Cericola, Fabio; Portis, Ezio; Toppino, Laura; Barchi, Lorenzo; Acciarri, Nazareno; Ciriaci, Tommaso; Sala, Tea; Rotino, Giuseppe Leonardo; Lanteri, Sergio

2013-01-01

A collection of 238 eggplant breeding lines, heritage varieties and selections within local landraces provenanced from Asia and the Mediterranean Basin was phenotyped with respect to key plant and fruit traits, and genotyped using 24 microsatellite loci distributed uniformly throughout the genome. STRUCTURE analysis based on the genotypic data identified two major sub-groups, which to a large extent mirrored the provenance of the entries. With the goal to identify true-breeding types, 38 of the entries were discarded on the basis of microsatellite-based residual heterozygosity, along with a further nine which were not phenotypically uniform. The remaining 191 entries were scored for a set of 19 fruit and plant traits in a replicated experimental field trial. The phenotypic data were subjected to principal component and hierarchical principal component analyses, allowing three major morphological groups to be identified. All three morphological groups were represented in both the “Occidental” and the “Oriental” germplasm, so the correlation between the phenotypic and the genotypic data sets was quite weak. The relevance of these results for evolutionary studies and the further improvement of eggplant are discussed. The population structure of the core set of germplasm shows that it can be used as a basis for an association mapping approach. PMID:24040032
The population structure and diversity of eggplant from Asia and the Mediterranean Basin.

PubMed

Cericola, Fabio; Portis, Ezio; Toppino, Laura; Barchi, Lorenzo; Acciarri, Nazareno; Ciriaci, Tommaso; Sala, Tea; Rotino, Giuseppe Leonardo; Lanteri, Sergio

2013-01-01

A collection of 238 eggplant breeding lines, heritage varieties and selections within local landraces provenanced from Asia and the Mediterranean Basin was phenotyped with respect to key plant and fruit traits, and genotyped using 24 microsatellite loci distributed uniformly throughout the genome. STRUCTURE analysis based on the genotypic data identified two major sub-groups, which to a large extent mirrored the provenance of the entries. With the goal to identify true-breeding types, 38 of the entries were discarded on the basis of microsatellite-based residual heterozygosity, along with a further nine which were not phenotypically uniform. The remaining 191 entries were scored for a set of 19 fruit and plant traits in a replicated experimental field trial. The phenotypic data were subjected to principal component and hierarchical principal component analyses, allowing three major morphological groups to be identified. All three morphological groups were represented in both the "Occidental" and the "Oriental" germplasm, so the correlation between the phenotypic and the genotypic data sets was quite weak. The relevance of these results for evolutionary studies and the further improvement of eggplant are discussed. The population structure of the core set of germplasm shows that it can be used as a basis for an association mapping approach.
Phenotypic diversity, population structure and stress protein-based capacitoring in populations of Xeropicta derbentina, a heat-tolerant land snail species.

PubMed

Di Lellis, Maddalena A; Sereda, Sergej; Geißler, Anna; Picot, Adrien; Arnold, Petra; Lang, Stefanie; Troschinski, Sandra; Dieterich, Andreas; Hauffe, Torsten; Capowiez, Yvan; Mazzia, Christophe; Knigge, Thomas; Monsinjon, Tiphaine; Krais, Stefanie; Wilke, Thomas; Triebskorn, Rita; Köhler, Heinz-R

2014-11-01

The shell colour of many pulmonate land snail species is highly diverse. Besides a genetic basis, environmentally triggered epigenetic mechanisms including stress proteins as evolutionary capacitors are thought to influence such phenotypic diversity. In this study, we investigated the relationship of stress protein (Hsp70) levels with temperature stress tolerance, population structure and phenotypic diversity within and among different populations of a xerophilic Mediterranean snail species (Xeropicta derbentina). Hsp70 levels varied considerably among populations, and were significantly associated with shell colour diversity: individuals in populations exhibiting low diversity expressed higher Hsp70 levels both constitutively and under heat stress than those of phenotypically diverse populations. In contrast, population structure (cytochrome c oxidase subunit I gene) did not correlate with phenotypic diversity. However, genetic parameters (both within and among population differences) were able to explain variation in Hsp70 induction at elevated but non-pathologic temperatures. Our observation that (1) population structure had a high explanatory potential for Hsp70 induction and that (2) Hsp70 levels, in turn, correlated with phenotypic diversity while (3) population structure and phenotypic diversity failed to correlate provides empirical evidence for Hsp70 to act as a mediator between genotypic variation and phenotype and thus for chaperone-driven evolutionary capacitance in natural populations.
Origin, Migration Routes and Worldwide Population Genetic Structure of the Wheat Yellow Rust Pathogen Puccinia striiformis f.sp. tritici

PubMed Central

Ali, Sajid; Gladieux, Pierre; Leconte, Marc; Gautier, Angélique; Justesen, Annemarie F.; Hovmøller, Mogens S.; Enjalbert, Jérôme; de Vallavieille-Pope, Claude

2014-01-01

Analyses of large-scale population structure of pathogens enable the identification of migration patterns, diversity reservoirs or longevity of populations, the understanding of current evolutionary trajectories and the anticipation of future ones. This is particularly important for long-distance migrating fungal pathogens such as Puccinia striiformis f.sp. tritici (PST), capable of rapid spread to new regions and crop varieties. Although a range of recent PST invasions at continental scales are well documented, the worldwide population structure and the center of origin of the pathogen were still unknown. In this study, we used multilocus microsatellite genotyping to infer worldwide population structure of PST and the origin of new invasions based on 409 isolates representative of distribution of the fungus on six continents. Bayesian and multivariate clustering methods partitioned the set of multilocus genotypes into six distinct genetic groups associated with their geographical origin. Analyses of linkage disequilibrium and genotypic diversity indicated a strong regional heterogeneity in levels of recombination, with clear signatures of recombination in the Himalayan (Nepal and Pakistan) and near-Himalayan regions (China) and a predominant clonal population structure in other regions. The higher genotypic diversity, recombinant population structure and high sexual reproduction ability in the Himalayan and neighboring regions suggests this area as the putative center of origin of PST. We used clustering methods and approximate Bayesian computation (ABC) to compare different competing scenarios describing ancestral relationship among ancestral populations and more recently founded populations. Our analyses confirmed the Middle East-East Africa as the most likely source of newly spreading, high-temperature-adapted strains; Europe as the source of South American, North American and Australian populations; and Mediterranean-Central Asian populations as the origin of South African populations. Although most geographic populations are not markedly affected by recent dispersal events, this study emphasizes the influence of human activities on recent long-distance spread of the pathogen. PMID:24465211
An unconventional family 1 uracil DNA glycosylase in Nitratifractor salsuginis.

PubMed

Li, Jing; Chen, Ran; Yang, Ye; Zhang, Zhemin; Fang, Guang-Chen; Xie, Wei; Cao, Weiguo

2017-12-01

The uracil DNA glycosylase superfamily consists of at least six families with a diverse specificity toward DNA base damage. Family 1 uracil N-glycosylase (UNG) exhibits exclusive specificity on uracil-containing DNA. Here, we report a family 1 UNG homolog from Nitratifractor salsuginis with distinct biochemical features that differentiate it from conventional family 1 UNGs. Globally, the crystal structure of N. salsuginisUNG shows a few additional secondary structural elements. Biochemical and enzyme kinetic analysis, coupled with structural determination, molecular modeling, and molecular dynamics simulations, shows that N. salsuginisUNG contains a salt bridge network that plays an important role in DNA backbone interactions. Disruption of the amino acid residues involved in the salt bridges greatly impedes the enzymatic activity. A tyrosine residue in motif 1 (GQDPY) is one of the distinct sequence features setting family 1 UNG apart from other families. The crystal structure of Y81G mutant indicates that several subtle changes may account for its inactivity. Unlike the conventional family 1 UNG enzymes, N. salsuginisUNG is not inhibited by Ugi, a potent inhibitor specific for family 1 UNG. This study underscores the diversity of paths that a uracil DNA glycosylase may take to acquire its unique structural and biochemical properties during evolution. Structure data are available in the PDB under accession numbers 5X3G and 5X3H. © 2017 Federation of European Biochemical Societies.
Structure of the Antibiotic Resistance Factor Spectinomycin Phosphotransferase from Legionella pneumophila

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

Fong, D.; Lemke, C; Huang, J

2010-01-01

Aminoglycoside phosphotransferases (APHs) constitute a diverse group of enzymes that are often the underlying cause of aminoglycoside resistance in the clinical setting. Several APHs have been extensively characterized, including the elucidation of the three-dimensional structure of two APH(3{prime}) isozymes and an APH(2{double_prime}) enzyme. Although many APHs are plasmid-encoded and are capable of inactivating numerous 2-deoxystreptmaine aminoglycosides with multiple regiospecificity, APH(9)-Ia, isolated from Legionella pneumophila, is an unusual enzyme among the APH family for its chromosomal origin and its specificity for a single non-2-deoxystreptamine aminoglycoside substrate, spectinomycin. We describe here the crystal structures of APH(9)-Ia in its apo form, its binarymore » complex with the nucleotide, AMP, and its ternary complex bound with ADP and spectinomycin. The structures reveal that APH(9)-Ia adopts the bilobal protein kinase-fold, analogous to the APH(3{prime}) and APH(2{double_prime}) enzymes. However, APH(9)-Ia differs significantly from the other two types of APH enzymes in its substrate binding area and that it undergoes a conformation change upon ligand binding. Moreover, kinetic assay experiments indicate that APH(9)-Ia has stringent substrate specificity as it is unable to phosphorylate substrates of choline kinase or methylthioribose kinase despite high structural resemblance. The crystal structures of APH(9)-Ia demonstrate and expand our understanding of the diversity of the APH family, which in turn will facilitate the development of new antibiotics and inhibitors.« less
Genetic diversity and structure in hill rice (Oryza sativa L.) landraces from the North-Eastern Himalayas of India.

PubMed

Roy, Somnath; Marndi, B C; Mawkhlieng, B; Banerjee, A; Yadav, R M; Misra, A K; Bansal, K C

2016-07-13

Hill rices (Oryza sativa L.) are direct seeded rices grown on hill slopes of different gradients. These landraces have evolved under rainfed and harsh environmental conditions and may possess genes governing adaptation traits such as tolerance to cold and moisture stress. In this study, 64 hill rice landraces were collected from the state of Arunachal Pradesh of North-Eastern region of India, and assessed by agro-morphological variability and microsatellite markers polymorphism. Our aim was to use phenotypic and genetic diversity data to understand the basis of farmers' classification of hill rice landraces into two groups: umte and tening. Another goal was to understand the genetic differentiation of hill rices into Indica or japonica subspecies. According to farmers' classification, hill rices were categorized into two groups: umte (large-grained, late maturing) and tening (small-grained, early maturing). We did not find significant difference in days to 50 % flowering between the groups. Principal component analysis revealed that two groups can be distinguished on the basis of kernel length-to-width ration (KLW), kernel length (KL), grain length (GrL), grain length-to-width ration (GrLW) and plant height (Ht). Stepwise canonical discriminant analysis identified KL and Ht as the main discriminatory characters between the cultivar groups. Genetic diversity analysis with 35 SSR markers revealed considerable genetic diversity in the hill rice germplasm (gene diversity: 0.66; polymorphism information content: 0.62). Pair-wise allelic difference between umte and tening groups was not statistically significant. The model-based population structure analysis showed that the hill rices were clustered into two broad groups corresponding to Indica and Japonica. The geographic distribution and cultivars grouping of hill rices were not congruent in genetic clusters. Both distance- and model-based approaches indicated that the hill rices were predominantly japonica or admixture among the groups within the subspecies. These findings were further supported by combined analysis hill rices with 150 reference rice accessions representing major genetic groups of rice. This study collected a valuable set of hill rice germplasm for rice breeding and for evolutionary studies. It also generated a new set of information on genetic and phenotypic diversity of hill rice landraces in North-Eastern region of India. The collected hill rices were mostly japonica or admixture among the subpopulations of Indica or Japonica. The findings are useful for utilization and conservation of hill rice germplasm.
Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences.

