bluuebunny/crossref_metadata_2025_split huggingface dataset:
From genomes to phenotypes: Traitar, the microbial trait analyzer
Authors: Weimann Aaron , Mooren Kyra , Frank Jeremy , Pope Phillip B. , Bremges Andreas , McHardy Alice C. 
Published: March 2016

AbstractThe number of sequenced genomes is growing exponentially, profoundly shifting the bottleneck from data generation to genome interpretation. Traits are often used to characterize and distinguish bacteria, and are likely a driving factor in microbial community composition, yet little is known about the traits of most microbes. We describe Traitar, the microbial trait analyzer, which is a fully automated software package for deriving phenotypes from the genome sequence. Traitar provides phenotype classifiers to predict 67 traits related to the use of various substrates as carbon and energy sources, oxygen requirement, morphology, antibiotic susceptibility, proteolysis and enzymatic activities. Furthermore, it suggests protein families associated with the presence of particular phenotypes. Our method uses L1-regularized L2-loss support vector machines for phenotype assignments based on phyletic patterns of protein families and their evolutionary histories across a diverse set of microbial species. We demonstrate reliable phenotype assignment for Traitar to bacterial genomes from 572 species of 8 phyla, also based on incomplete single-cell genomes and simulated draft genomes. We also showcase its application in metagenomics by verifying and complementing a manual metabolic reconstruction of two novel Clostridiales species based on draft genomes recovered from commercial biogas reactors. Traitar is available athttps://github.com/hzi-bifo/traitar.
Demographic stochasticity and resource autocorrelation control biological invasions in heterogeneous landscapes
Authors: Giometto Andrea , Altermatt Florian , Rinaldo Andrea 
Published: March 2016

AbstractClassical models of biological invasions assess species spread in homogeneous landscapes by assuming constant growth rates and random local movement. Mounting evidence suggests, however, that demographic stochasticity, environmental heterogeneity and non-random movement of individuals affect considerably the spread dynamics. Here, we show that the dynamics of biological invasions are controlled by the spatial heterogeneity of the resource distribution. We show theoretically that increasing the landscape resource autocorrelation length causes a reduction in the average speed of species spread. Demographic stochasticity plays a key role in the slowdown, which is streghtened when individuals can actively move towards resources. The reduction in the front propagation speed is verified in laboratory microcosm experiments with the flagellated protistEuglena gracilisby comparing spread in habitats characterized by different resource heterogeneity. Our theoretical and experimental findings highlight the need to account for the intrinsic stochasticity of population dynamics to describe spread in spatially extended landscapes, which are inevitably characterized by heterogeneous spatial distributions of resources controlling vital rates. Our work identifies the resource autocorrelation length as a key modulator and a simple measure of landscape susceptibility to biological invasions, with implications for predicting the characters of biological invasions within naturally heterogeneous environmental corridors.
Structural basis for acyl group discrimination by human Gcn5L2
Authors: Ringel Alison E. , Wolberger Cynthia 
Published: March 2016

AbstractGcn5 is a conserved acetyltransferase that regulates transcription by acetylating the N-terminal tails of histones. Motivated by recent studies identifying a chemically diverse array of lysine acyl modificationsin vivo, we examined the acyl chain specificity of the acetyltransferase, human Gcn5 (Gcn5L2). Whereas Gcn5L2 robustly catalyzes lysine acetylation, the acyltransferase activity of Gcn5L2 gets progressively weaker with increasing acyl chain length. To understand how Gcn5 discriminates between different acyl-CoA molecules, we determined structures of the catalytic domain of human Gcn5L2 bound to propionyl-CoA and butyryl-CoA. Although the active site of Gcn5L2 can accommodate propionyl-CoA and butyryl-CoA without major structural rearrangements, butyryl-CoA adopts a conformation incompatible with catalysis that obstructs the path of the incoming lysine residue and acts as a competitive inhibitor for Gcn5L2 versus acetyl-CoA. These structures demonstrate how Gcn5L2 discriminates between acyl chain donors and explain why Gcn5L2 has weak activity for acyl moieties that are larger than an acetyl group.
Can secondary contact following range expansion be distinguished from barriers to gene flow?
Authors: Bertl Johanna , Ringbauer Harald , Blum Michael G. B. 
Published: March 2016

AbstractSecondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of Linkage Disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index Ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.
Genome-wide association between transcription factor expression and chromatin accessibility reveals chromatin state regulators
Authors: Lamparter David , Marbach Daniel , Rueedi Rico , Bergmann Sven , Kutalik Zoltán 
Published: March 2016

ABSTRACTTo better understand genome regulation, it is important to uncover the role of transcription factors in the process of chromatin structure establishment and maintenance. Here we present a data-driven approach to systematically characterize transcription factors that are relevant for this process. Our method uses a linear mixed modeling approach to combine data sets of transcription factor binding motif enrichments in open chromatin and gene expression across the same set of cell lines. Applying this approach to the ENCODE data set we confirm already known and imply numerous novel transcription factors in playing a role in the establishment or maintenance of open chromatin.
Strength of functional signature correlates with effect size in autism
Authors: Ballouz Sara , Gillis Jesse 
Published: March 2016

AbstractBackgroundDisagreements over genetic signatures associated with disease have been particularly prominent in the field of psychiatric genetics, creating a sharp divide between disease burdens attributed to common and rare variation, with study designs independently targeting each. Meta-analysis within each of these study designs is routine, whether using raw data or summary statistics, but combining results across study designs is atypical. However, tests of functional convergence are used across all study designs, where candidate gene sets are assessed for overlaps with previously known properties. This suggests one possible avenue for combining not study data, but the functional conclusions that they reach.MethodIn this work, we test for functional convergence in autism spectrum disorder (ASD) across different study types, and specifically whether the degree to which a gene is implicated in autism is correlated with the degree to which it drives functional convergence. Because different study designs are distinguishable by their differences in effect size, this also provides a unified means of incorporating the impact of study design into the analysis of convergence.ResultsWe detected remarkably significant positive trends in aggregate (p < 2.2e-16) with 14 individually significant properties (FDR<0.01), many in areas researchers have targeted based on different reasoning, such as the fragile X mental retardation protein(FMRP)interactor enrichment (FDR 0.003). We are also able to detect novel technical effects and we see that network enrichment from protein-protein interaction data is heavily confounded with study design, arising readily in control data.ConclusionsWe see a convergent functional signal for a subset of known and novel functions in ASD from all sources of genetic variation. Meta-analytic approaches explicitly accounting for different study designs can be adapted to other diseases to discover novel functional associations and increase statistical power.
Computational Pan-Genomics: Status, Promises and Challenges
Authors:   The Computational Pan-Genomics Consortium, Marschall Tobias , Marz Manja , Abeel Thomas , Dijkstra Louis , Dutilh Bas E. , Ghaffaari Ali , Kersey Paul , Kloosterman Wigard P. , Mäkinen Veli , Novak Adam M. , Paten Benedict , Porubsky David , Rivals Eric , Alkan Can , Baaijens Jasmijn , De Bakker Paul I. W. , Boeva Valentina , Bonnal Raoul J. P. , Chiaromonte Francesca , Chikhi Rayan , Ciccarelli Francesca D. , Cijvat Robin , Datema Erwin , Van Duijn Cornelia M. , Eichler Evan E. , Ernst Corinna , Eskin Eleazar , Garrison Erik , El-Kebir Mohammed , Klau Gunnar W. , Korbel Jan O. , Lameijer Eric-Wubbo , Langmead Benjamin , Martin Marcel , Medvedev Paul , Mu John C. , Neerincx Pieter , Ouwens Klaasjan , Peterlongo Pierre , Pisanti Nadia , Rahmann Sven , Raphael Ben , Reinert Knut , de Ridder Dick , de Ridder Jeroen , Schlesner Matthias , Schulz-Trieglaff Ole , Sanders Ashley D. , Sheikhizadeh Siavash , Shneider Carl , Smit Sandra , Valenzuela Daniel , Wang Jiayin , Wessels Lodewyk , Zhang Ying , Guryev Victor , Vandin Fabio , Ye Kai , Schönhuth Alexander 
Published: March 2016

AbstractMany disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case ofHomo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic datasets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension ofcomputational pan-genomics, a new sub-area of research in computational biology. In this paper, we generalize existing definitions and understand apan-genomeas any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies, and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.
PCR-free library preparation greatly reduces stutter noise at short tandem repeats
Authors: Gymrek Melissa 
Published: March 2016

