bluuebunny/crossref_metadata_2025 huggingface dataset:
IPC - Isoelectric Point Calculator
Authors: Kozlowski Lukasz P.
Published: May 2016

Accurate estimation of the isoelectric point (pI) based on the amino acid sequence can be useful for many biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Here, I present the Isoelectric Point Calculator, a web service for the estimation ofpIusing different sets of dissociation constant (pKa) values, including two new, computationally optimizedpKasets. According to the presented benchmarks, IPC outperform previous algorithms by at least 14.9% for proteins and 0.9% for peptides (on average, 22.1% and 59.6%, respectively), which corresponds to an average error of thepIestimation equal to 0.87 and 0.25 pH units for proteins and peptides, respectively. Peptide and protein datasets used in the study and the precalculatedpIfor PDB, SwissProt databases are available for large-scale analysis and future development. The IPC can be accessed athttp://isoelectric.ovh.org.
Signatures of personality on dense 3D facial images
Authors: Hu Sile , Xiong Jieyi , Fu Pengcheng , Qiao Lu , Tan Jingze , Jin Li , Tang Kun
Published: May 2016

It has long been speculated that there exist cues on human face that allow observersto make reliable judgments of others’personality traits. However, direct evidences ofassociation between facial shapes and personality are missing. This study assessed thepersonality attributes for 834 Han Chinese volunteers (405 males and 429 females) utilizing the five-factor personality model (the ‘Big Five’ model), and collected their neutral 3D facial images. Dense anatomical correspondence was established across the 3D facial images to allow high-dimensional quantitative analyses on the face phenotypes. Two different approaches, Composite Partial Least Square Component(CPLSC) and principle component analysis (PCA) were used to test the associations between the self-testedpersonality scores and the dense 3D face image data. Among the fivepersonality factors, Agreeableness and Conscientiousness in male, and Extraversion in female were significantly associated to specific facial patterns. The personality-related facial patterns were extracted and their effects were extrapolated on simulated 3Dfacial models.
Aequatus: An open-source homology browser
Authors: Thanki Anil S. , Soranzo Nicola , Herrero Javier , Haerty Wilfried , Davey Robert P.
Published: May 2016

Background

Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as well as regions under positive or purifying selection within lineages. Gene family and orthogroup characterisation enables the identification of syntenic blocks, which can then be visualised with various tools. Unfortunately, currently available tools display only an overview of syntenic regions as a whole, limited to the gene level, and none provide further details about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes.

Findings

We present Aequatus, a standalone web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualisations. It relies on pre-calculated alignment and gene feature information typically held in, but not limited to, the Ensembl Compara and Core databases. We also offer Aequatus.js, a reusable JavaScript module that fulfils the visualisation aspects of Aequatus, available within the Galaxy web platform as a visualisation plugin, which can be used to visualise gene trees generated by the GeneSeqToFamily workflow.

Availability

Aequatus is an open-source tool freely available to download under the MIT license athttps://github.com/TGAC/Aequatus. A demo server is available athttp://aequatus.earlham.ac.uk/. A publicly available instance of the GeneSeqToFamily workflow to generate gene tree information and visualise it using Aequatus is available on the Galaxy EU server athttps://usegalaxy.eu.

Contacts

Anil.Thanki@earlham.ac.ukandRobert.Davey@earlham.ac.uk
Analysis of behavioral variables across domains and skin phenotypes in zebrafish: Role of brain monoamines
Authors: Lima Monica Gomes , Herculano Anderson Manoel , Maximino Caio
Published: May 2016

Important neurochemical variations between strains or linages which correlate with behavioral differences have been identified in different species. Here, we report neurochemical and behavioral differences in four common zebrafish wild-type phenotypes (blue shortfin, longfin stripped, leopard and albino). Leopad zebrafish have been shown to display increased scototaxis in relation to the other strains, while both albino and leopard zebrafish show increased geotaxis. Moreover, leopard displayed increased nocifensive behavior, while albino zebrafish showed increased neophobia in the novel object task. Longfin zebrafish showed decreased turn frequency in both the novel tank and light/dark tests, and habituated faster in the novel tank, as well as displaying increased 5-HT levels. Leopard zebrafish showed decreased brain 5-HT levels and increased 5-HT turnover than other strains, and albino had increased brain DA levels. Finally, specific behavioral endpoints co-varied in terms of the behavioral and neurochemical differences between strains, identifying cross-test domains which included response to novelty, exploration-avoidance, general arousal, and activity.
Biogeographic Ancestry and Socioeconomic Outcomes in the Americas: A Meta-Analysis
Authors: Kirkegaard Emil O. W. , Wang Mingrui , Fuerst John
Published: May 2016