PubMed

Aguilera-Mendoza, Longendri; Marrero-Ponce, Yovani; Tellez-Ibarra, Roberto; Llorente-Quesada, Monica T; Salgado, Jesús; Barigye, Stephen J; Liu, Jun

2015-08-01

The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are included in CAMP_Patent. However, the majority of databases have their own set of unique sequences, as well as some overlap with other databases. The complete set of non-duplicate sequences comprises 16 990 cases, which is almost half of the total number of reported peptides. On the other hand, the diversity analysis identifies the most and least diverse databases and proves that all databases exhibit some level of redundancy. Finally, we present a new parallel-free software, named Dover Analyzer, developed to compute the overlap and diversity between any number of databases and compile a set of non-redundant sequences. These results are useful for selecting or building a suitable representative set of AMPs, according to specific needs. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Dealing with AFLP genotyping errors to reveal genetic structure in Plukenetia volubilis (Euphorbiaceae) in the Peruvian Amazon

PubMed Central

Vašek, Jakub; Viehmannová, Iva; Ocelák, Martin; Cachique Huansi, Danter; Vejl, Pavel

2017-01-01

An analysis of the population structure and genetic diversity for any organism often depends on one or more molecular marker techniques. Nonetheless, these techniques are not absolutely reliable because of various sources of errors arising during the genotyping process. Thus, a complex analysis of genotyping error was carried out with the AFLP method in 169 samples of the oil seed plant Plukenetia volubilis L. from small isolated subpopulations in the Peruvian Amazon. Samples were collected in nine localities from the region of San Martin. Analysis was done in eight datasets with a genotyping error from 0 to 5%. Using eleven primer combinations, 102 to 275 markers were obtained according to the dataset. It was found that it is only possible to obtain the most reliable and robust results through a multiple-level filtering process. Genotyping error and software set up influence both the estimation of population structure and genetic diversity, where in our case population number (K) varied between 2–9 depending on the dataset and statistical method used. Surprisingly, discrepancies in K number were caused more by statistical approaches than by genotyping errors themselves. However, for estimation of genetic diversity, the degree of genotyping error was critical because descriptive parameters (He, FST, PLP 5%) varied substantially (by at least 25%). Due to low gene flow, P. volubilis mostly consists of small isolated subpopulations (ΦPT = 0.252–0.323) with some degree of admixture given by socio-economic connectivity among the sites; a direct link between the genetic and geographic distances was not confirmed. The study illustrates the successful application of AFLP to infer genetic structure in non-model plants. PMID:28910307
Architectural Design Drives the Biogeography of Indoor Bacterial Communities

PubMed Central

O’Connor, Timothy K.; Mhuireach, Gwynne; Northcutt, Dale; Kline, Jeff; Moriyama, Maxwell; Brown, G. Z.; Bohannan, Brendan J. M.; Green, Jessica L.

2014-01-01

Background Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. Results Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. Conclusions Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our health and well-being. PMID:24489843
Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity.

PubMed

Korkuć, Paula; Walther, Dirk

2015-01-01

To better understand and ultimately predict both the metabolic activities as well as the signaling functions of metabolites, a detailed understanding of the physical interactions of metabolites with proteins is highly desirable. Focusing in particular on protein binding specificity vs. promiscuity, we performed a comprehensive analysis of the physicochemical properties of compound-protein binding events as reported in the Protein Data Bank (PDB). We compared the molecular and structural characteristics obtained for metabolites to those of the well-studied interactions of drug compounds with proteins. Promiscuously binding metabolites and drugs are characterized by low molecular weight and high structural flexibility. Unlike reported for drug compounds, low rather than high hydrophobicity appears associated, albeit weakly, with promiscuous binding for the metabolite set investigated in this study. Across several physicochemical properties, drug compounds exhibit characteristic binding propensities that are distinguishable from those associated with metabolites. Prediction of target diversity and compound promiscuity using physicochemical properties was possible at modest accuracy levels only, but was consistently better for drugs than for metabolites. Compound properties capturing structural flexibility and hydrogen-bond formation descriptors proved most informative in PLS-based prediction models. With regard to diversity of enzymatic activities of the respective metabolite target enzymes, the metabolites benzylsuccinate, hypoxanthine, trimethylamine N-oxide, oleoylglycerol, and resorcinol showed very narrow process involvement, while glycine, imidazole, tryptophan, succinate, and glutathione were identified to possess broad enzymatic reaction scopes. Promiscuous metabolites were found to mainly serve as general energy currency compounds, but were identified to also be involved in signaling processes and to appear in diverse organismal systems (digestive and nervous system) suggesting specific molecular and physiological roles of promiscuous metabolites.
Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity

PubMed Central

Korkuć, Paula; Walther, Dirk

2015-01-01

To better understand and ultimately predict both the metabolic activities as well as the signaling functions of metabolites, a detailed understanding of the physical interactions of metabolites with proteins is highly desirable. Focusing in particular on protein binding specificity vs. promiscuity, we performed a comprehensive analysis of the physicochemical properties of compound-protein binding events as reported in the Protein Data Bank (PDB). We compared the molecular and structural characteristics obtained for metabolites to those of the well-studied interactions of drug compounds with proteins. Promiscuously binding metabolites and drugs are characterized by low molecular weight and high structural flexibility. Unlike reported for drug compounds, low rather than high hydrophobicity appears associated, albeit weakly, with promiscuous binding for the metabolite set investigated in this study. Across several physicochemical properties, drug compounds exhibit characteristic binding propensities that are distinguishable from those associated with metabolites. Prediction of target diversity and compound promiscuity using physicochemical properties was possible at modest accuracy levels only, but was consistently better for drugs than for metabolites. Compound properties capturing structural flexibility and hydrogen-bond formation descriptors proved most informative in PLS-based prediction models. With regard to diversity of enzymatic activities of the respective metabolite target enzymes, the metabolites benzylsuccinate, hypoxanthine, trimethylamine N-oxide, oleoylglycerol, and resorcinol showed very narrow process involvement, while glycine, imidazole, tryptophan, succinate, and glutathione were identified to possess broad enzymatic reaction scopes. Promiscuous metabolites were found to mainly serve as general energy currency compounds, but were identified to also be involved in signaling processes and to appear in diverse organismal systems (digestive and nervous system) suggesting specific molecular and physiological roles of promiscuous metabolites. PMID:26442281
A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

PubMed

Barberán, Albert; Casamayor, Emilio O

2014-12-01

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies. © 2014 John Wiley & Sons Ltd.
Building a Better Fragment Library for De Novo Protein Structure Prediction

PubMed Central

de Oliveira, Saulo H. P.; Shi, Jiye; Deane, Charlotte M.

2015-01-01

Fragment-based approaches are the current standard for de novo protein structure prediction. These approaches rely on accurate and reliable fragment libraries to generate good structural models. In this work, we describe a novel method for structure fragment library generation and its application in fragment-based de novo protein structure prediction. The importance of correct testing procedures in assessing the quality of fragment libraries is demonstrated. In particular, the exclusion of homologs to the target from the libraries to correctly simulate a de novo protein structure prediction scenario, something which surprisingly is not always done. We demonstrate that fragments presenting different predominant predicted secondary structures should be treated differently during the fragment library generation step and that exhaustive and random search strategies should both be used. This information was used to develop a novel method, Flib. On a validation set of 41 structurally diverse proteins, Flib libraries presents both a higher precision and coverage than two of the state-of-the-art methods, NNMake and HHFrag. Flib also achieves better precision and coverage on the set of 275 protein domains used in the two previous experiments of the the Critical Assessment of Structure Prediction (CASP9 and CASP10). We compared Flib libraries against NNMake libraries in a structure prediction context. Of the 13 cases in which a correct answer was generated, Flib models were more accurate than NNMake models for 10. “Flib is available for download at: http://www.stats.ox.ac.uk/research/proteins/resources”. PMID:25901595
Structure Diversity, Synthesis, and Biological Activity of Cyathane Diterpenoids in Higher Fungi.

PubMed

Tang, Hao-Yu; Yin, Xia; Zhang, Cheng-Chen; Jia, Qian; Gao, Jin-Ming

2015-01-01

Cyathane diterpenoids, occurring exclusively in higher basidiomycete (mushrooms), represent a structurally diverse class of natural products based on a characteristic 5-6-7 tricyclic carbon scaffold, including 105 members reported to date. These compounds show a diverse range of biological activities, such as antimicrobial, anti-MRSA, agonistic toward the kappa-opioid receptor, antiinflammatory, anti-proliferative and nerve growth factor (NGF)-like properties. The present review focuses on the structure diversity, structure elucidation and biological studies of these compounds, including mechanisms of actions and structure-activity relationships (SARs). In addition, new progress in chemical synthesis of cyathane diterpenoids is discussed.
Survival, momentum, and things that make me "me": patients' perceptions of goal setting after stroke.

PubMed

Brown, Melanie; Levack, William; McPherson, Kathryn M; Dean, Sarah G; Reed, Kirk; Weatherall, Mark; Taylor, William J

2014-01-01

Goal setting and patient-centredness are considered fundamental concepts in rehabilitation. However, the best way to involve patients in setting goals remains unclear. The purpose of this study was to explore patient experiences of goal setting in post-acute stroke rehabilitation to further understanding of its application to practice. Thematic analysis was used to analyse interview transcripts from 10 stroke survivors, recruited from 4 rehabilitation units as part of a pilot study investigating the effects of a structured means of eliciting patient-centred goals in post-acute stroke rehabilitation. Three key themes emerged: (1) "A Day by Day Momentum", comprising subordinate themes of "Unpredictability" and "Natural Progression" in which daily progress forwards was seen as an integral part of rehabilitation; (2) "Battle versus Alliance" in which issues of struggle versus support influenced participants' advancement; and (3) "The Special Things", consisting of subordinate themes of "What Makes Me 'Me'" and "Symbolic Achievements" concerning issues defining individuals and their rehabilitation experiences. Patients' discourse around goal setting can differ from the discourse conventionally used by clinicians when describing "best practice" in rehabilitation goal setting. Understanding patients' non-conventional views of goals may assist in supporting and motivating them, thus providing drive for their rehabilitation. Stroke patients think about goals very differently from health professionals. Individual patients have diverse ideas about goals within the context of the uncertainty of stroke, their life as a whole and recovery after formal rehabilitation is completed. To meet these diverse needs, health professionals need to communicate fully with patients to gain an understanding of their experiences of stroke and wider views on goals.
The value of protein structure classification information-Surveying the scientific literature

DOE PAGES

Fox, Naomi K.; Brenner, Steven E.; Chandonia, John -Marc

2015-08-27

The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP-extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012-2013 that cite SCOP, 439 actually use data from themore » resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non-SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings.« less
The value of protein structure classification information-Surveying the scientific literature

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

Fox, Naomi K.; Brenner, Steven E.; Chandonia, John -Marc

The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP-extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012-2013 that cite SCOP, 439 actually use data from themore » resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non-SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings.« less

Diversity and Evolution in the Genome of Clostridium difficile

PubMed Central

Knight, Daniel R.; Elliott, Briony; Chang, Barbara J.; Perkins, Timothy T.