AbstractOver the past several decades, the forensic and population genetic communities have increasingly leveraged short tandem repeats (STRs) for a variety of applications. The advent of next-generation sequencing technologies and STR-specific bioninformatic tools has enabled the profiling of hundreds of thousands of STRs across the genome. Nonetheless, these genotypes remain error-prone, hindering their utility in downstream analyses. One of the primary drivers of STR genotyping errors are “stutter” artifacts arising during the PCR amplification step of library preparation that add or delete copies of the repeat unit in observed sequencing reads. Recently, Illumina developed the TruSeq PCR-free library preparation protocol which eliminates the PCR step and theoretically should reduce stutter error. Here, I compare two high coverage whole genome sequencing datasets prepared with and without the PCR-free protocol. I find that this protocol reduces the percent of reads due to stutter by more than four-fold and results in higher confidence STR genotypes. Notably, stutter at homopolymers was decreased by more than 6fold, making these previously inaccessible loci amenable to STR calling. This technological improvement shows good promise for significantly increasing the feasibility of obtaining high quality STR genotypes from next-generation sequencing technologies.
Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae
Authors: Barker Michael S. , Li Zheng , Kidder Thomas I. , Reardon Chris R. , Lai Zhao , Oliveira Luiz O. , Scascitelli Moira , Rieseberg Loren H. 
Published: March 2016

AbstractPremise of the studyLike many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature.MethodsWe sequenced new transcriptomes forBarnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy.Key resultsWe found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae exceptBarnadesia.ConclusionsOur analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high densityLactucalinkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.
Biochemical effects of the flavanol‐rich lychee fruit extract on the melanin biosynthesis and reactive oxygen species
Authors: Hagiwara Kazuya , Okura Masae , Sumikawa Yasuyuki , Hida Tokimasa , Kuno Atsushi , Horio Yoshiyuki , Yamashita Toshiharu 
Published: March 2016

AbstractAn ingredient of fruit polyphenol, resveratrol, is known to have an inhibitory effect on melanogenesis. In order to examine the functional differences between resveratrol and other fruit polyphenols, we compared biochemical effects of a resveratrol‐free polyphenol, flavanol‐rich lychee fruit extract (FRLFE), with other phenolic compounds including resveratrol.FRLFEas well as hydroquinone and resveratrol suppressed growth of B16F1 melanoma cells more significantly than rhododendrol or arbutin. Resveratrol suppressed mushroom tyrosinase at the lowest concentration (23.0 μmol/L) among the compounds tested.FRLFEand hydroquinone suppressed tyrosinase at almost the same concentration (half maximal inhibitory concentration [IC50], 83.5 and 94.6 μmol/L, respectively), which was higher than rhododendrol, ascorbic acid and arbutin (IC50, 245, 345 and 421 μmol/L, respectively). Western blot analysis revealed that although resveratrol decreased expressions of tyrosinase and tyrosinase‐related protein 1,FRLFEdid not affect their expressions. BothFRLFEand resveratrol suppressed antimycin A‐mediated reactive oxygen species (ROS) production in melanocytic cells. Resveratrol‐mediatedROSsuppression was inhibited by nicotinamide, aSIRT1 inhibitor. However,FRLFE‐mediated suppression was not affected by nicotinamide. Moreover,FRLFEdirectly decreased superoxidein vitro, as detected by superoxide dismutase‐like scavenging activity assay. These results suggest thatFRLFEcan protect melanocytes from cytotoxicity caused by an excess amount of melanin andROSin a different manner from resveratrol.
Negative relationships between population density and metabolic rates are not general
Authors: Yashchenko Varvara , Fossen Erlend Ignacio , Kielland Øystein Nordeide , Einum Sigurd 
Published: March 2016

Summary

Population density has recently been suggested to be an important factor influencing metabolic rates and to represent an important ‘third axis’ explaining variation beyond that explained by body mass and temperature. In situations where population density influences food consumption, the immediate effect on metabolism acting through specific dynamic action (SDA), and downregulation due to fasting over longer periods, is well understood. However, according to a recent review, previous studies suggest a more general effect of population density per se, even in the absence of such effects. It has been hypothesized that this results from animals performing anticipatory responses (i.e. reduced activity) to expected declines in food availability.