Narrative reports suggest that socioeconomic status (SES) is associated with biogeographic ancestry (BGA) in the Americas. If so, SES potentially acts as a confound that needs to be taken into account when evaluating the relation between medical outcomes and BGA. To explore how systematic BGA-SES associations are, a meta-analysis of American studies was conducted. 40 studies were identified, yielding a total of 64 independent samples with directions of associations, including 48 independent samples with effect sizes. An analysis of association directions found a high degree of consistency. The square rootn-weighted directions were 0.83 (K=36), -0.81 (K= 41) and -0.82 (K= 39) for European, Amerindian and African BGA, respectively. An analysis of effect size magnitudes found that European BGA was positively associated with SES, with a meta-analytic effect size ofr= .18 [95% CI: .13 to .24,K= 28,n= 35,476.5], while both Amerindian and African BGA were negatively associated with SES, having meta-analytic effect sizes of -.14 [-.18 to -.10,K= 31,n= 28,937.5] and -.11 [-.15 to -.07,K= 28,n= 32,710.5], respectively. There was considerable cross-sample variation in effect sizes (mean I2= 92%), but the sample size was not enough for performing credible moderator analysis. Implications for future studies are discussed.
Genomic dimensions of Su(H)-targeted regulatory belts inDrosophila
Authors: Stroebele Elizabeth , Fuqua Timothy , Warren Madelyn , Herrig Danielle , Noblett Christian , Yuan Xin , Erives Albert
Published: May 2016

Asymmetric Notch signaling promotes divergent fates in select cells throughout metazoan development. In the receiving cell, signaling results in cleavage of the Notch intracellular domain and its import into the nucleus, where it binds Suppressor of Hairless [Su(H)] to promote gene expression in conjunction with contextual cues in the surrounding DNA sequence. To investigate the nature of this contextual logic, we identify 1344 Su(H)-site containing regulatory belts that are conserved across theDrosophilagenus. Each Su(H)-type regulatory belt (SUH-RB) is a 0.6-1.0 kb chain of conservation peaks consistent with a transcriptional enhancer or core promoter. These regulatory belts contain one or more canonical binding sites for Su(H) along with ~15-30 other binding sites. SUH-RBs are densely clustered in certain chromosomal regions such as the E(spl)-complex, theWntgene complex, and genes encoding Notch receptor ligands (Delta and Serrate). SUH-RBs overlap most known Su(H)/Notch-target enhancers and others, including non-embryonic enhancers that are not identified by embryonic ChIP-seq peaks. Thus, SUH-RBs overcome the stage-specific nature of embryonic ChIP-seq peaks and suggest a pervasive role for contextual tissue-specific pioneer and/or enhancer-licensing factors. SUH-RBs also delineate false positive ChIP-seq peaks, which do not overlap SUH-RBs, are missing even the weakest Su(H)-binding sequences, and have the shortest ChIP peak widths. Last, we characterize several novel enhancers including Su(H)-dependent enhancers atNotchandDelta, intestinal enhancers atA2bp1andhedgehog, and distinct enhancers atroughest,E2f1, andescargot.
Accurate prediction of single-cell DNA methylation states using deep learning
Authors: Angermueller Christof , Lee Heather J. , Reik Wolf , Stegle Oliver
Published: May 2016