2015-01-01

SUMMARY Clostridium difficile infection (CDI) is the leading cause of antimicrobial and health care-associated diarrhea in humans, presenting a significant burden to global health care systems. In the last 2 decades, PCR- and sequence-based techniques, particularly whole-genome sequencing (WGS), have significantly furthered our knowledge of the genetic diversity, evolution, epidemiology, and pathogenicity of this once enigmatic pathogen. C. difficile is taxonomically distinct from many other well-known clostridia, with a diverse population structure comprising hundreds of strain types spread across at least 6 phylogenetic clades. The C. difficile species is defined by a large diverse pangenome with extreme levels of evolutionary plasticity that has been shaped over long time periods by gene flux and recombination, often between divergent lineages. These evolutionary events are in response to environmental and anthropogenic activities and have led to the rapid emergence and worldwide dissemination of virulent clonal lineages. Moreover, genome analysis of large clinically relevant data sets has improved our understanding of CDI outbreaks, transmission, and recurrence. The epidemiology of CDI has changed dramatically over the last 15 years, and CDI may have a foodborne or zoonotic etiology. The WGS era promises to continue to redefine our view of this significant pathogen. PMID:26085550
Genetic diversity and structure of elite cotton germplasm (Gossypium hirsutum L.) using genome-wide SNP data.

PubMed

Ai, XianTao; Liang, YaJun; Wang, JunDuo; Zheng, JuYun; Gong, ZhaoLong; Guo, JiangPing; Li, XueYuan; Qu, YanYing

2017-10-01

Cotton (Gossypium spp.) is the most important natural textile fiber crop, and Gossypium hirsutum L. is responsible for 90% of the annual cotton crop in the world. Information on cotton genetic diversity and population structure is essential for new breeding lines. In this study, we analyzed population structure and genetic diversity of 288 elite Gossypium hirsutum cultivar accessions collected from around the world, and especially from China, using genome-wide single nucleotide polymorphisms (SNP) markers. The average polymorphsim information content (PIC) was 0.25, indicating a relatively low degree of genetic diversity. Population structure analysis revealed extensive admixture and identified three subgroups. Phylogenetic analysis supported the subgroups identified by STRUCTURE. The results from both population structure and phylogenetic analysis were, for the most part, in agreement with pedigree information. Analysis of molecular variance revealed a larger amount of variation was due to diversity within the groups. Establishment of genetic diversity and population structure from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in upland cotton.
3D-QSAR comparative molecular field analysis on opioid receptor antagonists: pooling data from different studies.

PubMed

Peng, Youyi; Keenan, Susan M; Zhang, Qiang; Kholodovych, Vladyslav; Welsh, William J

2005-03-10

Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were constructed using comparative molecular field analysis (CoMFA) on a series of opioid receptor antagonists. To obtain statistically significant and robust CoMFA models, a sizable data set of naltrindole and naltrexone analogues was assembled by pooling biological and structural data from independent studies. A process of "leave one data set out", similar to the traditional "leave one out" cross-validation procedure employed in partial least squares (PLS) analysis, was utilized to study the feasibility of pooling data in the present case. These studies indicate that our approach yields statistically significant and highly predictive CoMFA models from the pooled data set of delta, mu, and kappa opioid receptor antagonists. All models showed excellent internal predictability and self-consistency: q(2) = 0.69/r(2) = 0.91 (delta), q(2) = 0.67/r(2) = 0.92 (mu), and q(2) = 0.60/r(2) = 0.96 (kappa). The CoMFA models were further validated using two separate test sets: one test set was selected randomly from the pooled data set, while the other test set was retrieved from other published sources. The overall excellent agreement between CoMFA-predicted and experimental binding affinities for a structurally diverse array of ligands across all three opioid receptor subtypes gives testimony to the superb predictive power of these models. CoMFA field analysis demonstrated that the variations in binding affinity of opioid antagonists are dominated by steric rather than electrostatic interactions with the three opioid receptor binding sites. The CoMFA steric-electrostatic contour maps corresponding to the delta, mu, and kappa opioid receptor subtypes reflected the characteristic similarities and differences in the familiar "message-address" concept of opioid receptor ligands. Structural modifications to increase selectivity for the delta over mu and kappa opioid receptors have been predicted on the basis of the CoMFA contour maps. The structure-activity relationships (SARs) together with the CoMFA models should find utility for the rational design of subtype-selective opioid receptor antagonists.
Identification of a common neurobiological substrate for mental illness.

PubMed

Goodkind, Madeleine; Eickhoff, Simon B; Oathes, Desmond J; Jiang, Ying; Chang, Andrew; Jones-Hagata, Laura B; Ortega, Brissa N; Zaiko, Yevgeniya V; Roach, Erika L; Korgaonkar, Mayuresh S; Grieve, Stuart M; Galatzer-Levy, Isaac; Fox, Peter T; Etkin, Amit

2015-04-01

Psychiatric diagnoses are currently distinguished based on sets of specific symptoms. However, genetic and clinical analyses find similarities across a wide variety of diagnoses, suggesting that a common neurobiological substrate may exist across mental illness. To conduct a meta-analysis of structural neuroimaging studies across multiple psychiatric diagnoses, followed by parallel analyses of 3 large-scale healthy participant data sets to help interpret structural findings in the meta-analysis. PubMed was searched to identify voxel-based morphometry studies through July 2012 comparing psychiatric patients to healthy control individuals for the meta-analysis. The 3 parallel healthy participant data sets included resting-state functional magnetic resonance imaging, a database of activation foci across thousands of neuroimaging experiments, and a data set with structural imaging and cognitive task performance data. Studies were included in the meta-analysis if they reported voxel-based morphometry differences between patients with an Axis I diagnosis and control individuals in stereotactic coordinates across the whole brain, did not present predominantly in childhood, and had at least 10 studies contributing to that diagnosis (or across closely related diagnoses). The meta-analysis was conducted on peak voxel coordinates using an activation likelihood estimation approach. We tested for areas of common gray matter volume increase or decrease across Axis I diagnoses, as well as areas differing between diagnoses. Follow-up analyses on other healthy participant data sets tested connectivity related to regions arising from the meta-analysis and the relationship of gray matter volume to cognition. Based on the voxel-based morphometry meta-analysis of 193 studies comprising 15 892 individuals across 6 diverse diagnostic groups (schizophrenia, bipolar disorder, depression, addiction, obsessive-compulsive disorder, and anxiety), we found that gray matter loss converged across diagnoses in 3 regions: the dorsal anterior cingulate, right insula, and left insula. By contrast, there were few diagnosis-specific effects, distinguishing only schizophrenia and depression from other diagnoses. In the parallel follow-up analyses of the 3 independent healthy participant data sets, we found that the common gray matter loss regions formed a tightly interconnected network during tasks and at resting and that lower gray matter in this network was associated with poor executive functioning. We identified a concordance across psychiatric diagnoses in terms of integrity of an anterior insula/dorsal anterior cingulate-based network, which may relate to executive function deficits observed across diagnoses. This concordance provides an organizing model that emphasizes the importance of shared neural substrates across psychopathology, despite likely diverse etiologies, which is currently not an explicit component of psychiatric nosology.
Large-scale wind disturbances promote tree diversity in a Central Amazon forest.

PubMed

Marra, Daniel Magnabosco; Chambers, Jeffrey Q; Higuchi, Niro; Trumbore, Susan E; Ribeiro, Gabriel H P M; Dos Santos, Joaquim; Negrón-Juárez, Robinson I; Reu, Björn; Wirth, Christian

2014-01-01

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m(2)) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 to 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583 ± 46 trees ha(-1)) (mean ± 99% Confidence Interval) and basal area (26.7 ± 2.4 m(2) ha(-1)). Highly impacted areas had tree density and basal area as low as 120 trees ha(-1) and 14.9 m(2) ha(-1), respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m(2)) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level.
Genetic Patterns of Common-Bean Seed Acquisition and Early-Stage Adoption Among Farmer Groups in Western Uganda

PubMed Central

Wilkus, Erin L.; Berny Mier y Teran, Jorge C.; Mukankusi, Clare M.; Gepts, Paul

2018-01-01

Widespread adoption of new varieties can be valuable, especially where improved agricultural production technologies are hard to access. However, as farmers adopt new varieties, in situ population structure and genetic diversity of their seed holdings can change drastically. Consequences of adoption are still poorly understood due to a lack of crop genetic diversity assessments and detailed surveys of farmers' seed management practices. Common bean (Phaseolus vulgaris) is an excellent model for these types of studies, as it has a long history of cultivation among smallholder farmers, exhibits eco-geographic patterns of diversity (e.g., Andean vs. Mesoamerican gene-pools), and has been subjected to post-Columbian dispersal and recent introduction of improved cultivars. The Hoima district of western Uganda additionally provides an excellent social setting for evaluating consequences of adoption because access to improved varieties has varied across farmer groups in this production region. This study establishes a baseline understanding of the common bean diversity found among household producers in Uganda and compares the crop population structure, diversity and consequences of adoption of household producers with different adoption practices. Molecular diversity analysis, based on 4,955 single nucleotide polymorphism (SNP) markers, evaluated a total of 1,156 seed samples that included 196 household samples collected from household producers in the Hoima district, 19 breeder-selected varieties used in participatory breeding activities that had taken place prior to the study in the region, and a global bean germplasm collection. Households that had participated in regional participatory breeding efforts were more likely to adopt new varieties and, consequently, diversify their seed stocks than those that had not participated. Of the three farmer groups that participated in breeding efforts, households from the farmer group with the longest history of bean production were more likely to conserve “Seed Engufu”, a local “Calima”-type variety of the Andean bean gene pool, and, at the same time, introduce rare Mesoamerican gene pool varieties into household seed stocks. PMID:29868053
Large-Scale Wind Disturbances Promote Tree Diversity in a Central Amazon Forest

PubMed Central

Marra, Daniel Magnabosco; Chambers, Jeffrey Q.; Higuchi, Niro; Trumbore, Susan E.; Ribeiro, Gabriel H. P. M.; dos Santos, Joaquim; Negrón-Juárez, Robinson I.; Reu, Björn; Wirth, Christian

2014-01-01

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m2) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 to 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583±46 trees ha−1) (mean±99% Confidence Interval) and basal area (26.7±2.4 m2 ha−1). Highly impacted areas had tree density and basal area as low as 120 trees ha−1 and 14.9 m2 ha−1, respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m2) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level. PMID:25099118
Large-Scale Wind Disturbances Promote Tree Diversity in a Central Amazon Forest

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

Marra, Daniel Magnabosco; Chambers, Jeffrey Q.; Higuchi, Niro

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m 2) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 tomore » 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583±46 trees ha -1) (mean±99% Confidence Interval) and basal area (26.7±2.4 m 2 ha -1). Highly impacted areas had tree density and basal area as low as 120 trees ha -1 and 14.9 m 2 ha -1, respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m 2) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level.« less
Changes in Nematode Communities in Different Physiographic Sites of the Condor Seamount (North-East Atlantic Ocean) and Adjacent Sediments

PubMed Central

Zeppilli, Daniela; Bongiorni, Lucia; Serrão Santos, Ricardo; Vanreusel, Ann

2014-01-01

Several seamounts are known as ‘oases’ of high abundances and biomass and hotspots of biodiversity in contrast to the surrounding deep-sea environments. Recent studies have indicated that each single seamount can exhibit a high intricate habitat turnover. Information on alpha and beta diversity of single seamount is needed in order to fully understand seamounts contribution to regional and global biodiversity. However, while most of the seamount research has been focused on summits, studies considering the whole seamount structure are still rather poor. In the present study we analysed abundance, biomass and diversity of nematodes collected in distinct physiographic sites and surrounding sediments of the Condor Seamount (Azores, North-East Atlantic Ocean). Our study revealed higher nematode biomass in the seamount bases and values 10 times higher in the Condor sediments than in the far-field site. Although biodiversity indices did not showed significant differences comparing seamount sites and far-field sites, significant differences were observed in term of nematode composition. The Condor summit harboured a completely different nematode community when compared to the other seamount sites, with a high number of exclusive species and important differences in term of nematode trophic diversity. The oceanographic conditions observed around the Condor Seamount and the associated sediment mixing, together with the high quality of food resources available in seamount base could explain the observed patterns. Our results support the hypothesis that seamounts maintain high biodiversity through heightened beta diversity and showed that not only summits but also seamount bases can support rich benthic community in terms of standing stocks and diversity. Furthermore functional diversity of nematodes strongly depends on environmental conditions link to the local setting and seamount structure. This finding should be considered in future studies on seamounts, especially in view of the potential impacts due to current and future anthropogenic threats. PMID:25541988
Genetic Patterns of Common-Bean Seed Acquisition and Early-Stage Adoption Among Farmer Groups in Western Uganda.