Here, we test the generality of this finding by measuring density effects on metabolic rates in 10 clones from two different species of the zooplankton Daphnia (Daphnia pulex Leydig and D. magna Straus). Using fluorescence‐based respirometry, we obtain high‐precision measures of metabolism.

We also identify additional studies on this topic that were not included in the previous review, compare the results and evaluate the potential for measurement bias in all previous studies.

We demonstrate significant variation in mass‐specific metabolism among clones within both species. However, we find no evidence for a negative relationship between population density and mass‐specific metabolism. The previously reported pattern also disappeared when we extended the set of studies analysed.

We discuss potential reasons for the discrepancy among studies, including two main sources of potential bias (microbial respiration and declining oxygen consumption due to reduced oxygen availability). Only one of the previous studies gives sufficient information to conclude the absence of such biases, and consistent with our results, no effect of density on metabolism was found. We conclude that population density per se does not have a general effect on mass‐specific metabolic rate.
Quantifying pursuit‐diving seabirds’ associations with fine‐scale physical features in tidal stream environments
Authors: Waggitt James J. , Cazenave Pierre W. , Torres Ricardo , Williamson Benjamin J. , Scott Beth E. 
Published: March 2016

Summary

The rapid increase in the number of tidal stream turbine arrays will create novel and unprecedented levels of anthropogenic activity within habitats characterized by horizontal current speeds exceeding 2 ms−1. However, the potential impacts on pursuit‐diving seabirds exploiting these tidal stream environments remain largely unknown. Identifying similarities between the fine‐scale physical features (100s of metres) suitable for array installations, and those associated with foraging pursuit‐diving seabirds, could identify which species are most vulnerable to either collisions with moving components, or displacement from these installations.

A combination of vessel‐based observational surveys, Finite Volume Community Ocean Model outputs and hydroacoustic seabed surveys provided concurrent measures of foraging distributions and physical characteristics at a fine temporal (15 min) and spatial (500 m) resolution across a tidal stream environment suitable for array installations, during both breeding and non‐breeding seasons. These data sets were then used to test for associations between foraging pursuit‐diving seabirds (Atlantic puffins Fratercula arctica, black guillemots Cepphus grylle, common guillemots Uria aalge, European shags Phalacrocorax aristotelis) and physical features.

These species were associated with areas of fast horizontal currents, slow horizontal currents, high turbulence, downward vertical currents and also hard–rough seabeds. The identity and strength of associations differed among species, and also within species between seasons, indicative of interspecific and intraspecific variations in habitat use. However, Atlantic puffins were associated particularly strongly with areas of fast horizontal currents during breeding seasons, and European shags with areas of rough–hard seabeds and downward vertical currents during non‐breeding seasons.

Synthesis and applications. Atlantic puffins’ strong association with fast horizontal current speeds indicates that they are particularly likely to interact with installations during breeding seasons. Any post‐installation monitoring and mitigation measures should therefore focus on this species and season. The multi‐species associations with high turbulence and downward vertical currents, which often coincide with fast horizontal current speeds, also highlight useful pre‐installation mitigation measures via the omission of devices from these areas, reducing the overall likelihood of interactions. Environmental impact assessments (EIA) generally involve once‐a‐month surveys across 2‐year periods. However, the approaches used in this study show that more focussed surveys can greatly benefit management strategies aiming to reduce the likelihood of negative impacts by facilitating the development of targeted mitigation measures. It is therefore recommended that these approaches contribute towards EIA within development sites.
Packaging optimisation for portioned Canestrato di Moliterno cheese
Authors: Costa Cristina , Lucera Annalisa , Lacivita Valentina , Saccotelli Maria Antonietta , Conte Amalia , Del Nobile Matteo Alessandro 
Published: March 2016

Different polymeric films and various headspace conditions (air, vacuum and four different modified atmosphere packaging) were combined to select a packaging system that assured the desired shelf life for two types of portioned Canestrato di Moliterno cheese ripened for 4 and 12 months. To evaluate the quality deterioration of the packaged cheese samples under refrigerated conditions, texture change, weight loss, water activity, moisture content, microbial contamination, pH and sensory attributes were monitored during storage. The results highlighted that a high‐barrier multilayer film delayed proliferation of moulds and gave the best results for both types of ripened cheese.