Recent technological advances have enabled assaying DNA methylation at single-cell resolution. Current protocols are limited by incomplete CpG coverage and hence methods to predict missing methylation states are critical to enable genome-wide analyses. Here, we report DeepCpG, a computational approach based on deep neural networks to predict DNA methylation states from DNA sequence and incomplete methylation profiles in single cells. We evaluated DeepCpG on single-cell methylation data from five cell types generated using alternative sequencing protocols, finding that DeepCpG yields substantially more accurate predictions than previous methods. Additionally, we show that the parameters of our model can be interpreted, thereby providing insights into the effect of sequence composition on methylation variability.
Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters
Authors: Chen Yun , Pai Athma A. , Herudek Jan , Lubas Michal , Meola Nicola , Järvelin Aino I. , Andersson Robin , Pelechano Vicent , Steinmetz Lars M. , Heick Jensen Torben , Sandelin Albin
Published: May 2016

Mammalian transcriptomes are complex and formed by extensive promoter activity. In addition, gene promoters are largely divergent and initiate transcription of reverse-oriented promoter upstream transcripts (PROMPTs). Although PROMPTs are commonly terminated early, influenced by polyadenylation sites, promoters often cluster so that the divergent activity of one might impact another. Here, we find that the distance between promoters strongly correlates with the expression, stability and length of their associated PROMPTs. Adjacent promoters driving divergent mRNA transcription support PROMPT formation, but due to polyadenylation site constraints, these transcripts tend to spread into the neighboring mRNA on the same strand. This mechanism to derive new alternative mRNA transcription start sites (TSSs) is also evident at closely spaced promoters supporting convergent mRNA transcription. We suggest that basic building blocks of divergently transcribed core promoter pairs, in combination with the wealth of TSSs in mammalian genomes, provides a framework with which evolution shapes transcriptomes.
Controlling bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution
Authors: van Iterson Maarten , van Zwet Erik ,   the BIOS Consortium, Slagboom P. Eline , Heijmans Bastiaan T.
Published: May 2016

Association studies on omic-level data other then genotypes (GWAS) are becoming increasingly common, i.e., epigenome-and transcriptome-wide association studies (EWAS/TWAS). However, a tool box for the analysis of EWAS and TWAS studies is largely lacking and often approaches from GWAS are applied despite the fact that epigenome and transcriptome data have vedifferent characteristics than genotypes. Here, we show that EWASs and TWASs are prone not only to significant inflation but also bias of the test statistics and that these are not properly addressed by GWAS-based methodology (i.e. genomic control) and state-of-the-art approaches to control for unmeasured confounding (i.e. RUV, sva and cate). We developed a novel approach that is based on the estimation of the empirical null distribution using Bayesian statistics. Using simulation studies and empirical data, we demonstrate that our approach maximizes power while properly controlling the false positive rate. Finally, we illustrate the utility of our method in the application of meta-analysis by performing EWASs and TWASs on age and smoking which highlighted an overlap in differential methylation and expression of associated genes. An implementation of our new method is available fromhttp://bioconductor.org/packages/bacon/.
Convergent evolution of genes controlling mitonuclear balance in annual fishes
Authors: Sahm Arne , Bens Martin , Platzer Matthias , Cellerino Alessandro
Published: May 2016

Complexes of the respiratory chain are formed in a complex process where nuclearly-and mitochondrially-encoded components are assembled and inserted into the inner mitochondrial membrane. The coordination of this process is named mitonuclear balance and experimental manipulations of mitonuclear balance can increase longevity of laboratory species.

Here, we investigated the pattern of positive selection in annual (i.e. short-lived)and non-annual (i.e. long-lived) African killifishes to identify a genomic substrate for evolution of annual life history (and reduced lifespan).

We identified genes under positive selection in all mitonuclear balance: mitochondrial (mt) DNA replication, transcription from mt promoters, processing and stabilization of mt RNAs, mt translation, assembly of respiratory chain complexes and electron transport chain. Signs of convergent evolution are observed in four out of five steps. This strongly indicates that these genes are preferential genetic targets for the evolution of short lifespan and annual life cycle
Adapting Genotyping-by-Sequencing for Rice F2 Populations
Authors: Furuta Tomoyuki , Ashikari Motoyuki , Jena Kshirod K. , Doi Kazuyuki , Reuscher Stefan
Published: May 2016

Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross ofOryza sativassp.japonicacv. Nipponbare and the African wild rice speciesOryza longistaminata. While most GBS pipelines aim to analyze mainly homozygous populations we attempted to genotype a highly heterozygous F2 population. We show how species-and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average) we were able to generate up to 8,154 informative SNP markers in 1,081 F2 individuals. Additionally, the effects of enzyme choice, read coverage and data post-processing are evaluated. Using GBS-derived markers we were able to assemble a genetic map of 1,536 cM. To demonstrate the usefulness of our GBS pipeline we determined QTL for the number of tillers. We were able to map four QTLs to chromosomes 1, 3, 4 and 8 and confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform we show that the GBS method is flexible and cost-effective even for smaller laboratories
PIPI: PTM-Invariant Peptide Identification Using Coding Method
Authors: Yu Fengchao , Li Ning , Yu Weichuan
Published: May 2016

In computational proteomics, identification of peptides with an unlimited number of post-translational modification (PTM) types is a challenging task. The computational cost increases exponentially with respect to the number of modifiable amino acids and linearly with respect to the number of potential PTM types at each amino acid. The problem becomes intractable very quickly if we want to enumerate all possible modification patterns. Existing tools (e.g., MS-Alignment, ProteinProspector, and MODa) avoid enumerating modification patterns in database search by using an alignment-based approach to localize and characterize modified amino acids. This approach avoids enumerating all possible modification patterns in a database search. However, due to the large search space and PTM localization issue, the sensitivity of these tools is low. This paper proposes a novel method named PIPI to achieve PTM-invariant peptide identification. PIPI first codes peptide sequences into Boolean vectors and converts experimental spectra into real-valued vectors. Then, it finds the top 10 peptide-coded vectors for each spectrum-coded vector. After that, PIPI uses a dynamic programming algorithm to localize and characterize modified amino acids. Simulations and real data experiments have shown that PIPI outperforms existing tools by identifying more peptide-spectrum matches (PSMs) and reporting fewer false positives. It also runs much faster than existing tools when the database is large.
Rapid emergence of HCMV drug resistance in immunocompromised paediatric patients detected using target enrichment and deep sequencing
Authors: Houldcroft Charlotte , Bryant Josephine M. , Depledge Daniel P. , Margetts Ben K. , Simmonds Jacob , Nicolaou Stephanos , Tutill Helena , Williams Rachel , Worth Austen , Marks Stephen D. , Veys Paul , Whittaker Elizabeth , Breuer Judith ,   the PATHSEEK condortium
Published: May 2016

Background

Cytomegalovirus can cause fatal disease in immunocompromised patients. With the advent of new anti-HCMV drugs there is interest in using virus sequence data to monitor resistance and identify new mutations.

Methods

We used target-enrichment to deep sequence HCMV DNA from 11 immunosuppressed paediatric patients receiving single or combination anti-HCMV treatment, serially sampled over 1-27 weeks. Changes in consensus sequence and resistance mutations were analysed for three ORFs targeted by anti-HCMV drugs and the frequencies of drug resistance mutations monitored.

Results

Targeted-enriched sequencing of clinical material detected mutations occurring at frequencies of 2%. Seven patients showed no evidence of drug resistance mutations. Four patients developed drug resistance mutations a mean of 16 weeks after starting treatment. In two patients, multiple resistance mutations accumulated at frequencies of 20% or less, including putative resistance mutations P522Q (UL54) and C480F (UL97). In one patient, resistance was detected 14 days earlier than by PCR. Phylogenetic analysis suggested recombination or superinfection in one patient.

Conclusions

Deep sequencing of HCMV enriched from clinical samples excluded resistance in 7 of eleven subjects and identified resistance mutations earlier than conventional PCR-based resistance testing in 2 patients. Detection of multiple low level resistance mutations was associated with poor outcome.
α4-containing GABAAreceptors on dopamine D2 receptor-expressing neurons mediate instrumental responding for conditioned reinforcers, and its potentiation by cocaine
Authors: Macpherson Tom , Dixon Claire I , Janak Patricia H. , Belelli Delia , Lambert Jeremy J. , Stephens David N. , King Sarah
Published: May 2016