PubMed

Wilkus, Erin L; Berny Mier Y Teran, Jorge C; Mukankusi, Clare M; Gepts, Paul

2018-01-01

Widespread adoption of new varieties can be valuable, especially where improved agricultural production technologies are hard to access. However, as farmers adopt new varieties, in situ population structure and genetic diversity of their seed holdings can change drastically. Consequences of adoption are still poorly understood due to a lack of crop genetic diversity assessments and detailed surveys of farmers' seed management practices. Common bean ( Phaseolus vulgaris ) is an excellent model for these types of studies, as it has a long history of cultivation among smallholder farmers, exhibits eco-geographic patterns of diversity (e.g., Andean vs. Mesoamerican gene-pools), and has been subjected to post-Columbian dispersal and recent introduction of improved cultivars. The Hoima district of western Uganda additionally provides an excellent social setting for evaluating consequences of adoption because access to improved varieties has varied across farmer groups in this production region. This study establishes a baseline understanding of the common bean diversity found among household producers in Uganda and compares the crop population structure, diversity and consequences of adoption of household producers with different adoption practices. Molecular diversity analysis, based on 4,955 single nucleotide polymorphism (SNP) markers, evaluated a total of 1,156 seed samples that included 196 household samples collected from household producers in the Hoima district, 19 breeder-selected varieties used in participatory breeding activities that had taken place prior to the study in the region, and a global bean germplasm collection. Households that had participated in regional participatory breeding efforts were more likely to adopt new varieties and, consequently, diversify their seed stocks than those that had not participated. Of the three farmer groups that participated in breeding efforts, households from the farmer group with the longest history of bean production were more likely to conserve "Seed Engufu", a local "Calima"-type variety of the Andean bean gene pool, and, at the same time, introduce rare Mesoamerican gene pool varieties into household seed stocks.
Large-Scale Wind Disturbances Promote Tree Diversity in a Central Amazon Forest

DOE PAGES

Marra, Daniel Magnabosco; Chambers, Jeffrey Q.; Higuchi, Niro; ...

2014-08-06

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m 2) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 tomore » 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583±46 trees ha -1) (mean±99% Confidence Interval) and basal area (26.7±2.4 m 2 ha -1). Highly impacted areas had tree density and basal area as low as 120 trees ha -1 and 14.9 m 2 ha -1, respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m 2) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level.« less
Mass Spectra-Based Framework for Automated Structural Elucidation of Metabolome Data to Explore Phytochemical Diversity

PubMed Central

Matsuda, Fumio; Nakabayashi, Ryo; Sawada, Yuji; Suzuki, Makoto; Hirai, Masami Y.; Kanaya, Shigehiko; Saito, Kazuki

2011-01-01

A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method. PMID:22645535
CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON ...

EPA Pesticide Factsheets

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database. Standardizing chemical structure annotation of public toxicity databases
Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection

PubMed Central

Zheng, Heping; Shabalin, Ivan G.; Handing, Katarzyna B.; Bujnicki, Janusz M.; Minor, Wladek

2015-01-01

The ubiquitous presence of magnesium ions in RNA has long been recognized as a key factor governing RNA folding, and is crucial for many diverse functions of RNA molecules. In this work, Mg2+-binding architectures in RNA were systematically studied using a database of RNA crystal structures from the Protein Data Bank (PDB). Due to the abundance of poorly modeled or incorrectly identified Mg2+ ions, the set of all sites was comprehensively validated and filtered to identify a benchmark dataset of 15 334 ‘reliable’ RNA-bound Mg2+ sites. The normalized frequencies by which specific RNA atoms coordinate Mg2+ were derived for both the inner and outer coordination spheres. A hierarchical classification system of Mg2+ sites in RNA structures was designed and applied to the benchmark dataset, yielding a set of 41 types of inner-sphere and 95 types of outer-sphere coordinating patterns. This classification system has also been applied to describe six previously reported Mg2+-binding motifs and detect them in new RNA structures. Investigation of the most populous site types resulted in the identification of seven novel Mg2+-binding motifs, and all RNA structures in the PDB were screened for the presence of these motifs. PMID:25800744
A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters.

PubMed

Sun, Chia-Tsen; Chiang, Austin W T; Hwang, Ming-Jing

2017-10-27

Proteome-scale bioinformatics research is increasingly conducted as the number of completely sequenced genomes increases, but analysis of protein domains (PDs) usually relies on similarity in their amino acid sequences and/or three-dimensional structures. Here, we present results from a bi-clustering analysis on presence/absence data for 6,580 unique PDs in 2,134 species with a sequenced genome, thus covering a complete set of proteins, for the three superkingdoms of life, Bacteria, Archaea, and Eukarya. Our analysis revealed eight distinctive PD clusters, which, following an analysis of enrichment of Gene Ontology functions and CATH classification of protein structures, were shown to exhibit structural and functional properties that are taxa-characteristic. For examples, the largest cluster is ubiquitous in all three superkingdoms, constituting a set of 1,472 persistent domains created early in evolution and retained in living organisms and characterized by basic cellular functions and ancient structural architectures, while an Archaea and Eukarya bi-superkingdom cluster suggests its PDs may have existed in the ancestor of the two superkingdoms, and others are single superkingdom- or taxa (e.g. Fungi)-specific. These results contribute to increase our appreciation of PD diversity and our knowledge of how PDs are used in species, yielding implications on species evolution.
Computational predictive models for P-glycoprotein inhibition of in-house chalcone derivatives and drug-bank compounds.

PubMed

Ngo, Trieu-Du; Tran, Thanh-Dao; Le, Minh-Tri; Thai, Khac-Minh

2016-11-01

The human P-glycoprotein (P-gp) efflux pump is of great interest for medicinal chemists because of its important role in multidrug resistance (MDR). Because of the high polyspecificity as well as the unavailability of high-resolution X-ray crystal structures of this transmembrane protein, ligand-based, and structure-based approaches which were machine learning, homology modeling, and molecular docking were combined for this study. In ligand-based approach, individual two-dimensional quantitative structure-activity relationship models were developed using different machine learning algorithms and subsequently combined into the Ensemble model which showed good performance on both the diverse training set and the validation sets. The applicability domain and the prediction quality of the developed models were also judged using the state-of-the-art methods and tools. In our structure-based approach, the P-gp structure and its binding region were predicted for a docking study to determine possible interactions between the ligands and the receptor. Based on these in silico tools, hit compounds for reversing MDR were discovered from the in-house and DrugBank databases through virtual screening using prediction models and molecular docking in an attempt to restore cancer cell sensitivity to cytotoxic drugs.
A phylogenetic framework facilitates Y-STR variant discovery and classification via massively parallel sequencing.

PubMed

Huszar, Tunde I; Jobling, Mark A; Wetton, Jon H

2018-04-12

Short tandem repeats on the male-specific region of the Y chromosome (Y-STRs) are permanently linked as haplotypes, and therefore Y-STR sequence diversity can be considered within the robust framework of a phylogeny of haplogroups defined by single nucleotide polymorphisms (SNPs). Here we use massively parallel sequencing (MPS) to analyse the 23 Y-STRs in Promega's prototype PowerSeq™ Auto/Mito/Y System kit (containing the markers of the PowerPlex® Y23 [PPY23] System) in a set of 100 diverse Y chromosomes whose phylogenetic relationships are known from previous megabase-scale resequencing. Including allele duplications and alleles resulting from likely somatic mutation, we characterised 2311 alleles, demonstrating 99.83% concordance with capillary electrophoresis (CE) data on the same sample set. The set contains 267 distinct sequence-based alleles (an increase of 58% compared to the 169 detectable by CE), including 60 novel Y-STR variants phased with their flanking sequences which have not been reported previously to our knowledge. Variation includes 46 distinct alleles containing non-reference variants of SNPs/indels in both repeat and flanking regions, and 145 distinct alleles containing repeat pattern variants (RPV). For DYS385a,b, DYS481 and DYS390 we observed repeat count variation in short flanking segments previously considered invariable, and suggest new MPS-based structural designations based on these. We considered the observed variation in the context of the Y phylogeny: several specific haplogroup associations were observed for SNPs and indels, reflecting the low mutation rates of such variant types; however, RPVs showed less phylogenetic coherence and more recurrence, reflecting their relatively high mutation rates. In conclusion, our study reveals considerable additional diversity at the Y-STRs of the PPY23 set via MPS analysis, demonstrates high concordance with CE data, facilitates nomenclature standardisation, and places Y-STR sequence variants in their phylogenetic context. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.
Nature of the protein universe

PubMed Central

Levitt, Michael

2009-01-01

The protein universe is the set of all proteins of all organisms. Here, all currently known sequences are analyzed in terms of families that have single-domain or multidomain architectures and whether they have a known three-dimensional structure. Growth of new single-domain families is very slow: Almost all growth comes from new multidomain architectures that are combinations of domains characterized by ≈15,000 sequence profiles. Single-domain families are mostly shared by the major groups of organisms, whereas multidomain architectures are specific and account for species diversity. There are known structures for a quarter of the single-domain families, and >70% of all sequences can be partially modeled thanks to their membership in these families. PMID:19541617
Persistence of Multiple Genetic Lineages within Intrahost Populations of Ross River Virus▿

PubMed Central

Liu, Wen J.; Rourke, Michelle F.; Holmes, Edward C.; Aaskov, John G.

2011-01-01

We examined the structure and extent of genetic diversity in intrahost populations of Ross River virus (RRV) in samples from six human patients, focusing on the nonstructural (nsP3) and structural (E2) protein genes. Strikingly, although the samples were collected from contrasting ecological settings 3,000 kilometers apart in Australia, we observed multiple viral lineages in four of the six individuals, which is indicative of widespread mixed infections. In addition, a comparison with previously published RRV sequences revealed that these distinct lineages have been in circulation for at least 5 years, and we were able to document their long-term persistence over extensive geographical distances. PMID:21430052
Switchable regioselectivity in amine-catalysed asymmetric cycloadditions

NASA Astrophysics Data System (ADS)

Zhou, Zhi; Wang, Zhou-Xiang; Zhou, Yuan-Chun; Xiao, Wei; Ouyang, Qin; Du, Wei; Chen, Ying-Chun

2017-06-01

Building small-molecule libraries with structural and stereogenic diversity plays an important role in drug discovery. The development of switchable intermolecular cycloaddition reactions from identical substrates in different regioselective fashions would provide an attractive protocol. However, this also represents a challenge in organic chemistry, because it is difficult to control regioselectivity to afford the products exclusively and at the same time achieve high levels of stereoselectivity. Here, we report the diversified cycloadditions of α‧-alkylidene-2-cyclopentenones catalysed by cinchona-derived primary amines. An asymmetric γ,β‧-regioselective intermolecular [6+2] cycloaddition reaction with 3-olefinic (7-aza)oxindoles is realized through the in situ generation of formal 4-aminofulvenes, while a different β,γ-regioselective [2+2] cycloaddition reaction with maleimides to access fused cyclobutanes is disclosed. In contrast, an intriguing α,γ-regioselective [4+2] cycloaddition reaction is uncovered with the same set of substrates, by employing an unprecedented dual small-molecule catalysis of amines and thiols. All of the cycloaddition reactions exhibit excellent regio- and stereoselectivity, producing a broad spectrum of chiral architectures with high structural diversity and molecular complexity.

Linking Vegetation Structure and Spider Diversity in Riparian and Adjacent Habitats in Two Rivers of Central Argentina: An Analysis at Two Conceptual Levels.

PubMed

Griotti, Mariana; Muñoz-Escobar, Christian; Ferretti, Nelson E

2017-08-01

The link between vegetation structure and spider diversity has been well explored in the literature. However, few studies have compared spider diversity and its response to vegetation at two conceptual levels: assemblage (species diversity) and ensemble (guild diversity). Because of this, we studied spider diversity in riparian and adjacent habitats of a river system from the Chacoan subregion in central Argentina and evaluated their linkage with vegetation structure at these two levels. To assess vegetation structure, we measured plant species richness and vegetation cover in the herb and shrub - tree layers. We collected spiders for over 6 months by using vacuum netting, sweep netting and pitfall traps. We collected 3,808 spiders belonging to 119 morphospecies, 24 families and 9 guilds. At spider assemblage level, SIMPROF analysis showed significant differences among studied habitats. At spider ensemble level, nevertheless, we found no significant differences among habitats. Concerning the linkage with vegetation structure, BIOENV test showed that spider diversity at either assemblage or ensemble level was not significantly correlated with the vegetation variables assessed. Our results indicated that spider diversity was not affected by vegetation structure. Hence, even though we found a pattern in spider assemblages among habitats, this could not be attributed to vegetation structure. In this study, we show that analyzing a community at two conceptual levels will be useful for recognizing different responses of spider communities to vegetation structure in diverse habitat types. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Genomic patterns in Acropora cervicornis show extensive population structure and variable genetic diversity.

PubMed

Drury, Crawford; Schopmeyer, Stephanie; Goergen, Elizabeth; Bartels, Erich; Nedimyer, Ken; Johnson, Meaghan; Maxwell, Kerry; Galvan, Victor; Manfrino, Carrie; Lirman, Diego

2017-08-01

Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis , across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis , including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.
Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

PubMed Central

Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

2013-01-01

The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545
Temporally diverse firing patterns in olfactory receptor neurons underlie spatiotemporal neural codes for odors

PubMed Central

Raman, Baranidharan; Joseph, Joby; Tang, Jeff; Stopfer, Mark

2010-01-01

Odorants are represented as spatiotemporal patterns of spikes in neurons of the antennal lobe (AL, insects) and olfactory bulb (OB, vertebrates). These response patterns have been thought to arise primarily from interactions within the AL/OB, an idea supported, in part, by the assumption that olfactory receptor neurons (ORNs) respond to odorants with simple firing patterns. However, activating the AL directly with simple pulses of current evoked responses in AL neurons that were much less diverse, complex, and enduring than responses elicited by odorants. Similarly, models of the AL driven by simplistic inputs generated relatively simple output. How then are dynamic neural codes for odors generated? Consistent with recent results from several other species, our recordings from locust ORNs showed a great diversity of temporal structure. Further, we found that, viewed as a population, many response features of ORNs were remarkably similar to those observed within the AL. Using a set of computational models constrained by our electrophysiological recordings, we found that the temporal heterogeneity of responses of ORNs critically underlies the generation of spatiotemporal odor codes in the AL. A test then performed in vivo confirmed that, given temporally homogeneous input, the AL cannot create diverse spatiotemporal patterns on its own; however, given temporally heterogeneous input, the AL generated realistic firing patterns. Finally, given the temporally structured input provided by ORNs, we clarified several separate, additional contributions of the AL to olfactory information processing. Thus, our results demonstrate the origin and subsequent reformatting of spatiotemporal neural codes for odors. PMID:20147528
Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple (Malus × domestica Borkh.) during development

PubMed Central

Schaeffer, Scott M.; Christian, Ryan; Castro-Velasquez, Nohely; Hyden, Brennan; Lynch-Holm, Valerie

2017-01-01

Plastids are the defining organelle for a plant cell and are critical for myriad metabolic functions. The role of leaf plastid, chloroplast, is extensively documented; however, fruit plastids—chromoplasts—are poorly understood, especially in the context of the diverse metabolic processes operating in these diverse plant organs. Recently, in a comparative study of the predicted plastid-targeted proteomes across seven plant species, we reported that each plant species is predicted to harbor a unique set of plastid-targeted proteins. However, the temporal and developmental context of these processes remains unknown. In this study, an ultrastructural analysis approach was used to characterize fruit plastids in the epidermal and collenchymal cell layers at 11 developmental timepoints in three genotypes of apple (Malus × domestica Borkh.): chlorophyll-predominant ‘Granny Smith’, carotenoid-predominant ‘Golden Delicious’, and anthocyanin-predominant ‘Top Red Delicious’. Plastids transitioned from a proplastid-like plastid to a chromoplast-like plastid in epidermis cells, while in the collenchyma cells, they transitioned from a chloroplast-like plastid to a chloro-chromo-amyloplast plastid. Plastids in the collenchyma cells of the three genotypes demonstrated a diverse array of structures and features. This study enabled the identification of discrete developmental stages during which specific functions are most likely being performed by the plastids as indicated by accumulation of plastoglobuli, starch granules, and other sub-organeller structures. Information regarding the metabolically active developmental stages is expected to facilitate biologically relevant omics studies to unravel the complex biochemistry of plastids in perennial non-model systems. PMID:28698906
Topographical mapping of α- and β-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives

PubMed Central

Wu, Ping; Ng, Chen Siang; Yan, Jie; Lai, Yung-Chih; Chen, Chih-Kuan; Lai, Yu-Ting; Wu, Siao-Man; Chen, Jiun-Jie; Luo, Weiqi; Widelitz, Randall B.; Li, Wen-Hsiung; Chuong, Cheng-Ming

2015-01-01

Avian integumentary organs include feathers, scales, claws, and beaks. They cover the body surface and play various functions to help adapt birds to diverse environments. These keratinized structures are mainly composed of corneous materials made of α-keratins, which exist in all vertebrates, and β-keratins, which only exist in birds and reptiles. Here, members of the keratin gene families were used to study how gene family evolution contributes to novelty and adaptation, focusing on tissue morphogenesis. Using chicken as a model, we applied RNA-seq and in situ hybridization to map α- and β-keratin genes in various skin appendages at embryonic developmental stages. The data demonstrate that temporal and spatial α- and β-keratin expression is involved in establishing the diversity of skin appendage phenotypes. Embryonic feathers express a higher proportion of β-keratin genes than other skin regions. In feather filament morphogenesis, β-keratins show intricate complexity in diverse substructures of feather branches. To explore functional interactions, we used a retrovirus transgenic system to ectopically express mutant α- or antisense β-keratin forms. α- and β-keratins show mutual dependence and mutations in either keratin type results in disrupted keratin networks and failure to form proper feather branches. Our data suggest that combinations of α- and β-keratin genes contribute to the morphological and structural diversity of different avian skin appendages, with feather-β-keratins conferring more possible composites in building intrafeather architecture complexity, setting up a platform of morphological evolution of functional forms in feathers. PMID:26598683
7 CFR 930.158 - Grower diversion and grower diversion certificates.

Code of Federal Regulations, 2014 CFR

2014-01-01

... will not be granted to growers whose fruit was destroyed before it set and/or matured on the tree, or... as storms or hail diversion credit could be granted. (b) Application and mapping for diversion. Any.... Trees that are four years or younger do not qualify for diversion. Annual resubmissions of either the...
7 CFR 930.158 - Grower diversion and grower diversion certificates.

Code of Federal Regulations, 2011 CFR

2011-01-01

... will not be granted to growers whose fruit was destroyed before it set and/or matured on the tree, or... as storms or hail diversion credit could be granted. (b) Application and mapping for diversion. Any.... Trees that are four years or younger do not qualify for diversion. Annual resubmissions of either the...
7 CFR 930.158 - Grower diversion and grower diversion certificates.

Code of Federal Regulations, 2012 CFR

2012-01-01

... will not be granted to growers whose fruit was destroyed before it set and/or matured on the tree, or... as storms or hail diversion credit could be granted. (b) Application and mapping for diversion. Any.... Trees that are four years or younger do not qualify for diversion. Annual resubmissions of either the...
7 CFR 930.158 - Grower diversion and grower diversion certificates.

Code of Federal Regulations, 2013 CFR

2013-01-01

... will not be granted to growers whose fruit was destroyed before it set and/or matured on the tree, or... as storms or hail diversion credit could be granted. (b) Application and mapping for diversion. Any.... Trees that are four years or younger do not qualify for diversion. Annual resubmissions of either the...
Demystifying Multitask Deep Neural Networks for Quantitative Structure-Activity Relationships.

PubMed

Xu, Yuting; Ma, Junshui; Liaw, Andy; Sheridan, Robert P; Svetnik, Vladimir

2017-10-23

Deep neural networks (DNNs) are complex computational models that have found great success in many artificial intelligence applications, such as computer vision1,2 and natural language processing.3,4 In the past four years, DNNs have also generated promising results for quantitative structure-activity relationship (QSAR) tasks.5,6 Previous work showed that DNNs can routinely make better predictions than traditional methods, such as random forests, on a diverse collection of QSAR data sets. It was also found that multitask DNN models-those trained on and predicting multiple QSAR properties simultaneously-outperform DNNs trained separately on the individual data sets in many, but not all, tasks. To date there has been no satisfactory explanation of why the QSAR of one task embedded in a multitask DNN can borrow information from other unrelated QSAR tasks. Thus, using multitask DNNs in a way that consistently provides a predictive advantage becomes a challenge. In this work, we explored why multitask DNNs make a difference in predictive performance. Our results show that during prediction a multitask DNN does borrow "signal" from molecules with similar structures in the training sets of the other tasks. However, whether this borrowing leads to better or worse predictive performance depends on whether the activities are correlated. On the basis of this, we have developed a strategy to use multitask DNNs that incorporate prior domain knowledge to select training sets with correlated activities, and we demonstrate its effectiveness on several examples.
Scaffold hopping in drug discovery using inductive logic programming.

PubMed

Tsunoyama, Kazuhisa; Amini, Ata; Sternberg, Michael J E; Muggleton, Stephen H

2008-05-01

In chemoinformatics, searching for compounds which are structurally diverse and share a biological activity is called scaffold hopping. Scaffold hopping is important since it can be used to obtain alternative structures when the compound under development has unexpected side-effects. Pharmaceutical companies use scaffold hopping when they wish to circumvent prior patents for targets of interest. We propose a new method for scaffold hopping using inductive logic programming (ILP). ILP uses the observed spatial relationships between pharmacophore types in pretested active and inactive compounds and learns human-readable rules describing the diverse structures of active compounds. The ILP-based scaffold hopping method is compared to two previous algorithms (chemically advanced template search, CATS, and CATS3D) on 10 data sets with diverse scaffolds. The comparison shows that the ILP-based method is significantly better than random selection while the other two algorithms are not. In addition, the ILP-based method retrieves new active scaffolds which were not found by CATS and CATS3D. The results show that the ILP-based method is at least as good as the other methods in this study. ILP produces human-readable rules, which makes it possible to identify the three-dimensional features that lead to scaffold hopping. A minor variant of a rule learnt by ILP for scaffold hopping was subsequently found to cover an inhibitor identified by an independent study. This provides a successful result in a blind trial of the effectiveness of ILP to generate rules for scaffold hopping. We conclude that ILP provides a valuable new approach for scaffold hopping.
Genotyping-by-Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins.

PubMed

Kumar, Anil; Sharma, Divya; Tiwari, Apoorv; Jaiswal, J P; Singh, N K; Sood, Salej

2016-07-01

Finger millet [ (L.) Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of finger millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the present investigation, attempts have been made to characterize the genetically diverse collection of 113 finger millet accessions through whole-genome genotyping-by-sequencing (GBS), which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the presence of three subpopulations among the finger millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that finger millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO) terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput genotyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of finger millet. Copyright © 2016 Crop Science Society of America.
Effects of Habitat Structure and Fragmentation on Diversity and Abundance of Primates in Tropical Deciduous Forests in Bolivia.