Extrasynaptic GABAAreceptors (GABAARs) composed of α4, β and δ subunits mediate GABAergic tonic inhibition and are pertinent molecular targets in the modulation of behavioural responses to drugs of abuse, including ethanol and cocaine. These GABAARs are highly expressed within the nucleus accumbens (NAc) where they influence the excitability of the medium spiny neurons (MSNs). Here we explore their role in modulating behavioural responses to reward-conditioned cues and the behaviour-potentiating effects of cocaine. α4-subunit constitutive knockout mice (α4-/-) showed higher rates of instrumental responding for reward-paired stimuli in a test of conditioned reinforcement (CRf). A similar effect was seen following viral knockdown of GABAAR α4 subunits within the NAc. Local infusion of the δ-GABAAR-preferring agonist, THIP, into the NAc had no effect on responding when given alone, but reduced cocaine potentiation of responding for conditioned reinforcers in wildtype but not α4-/- mice. Finally, specific deletion of α4-subunits from dopamine D2-, but not D1-receptor-expressing neurons, mimicked the phenotype of the constitutive knockout, potentiating CRf responding and blocking intra-accumbal THIP attenuation of cocaine-potentiated CRf responding. These data demonstrate that α4-GABAAR mediated inhibition of dopamine D2 receptor-expressing neurons reduces instrumental-responding for a conditioned reinforcer, and its potentiation by cocaine, and emphasise the potential importance of GABAergic signalling within the NAc in mediating cocaine’s effects.
Population structure of UK Biobank and ancient Eurasians reveals adaptation at genes influencing blood pressure
Authors: Galinsky Kevin J. , Loh Po-Ru , Swapan Mallick , Patterson Nick J. , Price Alkes L.
Published: May 2016

Analyzing genetic differences between closely related populations can be a powerful way to detect recent adaptation. The very large sample size of the UK Biobank is ideal for detecting selection using population differentiation, and enables an analysis of UK population structure at fine resolution. In analyses of 113,851 UK Biobank samples, population structure in the UK is dominated by 5 principal components (PCs) spanning 6 clusters: Northern Ireland, Scotland, northern England, southern England, and two Welsh clusters. Analyses with ancient Eurasians show that populations in the northern UK have higher levels of Steppe ancestry, and that UK population structure cannot be explained as a simple mixture of Celts and Saxons. A scan for unusual population differentiation along top PCs identified a genome-wide significant signal of selection at the coding variant rs601338 inFUT2(p= 9.16 × 10−9). In addition, by combining evidence of unusual differentiation within the UK with evidence from ancient Eurasians, we identified new genome-wide significant (p< 5 × 10−8) signals of recent selection at two additional loci:CYP1A2/CSKandF12. We detected strong associations to diastolic blood pressure in the UK Biobank for the variants with new selection signals atCYP1A2/CSK(p= 1.10 × 10−19)) and for variants with ancient Eurasian selection signals in theATXN2/SH2B3locus (p= 8.00 × 10−33), implicating recent adaptation related to blood pressure.
Rapidly evolving homing CRISPR barcodes
Authors: Kalhor Reza , Mali Prashant , Church George M.
Published: May 2016

We present here an approach for engineering evolving DNA barcodes in living cells. The methodology entails using a homing guide RNA (hgRNA) scaffold that directs the Cas9-hgRNA complex to target the DNA locus of the hgRNA itself. We show that this homing CRISPR-Cas9 system acts as an expressed genetic barcode that diversifies its sequence and that the rate of diversification can be controlled in cultured cells. We further evaluate these barcodes in cultured cell populations and show that they can record lineage history and and that their RNA can be assayed as single moleculesin situ. This integrated approach will have wide ranging applications, such as in deep lineage tracing, cellular barcoding, molecular recording, dissecting cancer biology, and connectome mapping.
The Coevolutionary Romance of Social Learning and Parasitic Behavior
Authors: McElreath Richard
Published: May 2016

Once an animal begins to acquire behavior by social learning, it may be seduced by parasitic parasitic, behavior that reduces the animal’s fitness and thereby increases its own spread. However, the animal’s psychology will coevolve, potentially limiting the influence and spread of parasitic behavior. I revisit prominent models of the evolution of social learning and introduce the possibility of parasitic behavior. First, I explore a courtship between primitive social learning and parasitic behavior. Parasitic behavior can spread, but selection on the host then reduces social learning and limits its importance. Both parties are frustrated. In the second part, I study a reconciliation dynamic in which social learning becomes strategic about who it partners with. In this model, parasitic behavior can become prevalent and substantially reduce host fitness. However, it may also evolve to be mutualistic and raise the mean fitness of the host organism. When this occurs, natural selection may favor psychological susceptibility to parasitic behavior. Both social learning and socially learned behavior can enjoy a happy ending.
Improved Insights into Protein Thermal Stability: From the Molecular to the Structurome Scale
Authors: Pucci Fabrizio , Rooman Marianne
Published: May 2016

Despite the intense efforts of the last decades to understand the thermal stability of proteins, the mechanisms responsible for its modulation still remain debated. In this investigation, we tackle this issue by showing how a multi-scale perspective can yield new insights. With the help of temperature-dependent statistical potentials, we analyzed some amino acid interactions at the molecular level, which are suggested to be relevant for the enhancement of thermal resistance. We then investigated the thermal stability at the protein level by quantifying its modification upon amino acid substitutions. Finally, a large scale analysis of protein stability - at the structurome level - contributed to the clarification of the relation between stability and natural evolution, thereby showing that the mutational profile of thermostable and mesostable proteins differ. Some final considerations on how the multi-scale approach could help unraveling the protein stability mechanisms are briefly discussed.
Scale-free versus multi-scale: Statistical analysis of livestock mobility patterns across species
Authors: Sakamoto Takuto , Sanders Lloyd , Inazumi Nobu
Published: May 2016

In quantitative studies on animal movements and foraging, there has been ongoing debate over the relevance of Lévy walk and related stochastic models to understanding mobility patterns of diverse organisms. In this study, we collected and analyzed a large number of GPS logs that tracked the movements of different livestock species in northwestern Kenya. Statistically principled analysis has only found limited evidence for the scale-free movement patterns of the Lévy walk and its variants, even though most of the tracked movements clearly show super-diffusive behavior within the relevant temporal duration. Instead, the analysis has given strong support to composite exponential distributions (composite Brownian walks) as the best description of livestock movement trajectories in a wide array of parameter settings. Furthermore, this support has become overwhelming and near universal under an alternative criterion for model selection. These results illuminate the multi-scale and multi-modal nature of livestock spatial behavior. They also have broader theoretical and empirical implications for the related literature.
Tribe: The collaborative platform for reproducible web-based analysis of gene sets
Authors: Zelaya René A. , Wong Aaron K. , Frase Alex T. , Ritchie Marylyn D. , Greene Casey S.
Published: May 2016

Background

The adoption of new bioinformatics webservers provides biological researchers with new analytical opportunities but also raises workflow challenges. These challenges include sharing collections of genes with collaborators, translating gene identifiers to the most appropriate nomenclature for each server, tracking these collections across multiple analysis tools and webservers, and maintaining effective records of the genes used in each analysis.

Description

In this paper, we present the Tribe webserver (available athttps://tribe.greenelab.com), which addresses these challenges in order to make multi-server workflows seamless and reproducible. This allows users to create analysis pipelines that use their own sets of genes in combinations of specialized data mining webservers and tools while seamlessly maintaining gene set version control. Tribe’s web interface facilitates collaborative editing: users can share with collaborators, who can then view, download, and edit these collections. Tribe’s fully-featured API allows users to interact with Tribe programmatically if desired. Tribe implements the OAuth 2.0 standard as well as gene identifier mapping, which facilitates its integration into existing servers. Access to Tribe’s resources is facilitated by an easy-to-install Python application calledtribe-client. We provide Tribe and tribe-client under a permissive open-source license to encourage others to download the source code and set up a local instance or to extend its capabilities.