PubMed

Pyritz, Lennart W; Büntge, Anna B S; Herzog, Sebastian K; Kessler, Michael

2010-10-01

Habitat structure and anthropogenic disturbance are known to affect primate diversity and abundance. However, researchers have focused on lowland rain forests, whereas endangered deciduous forests have been neglected. We aimed to investigate the relationships between primate diversity and abundance and habitat parameters in 10 deciduous forest fragments southeast of Santa Cruz, Bolivia. We obtained primate data via line-transect surveys and visual and acoustic observations. In addition, we assessed the vegetation structure (canopy height, understory density), size, isolation time, and surrounding forest area of the fragments. We interpreted our results in the context of the historical distribution data for primates in the area before fragmentation and interviews with local people. We detected 5 of the 8 historically observed primate species: Alouatta caraya, Aotus azarae boliviensis, Callithrix melanura, Callicebus donacophilus, and Cebus libidinosus juruanus. Total species number and detection rates decreased with understory density. Detection rates also negatively correlated with forest areas in the surroundings of a fragment, which may be due to variables not assessed, i.e., fragment shape, distance to nearest town. Observations for Alouatta and Aotus were too few to conduct further statistics. Cebus and Callicebus were present in 90% and 70% of the sites, respectively, and their density did not correlate with any of the habitat variables assessed, signaling high ecological plasticity and adaptability to anthropogenic impact in these species. Detections of Callithrix were higher in areas with low forest strata. Our study provides baseline data for future fragmentation studies in Neotropical dry deciduous forests and sets a base for specific conservation measures.
Virtual screening for novel Staphylococcus Aureus NorA efflux pump inhibitors from natural products.

PubMed

Thai, Khac-Minh; Ngo, Trieu-Du; Phan, Thien-Vy; Tran, Thanh-Dao; Nguyen, Ngoc-Vinh; Nguyen, Thien-Hai; Le, Minh-Tri

2015-01-01

NorA is a member of the Major Facilitator Superfamily (MFS) drug efflux pumps that have been shown to mediate antibiotic resistance in Staphylococcus aureus (SA). In this study, QSAR analysis, virtual screening and molecular docking were implemented in an effort to discover novel SA NorA efflux pump inhibitors. Originally, a set of 47 structurally diverse compounds compiled from the literature was used to develop linear QSAR models and another set of 15 different compounds were chosen for extra validation. The final model which was estimated by statistical values for the full data set (n = 45, Q(2) = 0.80, RMSE = 0.20) and for the external test set (n = 15, R(2) = 0.60, |res|max = 0.75, |res|min = 0.02) was applied on the collection of 182 flavonoides and the traditional Chinese medicine (TCM) database to screen for novel NorA inhibitors. Finally, 33 lead compounds that met the Lipinski's rules of five/three and had good predicted pIC50 values from in silico screening process were employed to analyze the binding ability by docking studies on NorA homology model in place of its unavailable crystal structures at two active sites, the central channel and the Walker B.
An Unbiased Method To Build Benchmarking Sets for Ligand-Based Virtual Screening and its Application To GPCRs

PubMed Central

2015-01-01

Benchmarking data sets have become common in recent years for the purpose of virtual screening, though the main focus had been placed on the structure-based virtual screening (SBVS) approaches. Due to the lack of crystal structures, there is great need for unbiased benchmarking sets to evaluate various ligand-based virtual screening (LBVS) methods for important drug targets such as G protein-coupled receptors (GPCRs). To date these ready-to-apply data sets for LBVS are fairly limited, and the direct usage of benchmarking sets designed for SBVS could bring the biases to the evaluation of LBVS. Herein, we propose an unbiased method to build benchmarking sets for LBVS and validate it on a multitude of GPCRs targets. To be more specific, our methods can (1) ensure chemical diversity of ligands, (2) maintain the physicochemical similarity between ligands and decoys, (3) make the decoys dissimilar in chemical topology to all ligands to avoid false negatives, and (4) maximize spatial random distribution of ligands and decoys. We evaluated the quality of our Unbiased Ligand Set (ULS) and Unbiased Decoy Set (UDS) using three common LBVS approaches, with Leave-One-Out (LOO) Cross-Validation (CV) and a metric of average AUC of the ROC curves. Our method has greatly reduced the “artificial enrichment” and “analogue bias” of a published GPCRs benchmarking set, i.e., GPCR Ligand Library (GLL)/GPCR Decoy Database (GDD). In addition, we addressed an important issue about the ratio of decoys per ligand and found that for a range of 30 to 100 it does not affect the quality of the benchmarking set, so we kept the original ratio of 39 from the GLL/GDD. PMID:24749745
An unbiased method to build benchmarking sets for ligand-based virtual screening and its application to GPCRs.

PubMed

Xia, Jie; Jin, Hongwei; Liu, Zhenming; Zhang, Liangren; Wang, Xiang Simon

2014-05-27

Benchmarking data sets have become common in recent years for the purpose of virtual screening, though the main focus had been placed on the structure-based virtual screening (SBVS) approaches. Due to the lack of crystal structures, there is great need for unbiased benchmarking sets to evaluate various ligand-based virtual screening (LBVS) methods for important drug targets such as G protein-coupled receptors (GPCRs). To date these ready-to-apply data sets for LBVS are fairly limited, and the direct usage of benchmarking sets designed for SBVS could bring the biases to the evaluation of LBVS. Herein, we propose an unbiased method to build benchmarking sets for LBVS and validate it on a multitude of GPCRs targets. To be more specific, our methods can (1) ensure chemical diversity of ligands, (2) maintain the physicochemical similarity between ligands and decoys, (3) make the decoys dissimilar in chemical topology to all ligands to avoid false negatives, and (4) maximize spatial random distribution of ligands and decoys. We evaluated the quality of our Unbiased Ligand Set (ULS) and Unbiased Decoy Set (UDS) using three common LBVS approaches, with Leave-One-Out (LOO) Cross-Validation (CV) and a metric of average AUC of the ROC curves. Our method has greatly reduced the "artificial enrichment" and "analogue bias" of a published GPCRs benchmarking set, i.e., GPCR Ligand Library (GLL)/GPCR Decoy Database (GDD). In addition, we addressed an important issue about the ratio of decoys per ligand and found that for a range of 30 to 100 it does not affect the quality of the benchmarking set, so we kept the original ratio of 39 from the GLL/GDD.
High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia

PubMed Central

Shi, Mang; Neville, Peter; Nicholson, Jay; Eden, John-Sebastian

2017-01-01

ABSTRACT Mosquitoes harbor a high diversity of RNA viruses, including many that impact human health. Despite a growing effort to describe the extent and nature of the mosquito virome, little is known about how these viruses persist, spread, and interact with both their hosts and other microbes. To address this issue we performed a metatranscriptomics analysis of 12 Western Australian mosquito populations structured by species and geographic location. Our results identified the complete genomes of 24 species of RNA viruses from a diverse range of viral families and orders, among which 19 are newly described. Comparisons of viromes revealed a striking difference between the two mosquito genera, with viromes of mosquitoes of the Aedes genus exhibiting substantially less diversity and lower abundances than those of mosquitoes of the Culex genus, within which the viral abundance reached 16.87% of the total non-rRNA. In addition, there was little overlap in viral diversity between the two genera, although the viromes were very similar among the three Culex species studied, suggesting that the host taxon plays a major role in structuring virus diversity. In contrast, we found no evidence that geographic location played a major role in shaping RNA virus diversity, and several viruses discovered here exhibited high similarity (95 to 98% nucleotide identity) to those from Indonesia and China. Finally, using abundance-level and phylogenetic relationships, we were able to distinguish potential mosquito viruses from those present in coinfecting bacteria, fungi, and protists. In sum, our metatranscriptomics approach provides important insights into the ecology of mosquito RNA viruses. IMPORTANCE Studies of virus ecology have generally focused on individual viral species. However, recent advances in bulk RNA sequencing make it possible to utilize metatranscriptomic approaches to reveal both complete virus diversity and the relative abundance of these viruses. We used such a metatranscriptomic approach to determine key aspects of the ecology of mosquito viruses in Western Australia. Our results show that RNA viruses are some of the most important components of the mosquito transcriptome, and we identified 19 new virus species from a diverse set of virus families. A key result was that host genetic background plays a more important role in shaping virus diversity than sampling location, with Culex species harboring more viruses at higher abundance than those from Aedes mosquitoes. PMID:28637756
Fish communities in coastal freshwater ecosystems: the role of the physical and chemical setting.

PubMed

Arend, Kristin K; Bain, Mark B

2008-12-29

We explored how embayment watershed inputs, morphometry, and hydrology influence fish community structure among eight embayments located along the southeastern shoreline of Lake Ontario, New York, USA. Embayments differed in surface area and depth, varied in their connections to Lake Ontario and their watersheds, and drained watersheds representing a gradient of agricultural to forested land use. We related various physicochemical factors, including total phosphorus load, embayment area, and submerged vegetation, to differences in fish species diversity and community relative abundance, biomass, and size structure both among and within embayments. Yellow perch (Perca flavescens) and centrarchids numerically dominated most embayment fish communities. Biomass was dominated by piscivorous fishes including brown bullhead (Ameiurus nebulosus), bowfin (Amia calva), and northern pike (Esox lucius). Phosphorus loading influenced relative biomass, but not species diversity or relative abundance. Fish relative abundance differed among embayments; within embayments, fish abundance at individual sampling stations increased significantly with submerged vegetative cover. Relative biomass differed among embayments and was positively related to total phophorus loading and embayment area. Fish community size structure, based on size spectra analysis, differed among embayments, with the frequency of smaller-bodied fishes positively related to percent vegetation. The importance of total phosphorus loading and vegetation in structuring fish communities has implications for anthropogenic impacts to embayment fish communities through activities such as farming and residential development, reduction of cultural eutrophication, and shoreline development and maintenance.
Diversity rankings among bacterial lineages in soil.

PubMed

Youssef, Noha H; Elshahed, Mostafa S

2009-03-01

We used rarefaction curve analysis and diversity ordering-based approaches to rank the 11 most frequently encountered bacterial lineages in soil according to diversity in 5 previously reported 16S rRNA gene clone libraries derived from agricultural, undisturbed tall grass prairie and forest soils (n=26,140, 28 328, 31 818, 13 001 and 53 533). The Planctomycetes, Firmicutes and the delta-Proteobacteria were consistently ranked among the most diverse lineages in all data sets, whereas the Verrucomicrobia, Gemmatimonadetes and beta-Proteobacteria were consistently ranked among the least diverse. On the other hand, the rankings of alpha-Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes and Chloroflexi varied widely in different soil clone libraries. In general, lineages exhibiting largest differences in diversity rankings also exhibited the largest difference in relative abundance in the data sets examined. Within these lineages, a positive correlation between relative abundance and diversity was observed within the Acidobacteria, Actinobacteria and Chloroflexi, and a negative diversity-abundance correlation was observed within the Bacteroidetes. The ecological and evolutionary implications of these results are discussed.

Hydrologic connection between ponds positively affects macrophyte alpha and gamma diversity but negatively affects beta diversity.