Conclusions

The Tribe webserver addresses challenges that have made reproducible multi-webserver workflows difficult to implement until now. It is open source, has a user-friendly web interface, and provides a means for researchers to perform reproducible gene set based analyses seamlessly across webservers and command line tools.
Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation
Authors: Duarte Fabiana M. , Fuda Nicholas J. , Mahat Dig B. , Core Leighton J. , Guertin Michael J. , Lis John T.
Published: May 2016

The coordinated regulation of gene expression at the transcriptional level is fundamental to organismal development and homeostasis. Inducible systems are invaluable when studying transcription because the regulatory process can be triggered instantaneously, allowing the tracking of ordered mechanistic events. Here, we use Precision Run-On sequencing (PRO-seq) to examine the genome-wide Heat Shock (HS) response inDrosophilaand the function of two key transcription factors on the immediate transcription activation or repression of all genes regulated by HS. We identify the primary HS response genes and the rate-limiting steps in the transcription cycle that GAGA-Associated Factor (GAF) and HS Factor (HSF) regulate. We demonstrate that GAF acts upstream of promoter-proximally paused RNA Polymerase II (Pol II) formation, likely at the step of chromatin opening, and that GAF-facilitated Pol II pausing is critical for HS activation. In contrast, HSF is dispensable for establishing or maintaining Pol II pausing, but is critical for the release of paused Pol II into the gene body at a subset of highly-activated genes. Additionally, HSF has no detectable role in the rapid HS-repression of thousands of genes.
The reciprocal relationship between competition and intraspecific trait variation
Authors: Bennett Jonathan A. , Riibak Kersti , Tamme Riin , Lewis Rob J. , Pärtel Meelis
Published: May 2016

Trait differences among plants are expected to influence the outcome of competition; competition should be strongest between similar species (or individuals) under limiting similarity, and between dissimilar species within competitive hierarchies. These hypotheses are often used to infer competitive dynamics from trait patterns within communities. However, plant traits are frequently plastic in response to competition. This variation is poorly accounted for in trait‐based studies of competition and community assembly.

To explore the relationship between trait responses and competitive outcomes, we grew 15 species alone, in monoculture and in mixture. We measured traits relating to leaf and root tissue morphology as well as biomass allocation and related competition‐induced changes in these traits to intra‐ and interspecific competition using multi‐model inference. Additionally, we tested how traits from different competitive environments influenced potential community assembly inferences.

The competitive environment had large effects on species’ traits, although many effects were species specific. Differences among species in how competition affected trait expression were linked to both intra‐ and interspecific competition, frequently affecting competitive hierarchies. Intraspecific competition was lower for species that limited competition‐induced increases in root allocation and had less variability in this trait overall. Interspecific competition was lower for species with larger leaves and lower specific leaf area than their neighbours. Switching to more stress‐tolerant strategies by increasing root diameter and leaf tissue density also reduced competition. However, dissimilarity in root tissue density also minimized competition, consistent with limiting similarity affecting competitive outcomes. Moreover, changes in these traits were linked to changes in functional diversity, suggesting that competition affects functional diversity by affecting trait expression.

Synthesis. Both trait hierarchies and trait dissimilarity affect the outcome of competition by acting on different traits, although competition‐induced changes in trait expression can alter competitive outcomes. Moreover, the magnitude of these trait changes suggests that the source environment where plant traits are collected can affect the inferences drawn from trait patterns within communities. Combined, our results suggest that considering the effect of competition on trait expression is critical to understanding the relationship between traits and community assembly.
Soil abiotic and biotic controls on plant performance during primary succession in a glacial landscape
Authors: Castle Sarah C. , Lekberg Ylva , Affleck David , Cleveland Cory C.
Published: May 2016

Plant–soil interactions are temporally dynamic in ways that are important for the development of plant communities. Yet, during primary succession, the degree to which changing soil characteristics (e.g. increasing nutrient availabilities) and developing communities of soil biota influence plant growth and species turnover is not well understood.

We conducted a two‐phase glasshouse experiment with two native plant species and soils collected from three ages (early, mid‐ and late succession) of an actively developing glacial chronosequence ranging from approximately 5 to <100 years in age. The first phase assessed how soil abiotic characteristics and soil biota immediately influenced plant performance. In the second phase, we used conditioned soils to grow the same plant species and assessed how the direction and strength of plant–soil feedback (PSF) varied through succession. We used high and low nutrient and soil sterilization treatments to isolate effects of abiotic and biotic factors on plant performance and to assess how patterns of PSF related to soil nutrients.