PubMed

Akasaka, Munemitsu; Takamura, Noriko

2012-05-01

Connections between habitat patches can positively influence the number of species in respective patches, providing a basis for preferentially conserving interconnected patches. However, from a regional perspective, it is not known whether conserving multiple sets of interconnected habitat patches would include more species (i.e., show higher gamma diversity) than conserving multiple, unconnected, solitary patches. We studied aquatic macrophytes in 15 sets of unidirectionally interconnected ponds and 19 unconnected ponds and also tested whether alpha and beta diversity, expressed as the number of species and dissimilarity in species composition, respectively, differed between connected and unconnected ponds. We found that gamma diversity was higher in connected ponds than in unconnected ponds, even after controlling for surface area. This resulted from a higher alpha diversity in connected ponds, despite lower beta diversity. These results suggest that connections between habitat patches positively influence diversity at both local and regional scales. When the total surface area available for conservation is limited, interconnected habitat patches should be preferentially conserved.
Evaluating an accelerated nursing program: a dashboard for diversity.

PubMed

Schmidt, Bonnie J; MacWilliams, Brent R

2015-01-01

Diversity is a topic of increasing attention in higher education and the nursing workforce. Experts have called for a nursing workforce that mirrors the population it serves. Students in nursing programs in the United States do not reflect our country's diverse population; therefore, much work is needed before that goal can be reached. Diversity cannot be successfully achieved in nursing education without inclusion and attention to quality. The Inclusive Excellence framework can be used by nurse educators to promote inclusion, diversity, and excellence. In this framework, excellence and diversity are linked in an intentional metric-driven process. Accelerated programs offer a possible venue to promote diversity, and one accelerated program is examined using a set of metrics and a dashboard approach commonly used in business settings. Several recommendations were made for future assessment, interventions, and monitoring. Nurse educators are called to examine and adopt a diversity dashboard in all nursing programs. Copyright © 2015 Elsevier Inc. All rights reserved.
Music viewed by its entropy content: A novel window for comparative analysis

PubMed Central

Febres, Gerardo; Jaffe, Klaus

2017-01-01

Polyphonic music files were analyzed using the set of symbols that produced the Minimal Entropy Description, which we call the Fundamental Scale. This allowed us to create a novel space to represent music pieces by developing: (a) a method to adjust a textual description from its original scale of observation to an arbitrarily selected scale, (b) a method to model the structure of any textual description based on the shape of the symbol frequency profiles, and (c) the concept of higher order entropy as the entropy associated with the deviations of a frequency-ranked symbol profile from a perfect Zipfian profile. We call this diversity index the ‘2nd Order Entropy’. Applying these methods to a variety of musical pieces showed how the space of ‘symbolic specific diversity-entropy’ and that of ‘2nd order entropy’ captures characteristics that are unique to each music type, style, composer and genre. Some clustering of these properties around each musical category is shown. These methods allow us to visualize a historic trajectory of academic music across this space, from medieval to contemporary academic music. We show that the description of musical structures using entropy, symbol frequency profiles and specific symbolic diversity allows us to characterize traditional and popular expressions of music. These classification techniques promise to be useful in other disciplines for pattern recognition and machine learning. PMID:29040288
State-dependent compound inhibition of Nav1.2 sodium channels using the FLIPR Vm dye: on-target and off-target effects of diverse pharmacological agents.

PubMed

Benjamin, Elfrida R; Pruthi, Farhana; Olanrewaju, Shakira; Ilyin, Victor I; Crumley, Gregg; Kutlina, Elena; Valenzano, Kenneth J; Woodward, Richard M

2006-02-01

Voltage-gated sodium channels (NaChs) are relevant targets for pain, epilepsy, and a variety of neurological and cardiac disorders. Traditionally, it has been difficult to develop structure-activity relationships for NaCh inhibitors due to rapid channel kinetics and state-dependent compound interactions. Membrane potential (Vm) dyes in conjunction with a high-throughput fluorescence imaging plate reader (FLIPR) offer a satisfactory 1st-tier solution. Thus, the authors have developed a FLIPR Vm assay of rat Nav1.2 NaCh. Channels were opened by addition of veratridine, and Vm dye responses were measured. The IC50 values from various structural classes of compounds were compared to the resting state binding constant (Kr)and inactivated state binding constant (Ki)obtained using patch-clamp electrophysiology (EP). The FLIPR values correlated with Ki but not Kr. FLIPRIC50 values fell within 0.1-to 1.5-fold of EP Ki values, indicating that the assay generally reports use-dependent inhibition rather than resting state block. The Library of Pharmacologically Active Compounds (LOPAC, Sigma) was screened. Confirmed hits arose from diverse classes such as dopamine receptor antagonists, serotonin transport inhibitors, and kinase inhibitors. These data suggest that NaCh inhibition is inherent in a diverse set of biologically active molecules and may warrant counterscreening NaChs to avoid unwanted secondary pharmacology.
Music viewed by its entropy content: A novel window for comparative analysis.

PubMed

Febres, Gerardo; Jaffe, Klaus

2017-01-01

Polyphonic music files were analyzed using the set of symbols that produced the Minimal Entropy Description, which we call the Fundamental Scale. This allowed us to create a novel space to represent music pieces by developing: (a) a method to adjust a textual description from its original scale of observation to an arbitrarily selected scale, (b) a method to model the structure of any textual description based on the shape of the symbol frequency profiles, and (c) the concept of higher order entropy as the entropy associated with the deviations of a frequency-ranked symbol profile from a perfect Zipfian profile. We call this diversity index the '2nd Order Entropy'. Applying these methods to a variety of musical pieces showed how the space of 'symbolic specific diversity-entropy' and that of '2nd order entropy' captures characteristics that are unique to each music type, style, composer and genre. Some clustering of these properties around each musical category is shown. These methods allow us to visualize a historic trajectory of academic music across this space, from medieval to contemporary academic music. We show that the description of musical structures using entropy, symbol frequency profiles and specific symbolic diversity allows us to characterize traditional and popular expressions of music. These classification techniques promise to be useful in other disciplines for pattern recognition and machine learning.
A cluster-based strategy for assessing the overlap between large chemical libraries and its application to a recent acquisition.

PubMed

Engels, Michael F M; Gibbs, Alan C; Jaeger, Edward P; Verbinnen, Danny; Lobanov, Victor S; Agrafiotis, Dimitris K

2006-01-01

We report on the structural comparison of the corporate collections of Johnson & Johnson Pharmaceutical Research & Development (JNJPRD) and 3-Dimensional Pharmaceuticals (3DP), performed in the context of the recent acquisition of 3DP by JNJPRD. The main objective of the study was to assess the druglikeness of the 3DP library and the extent to which it enriched the chemical diversity of the JNJPRD corporate collection. The two databases, at the time of acquisition, collectively contained more than 1.1 million compounds with a clearly defined structural description. The analysis was based on a clustering approach and aimed at providing an intuitive quantitative estimate and visual representation of this enrichment. A novel hierarchical clustering algorithm called divisive k-means was employed in combination with Kelley's cluster-level selection method to partition the combined data set into clusters, and the diversity contribution of each library was evaluated as a function of the relative occupancy of these clusters. Typical 3DP chemotypes enriching the diversity of the JNJPRD collection were catalogued and visualized using a modified maximum common substructure algorithm. The joint collection of JNJPRD and 3DP compounds was also compared to other databases of known medicinally active or druglike compounds. The potential of the methodology for the analysis of very large chemical databases is discussed.
Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs.

PubMed

Dupont, A Ö C; Griffiths, R I; Bell, T; Bass, D

2016-06-01

A recent large-scale assessment of bacterial communities across a range of UK soil types showed that bacterial community structure was strongly determined by soil pH. We analysed a data set of eukaryotic 454 sequencing 18S rDNA from the surveyed samples and showed significant differences in eukaryotic assemblages according to pH class, mostly between low pH and higher pH soils. Soil eukaryote communities (per sample) differed most at the taxonomic rank approximating to order level. Taxonomies assigned with the Protist Ribosomal Reference and the Silva 119 databases were taxonomically inconsistent, mostly due to differing 18S annotations, although general structure and composition according to pH were coherent. A relatively small number of lineages, mostly putative parasitic protists and fungi, drive most differences between pH classes, with weaker contributions from bacterivores and autotrophs. Overall, soil parasites included a large diversity of alveolates, in particular apicomplexans. Phylogenetic analysis of alveolate lineages demonstrates a large diversity of unknown gregarines, novel perkinsids, coccidians, colpodellids and uncharacterized alveolates. Other novel and/or divergent lineages were revealed across the eukaryote tree of life. Our study provides an in-depth taxonomic evaluation of micro-eukaryotic diversity, and reveals novel lineages and insights into their relationships with environmental variables across soil gradients. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.
Light-induced plasticity in leaf hydraulics, venation, anatomy, and gas exchange in ecologically diverse Hawaiian lobeliads.

PubMed

Scoffoni, Christine; Kunkle, Justin; Pasquet-Kok, Jessica; Vuong, Christine; Patel, Amish J; Montgomery, Rebecca A; Givnish, Thomas J; Sack, Lawren

2015-07-01

Leaf hydraulic conductance (Kleaf ) quantifies the capacity of a leaf to transport liquid water and is a major constraint on light-saturated stomatal conductance (gs ) and photosynthetic rate (Amax ). Few studies have tested the plasticity of Kleaf and anatomy across growth light environments. These provided conflicting results. The Hawaiian lobeliads are an excellent system to examine plasticity, given the striking diversity in the light regimes they occupy, and their correspondingly wide range of Amax , allowing maximal carbon gain for success in given environments. We measured Kleaf , Amax , gs and leaf anatomical and structural traits, focusing on six species of lobeliads grown in a common garden under two irradiances (300/800 μmol photons m(-2) s(-1) ). We tested hypotheses for light-induced plasticity in each trait based on expectations from optimality. Kleaf , Amax , and gs differed strongly among species. Sun/shade plasticity was observed in Kleaf , Amax, and numerous traits relating to lamina and xylem anatomy, venation, and composition, but gs was not plastic with growth irradiance. Species native to higher irradiance showed greater hydraulic plasticity. Our results demonstrate that a wide set of leaf hydraulic, stomatal, photosynthetic, anatomical, and structural traits tend to shift together during plasticity and adaptation to diverse light regimes, optimizing performance from low to high irradiance. © 2015 The Authors New Phytologist © 2015 New Phytologist Trust.
Innovative partnerships: the clinical nurse leader role in diverse clinical settings.

PubMed

Lammon, Carol Ann Barnett; Stanton, Marietta P; Blakney, John L

2010-01-01

The American Association of Colleges of Nursing in collaboration with leaders in the health care arena has developed a new role in nursing, the clinical nurse leader (CNL). The CNL is a master's-prepared advanced nurse generalist, accountable for providing high-quality, cost-effective care for a cohort of patients in a specific microsystem. Although initial implementation of the CNL has been predominantly in urban acute care settings, the skill set of the CNL role is equally applicable to diverse clinical settings, such as smaller rural hospitals, home-based home care providers, long-term care facilities, schools, Veteran's Administration facilities, and public health settings. This article reports the strategies used and the progress made at The University of Alabama Capstone College of Nursing in the development of innovative partnerships to develop the role of the CNL in diverse clinical settings. With academia and practice working in partnership, the goal of transforming health care and improving patient outcomes can be achieved. Copyright © 2010 Elsevier Inc. All rights reserved.
Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set.

PubMed

Hinze, Lori L; Gazave, Elodie; Gore, Michael A; Fang, David D; Scheffler, Brian E; Yu, John Z; Jones, Don C; Frelichowski, James; Percy, Richard G

2016-05-01

A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources. Published by Oxford University Press on behalf of the American Genetic Association 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.
Analysis of genetic and cultural conservation value of three indigenous Croatian cattle breeds in a local and global context.

PubMed

Ramljak, J; Ivanković, A; Veit-Kensch, C E; Förster, M; Medugorac, I

2011-02-01

It is widely accepted that autochthonous cattle breeds can be important genetic resources for unforeseeable environmental conditions in the future. Apart from that, they often represent local culture and tradition and thus assist in the awareness of ethnic identity of a country. In Croatia, there are only three indigenous cattle breeds, Croatian Buša, Slavonian Syrmian Podolian and Istrian Cattle. All of them are threatened but specialized in a particular habitat and production system. We analysed 93 microsatellites in 51 animals of each breed to get thorough information about genetic diversity and population structure. We further set them within an existing frame of additional 16 breeds that have been genotyped for the same marker set and cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the north-west of Europe. The cultural value was evaluated regarding the role in landscape, gastronomy, folklore and handicraft. The overall results recognize Croatian Buša being partly admixed but harbouring an enormous genetic diversity comparable with other traditional unselected Buša breeds in the Anatolian and Balkan areas. The Podolian cattle showed the lowest genetic diversity at the highest genetic distance to all remaining breeds but are playing an important role as part of the cultural landscape and thus contribute to the tourist industry. The genetic diversity of the Istrian cattle was found in the middle range of this study. It is already included in the tourist industry as a local food speciality. Current and future conservation strategies are discussed. © 2010 Blackwell Verlag GmbH.
Mitochondrial and microsatellite DNA markers reveal a Balkan origin for the highly invasive horse-chestnut leaf miner Cameraria ohridella (Lepidoptera, Gracillariidae).

PubMed

Valade, R; Kenis, M; Hernandez-Lopez, A; Augustin, S; Mari Mena, N; Magnoux, E; Rougerie, R; Lakatos, F; Roques, A; Lopez-Vaamonde, C

2009-08-01

Biological invasions usually start with a small number of founder individuals. These founders are likely to represent a small fraction of the total genetic diversity found in the source population. Our study set out to trace genetically the geographical origin of the horse-chestnut leafminer, Cameraria ohridella, an invasive microlepidopteran whose area of origin is still unkown. Since its discovery in Macedonia 25 years ago, this insect has experienced an explosive westward range expansion, progressively colonizing all of Central and Western Europe. We used cytochrome oxidase I sequences (DNA barcode fragment) and a set of six polymorphic microsatellites to assess the genetic variability of C. ohridella populations, and to test the hypothesis that C. ohridella derives from the southern Balkans (Albania, Macedonia and Greece). Analysis of mtDNA of 486 individuals from 88 localities allowed us to identify 25 geographically structured haplotypes. In addition, 480 individuals from 16 populations from Europe and the southern Balkans were genotyped for 6 polymorphic microsatellite loci. High haplotype diversity and low measures of nucleotide diversities including a significantly negative Tajima's D indicate that C. ohridella has experienced rapid population expansion during its dispersal across Europe. Both mtDNA and microsatellites show a reduction in genetic diversity of C. ohridella populations sampled from artificial habitats (e.g. planted trees in public parks, gardens, along roads in urban or sub-urban areas) across Europe compared with C. ohridella sampled in natural stands of horse-chestnuts in the southern Balkans. These findings suggest that European populations of C. ohridella may indeed derive from the southern Balkans.
Understanding the ways in which health visitors manage anxiety in cross-cultural work: a qualitative study.

PubMed

Cuthill, Fiona

2014-10-01

This paper is a report of part of a study that explored the ways in which health visitors manage uncertainty and anxiety when working with clients across cultures. Internationally health care professionals are required to deliver a high standard of culturally appropriate care to increasingly diverse communities and yet problems persist. Research evidence informing cultural 'competence' is focused largely around student experience and consequently little is known about the day-to-day experiences of health professionals in diverse community settings. Anxiety and uncertainty are increasingly recognised as important emotions experienced by a variety of health care professionals when working across cultures and yet the ways in which anxiety and uncertainty is managed in practice is less well understood. Grounded theory methodology was used and 21 semi-structured interviews were conducted with participating health visitors in the North East of England between May 2008 and September 2009. All participants described themselves as white. This study identified three different positions adopted by the health visitors to manage uncertainty and anxiety in their work across cultures. Identified as, 'Fixing a culture', 'Reworking the equality agenda' and 'Asserting the professional self', these strategies identify the ways in which health visitors try to manage the uncertainty and anxiety they feel when working in diverse communities. All of these strategies attempt in different ways to negate cultural difference and to render culture as static and known. Given that health professionals report anxiety and uncertainty when working across diverse community settings, identification of the strategies used by health visitors to manage that anxiety is important for both policy and practice. New strategies need to be developed to help health professionals to manage uncertainty and anxiety in ways that promote both cultural safe care and health equity.
Chemoinformatic expedition of the chemical space of fungal products.

PubMed

González-Medina, Mariana; Prieto-Martínez, Fernando D; Naveja, J Jesús; Méndez-Lucio, Oscar; El-Elimat, Tamam; Pearce, Cedric J; Oberlies, Nicholas H; Figueroa, Mario; Medina-Franco, José L

2016-08-01

Fungi are valuable resources for bioactive secondary metabolites. However, the chemical space of fungal secondary metabolites has been studied only on a limited basis. Herein, we report a comprehensive chemoinformatic analysis of a unique set of 207 fungal metabolites isolated and characterized in a USA National Cancer Institute funded drug discovery project. Comparison of the molecular complexity of the 207 fungal metabolites with approved anticancer and nonanticancer drugs, compounds in clinical studies, general screening compounds and molecules Generally Recognized as Safe revealed that fungal metabolites have high degree of complexity. Molecular fingerprints showed that fungal metabolites are as structurally diverse as other natural products and have, in general, drug-like physicochemical properties. Fungal products represent promising candidates to expand the medicinally relevant chemical space. This work is a significant expansion of an analysis reported years ago for a smaller set of compounds (less than half of the ones included in the present work) from filamentous fungi using different structural properties.
Quantitative structure-toxicity relationship of the aquatic toxicity for various narcotic pollutants using the norm indexes.

PubMed

Wang, Qiang; Jia, Qingzhu; Yan, Lihong; Xia, Shuqian; Ma, Peisheng

2014-08-01

The aquatic toxicity value of hazardous contaminants plays an important role in the risk assessments of aquatic ecosystems. The following study presents a stable and accurate structure-toxicity relationship model based on the norm indexes for the prediction of toxicity value (log(LC50)) for 190 diverse narcotic pollutants (96 h LC50 data for Poecilia reticulata). Research indicates that this new model is very efficient and provides satisfactory results. The suggested prediction model is evidenced by R(2) (square correlation coefficient) and ARD (average relative difference) values of 0.9376 and 10.45%, respectively, for the training set, and 0.9264 and 13.90% for the testing set. Comparison results with reference models demonstrate that this new method, based on the norm indexes proposed in this work, results in significant improvements, both in accuracy and stability for predicting aquatic toxicity values of narcotic pollutants. Copyright © 2014 Elsevier Ltd. All rights reserved.
Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics.

PubMed

Kimura, S Roy; Hu, Hai Peng; Ruvinsky, Anatoly M; Sherman, Woody; Favia, Angelo D

2017-06-26

In recent years, molecular dynamics simulations of proteins in explicit mixed solvents have been applied to various problems in protein biophysics and drug discovery, including protein folding, protein surface characterization, fragment screening, allostery, and druggability assessment. In this study, we perform a systematic study on how mixtures of organic solvent probes in water can reveal cryptic ligand binding pockets that are not evident in crystal structures of apo proteins. We examine a diverse set of eight PDB proteins that show pocket opening induced by ligand binding and investigate whether solvent MD simulations on the apo structures can induce the binding site observed in the holo structures. The cosolvent simulations were found to induce conformational changes on the protein surface, which were characterized and compared with the holo structures. Analyses of the biological systems, choice of probes and concentrations, druggability of the resulting induced pockets, and application to drug discovery are discussed here.
Amyloid Fibrils as Building Blocks for Natural and Artificial Functional Materials.

PubMed

Knowles, Tuomas P J; Mezzenga, Raffaele

2016-08-01

Proteinaceous materials based on the amyloid core structure have recently been discovered at the origin of biological functionality in a remarkably diverse set of roles, and attention is increasingly turning towards such structures as the basis of artificial self-assembling materials. These roles contrast markedly with the original picture of amyloid fibrils as inherently pathological structures. Here we outline the salient features of this class of functional materials, both in the context of the functional roles that have been revealed for amyloid fibrils in nature, as well as in relation to their potential as artificial materials. We discuss how amyloid materials exemplify the emergence of function from protein self-assembly at multiple length scales. We focus on the connections between mesoscale structure and material function, and demonstrate how the natural examples of functional amyloids illuminate the potential applications for future artificial protein based materials. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein.

PubMed

Tanaka, Yoshiki; Iwaki, Shigehiro; Tsukazaki, Tomoya

2017-09-05

The multidrug and toxic compound extrusion (MATE) family of proteins consists of transporters responsible for multidrug resistance in prokaryotes. In plants, a number of MATE proteins were identified by recent genomic and functional studies, which imply that the proteins have substrate-specific transport functions instead of multidrug extrusion. The three-dimensional structure of eukaryotic MATE proteins, including those of plants, has not been reported, preventing a better understanding of the molecular mechanism of these proteins. Here, we describe the crystal structure of a MATE protein from the plant Camelina sativa at 2.9 Å resolution. Two sets of six transmembrane α helices, assembled pseudo-symmetrically, possess a negatively charged internal pocket with an outward-facing shape. The crystal structure provides insight into the diversity of plant MATE proteins and their substrate recognition and transport through the membrane. Copyright © 2017 Elsevier Ltd. All rights reserved.
Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.

PubMed

Kuzmanic, Antonija; Zagrovic, Bojan

2010-03-03

Root mean-square deviation (RMSD) after roto-translational least-squares fitting is a measure of global structural similarity of macromolecules used commonly. On the other hand, experimental x-ray B-factors are used frequently to study local structural heterogeneity and dynamics in macromolecules by providing direct information about root mean-square fluctuations (RMSF) that can also be calculated from molecular dynamics simulations. We provide a mathematical derivation showing that, given a set of conservative assumptions, a root mean-square ensemble-average of an all-against-all distribution of pairwise RMSD for a single molecular species, (1/2), is directly related to average B-factors () and (1/2). We show this relationship and explore its limits of validity on a heterogeneous ensemble of structures taken from molecular dynamics simulations of villin headpiece generated using distributed-computing techniques and the Folding@Home cluster. Our results provide a basis for quantifying global structural diversity of macromolecules in crystals directly from x-ray experiments, and we show this on a large set of structures taken from the Protein Data Bank. In particular, we show that the ensemble-average pairwise backbone RMSD for a microscopic ensemble underlying a typical protein x-ray structure is approximately 1.1 A, under the assumption that the principal contribution to experimental B-factors is conformational variability. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Determination of Ensemble-Average Pairwise Root Mean-Square Deviation from Experimental B-Factors

PubMed Central

Kuzmanic, Antonija; Zagrovic, Bojan

2010-01-01

Abstract Root mean-square deviation (RMSD) after roto-translational least-squares fitting is a measure of global structural similarity of macromolecules used commonly. On the other hand, experimental x-ray B-factors are used frequently to study local structural heterogeneity and dynamics in macromolecules by providing direct information about root mean-square fluctuations (RMSF) that can also be calculated from molecular dynamics simulations. We provide a mathematical derivation showing that, given a set of conservative assumptions, a root mean-square ensemble-average of an all-against-all distribution of pairwise RMSD for a single molecular species, 1/2, is directly related to average B-factors () and 1/2. We show this relationship and explore its limits of validity on a heterogeneous ensemble of structures taken from molecular dynamics simulations of villin headpiece generated using distributed-computing techniques and the Folding@Home cluster. Our results provide a basis for quantifying global structural diversity of macromolecules in crystals directly from x-ray experiments, and we show this on a large set of structures taken from the Protein Data Bank. In particular, we show that the ensemble-average pairwise backbone RMSD for a microscopic ensemble underlying a typical protein x-ray structure is ∼1.1 Å, under the assumption that the principal contribution to experimental B-factors is conformational variability. PMID:20197040

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