For both species, our experiments revealed that the initial effect of soil biota on plant performance depended on successional stage. In soils collected from early‐, mid‐ and late‐succession stages, we observed neutral to negative, negative and positive effects of soil biota on plant performance, respectively.

Plant–soil feedback varied with successional stage and depended on whether microcosms were supplied with nutrients. Under low nutrient conditions, soil conditioning by plants, unrelated to initial soil biota, was an important mechanism for positive PSF. Under high nutrient conditions, PSFs differed by plant species in early‐ and mid‐succession soils, but were consistently neutral in late succession.

Synthesis. Soil biota can affect the performance of pioneer plants over short gradients of ecosystem development, but the strength and direction of interactions depend on nutrient availability. Conceptual frameworks describing mechanisms of primary succession should acknowledge soil conditioning by previous plants as a potential mechanism of positive feedback.
A multiproxy approach to evaluate biocidal treatments on biodeteriorated majolica glazed tiles
Authors: Coutinho M. L. , Miller A. Z. , Martin‐Sanchez P. M. , Mirão J. , Gomez‐Bolea A. , Machado‐Moreira B. , Cerqueira‐Alves L. , Jurado V. , Saiz‐Jimenez C. , Lima A. , Phillips A. J. L. , Pina F. , Macedo M. F.
Published: May 2016

The Fishing House located on the grounds of the Marquis of Pombal Palace, Oeiras, Portugal, was built in the 18th century. During this epoch, Portuguese gardens, such as the one surrounding the Fishing House, were commonly ornamented with glazed wall tile claddings. Currently, some of these outdoor tile panels are covered with dark colored biofilms, contributing to undesirable aesthetic changes and eventually inducing chemical and physical damage to the tile surfaces. Phylogenetic analyses revealed that the investigated biofilms are mainly composed of green algae, cyanobacteria and dematiaceous fungi. With the aim of mitigating biodeterioration, four different biocides (TiO2 nanoparticles, Biotin® T, Preventol® RI 80 and Albilex Biostat®) were applied in situ to the glazed wall tiles. Their efficacy was monitored by visual examination, epifluorescence microscopy and DNA‐based analysis. Significant changes in the microbial community composition were observed 4 months after treatment with Preventol® RI 80 and Biotin® T. Although the original community was inactivated after these treatments, an early stage of re‐colonization was detected 6 months after the biocide application. TiO2 nanoparticles showed promising results due to their self‐cleaning effect, causing the detachment of the biofilm from the tile surface, which remained clean 6 and even 24 months after biocide application. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd
Native plasmids restrict growth of Phaeobacter inhibens DSM 17395: Energetic costs of plasmids assessed by quantitative physiological analyses
Authors: Trautwein Kathleen , Will Sabine Eva , Hulsch Reiner , Maschmann Uwe , Wiegmann Katharina , Hensler Michael , Michael Victoria , Ruppersberg Hanna , Wünsch Daniel , Feenders Christoph , Neumann‐Schaal Meina , Kaltenhäuser Sabine , Ulbrich Marcus , Schmidt‐Hohagen Kerstin , Blasius Bernd , Petersen Jörn , Schomburg Dietmar , Rabus Ralf
Published: May 2016

Plasmid carriage is associated with energetic costs, and thus only those plasmids providing fitness benefits are stably maintained in the host lineage. Marine bacteria of the Roseobacter clade harbor up to 11 extrachromosomal replicons, adding lifestyle‐relevant and possibly habitat success‐promoting functions to their genomic repertoire. Phaeobacter inhibens DSM 17395 is a nutritionally versatile representative, carrying three stable and functionally distinct plasmids (65, 78, and 262 kb). The present study investigates the physiological and energetic consequences of plasmid carriage in P. inhibens DSM 17395, employing mutants cured from all native plasmids in every possible combination (seven different). Cultivation in process‐controlled bioreactors with casamino acids as organic substrate revealed a complex physiological response, suggesting existence of functional interconnections between the replicons. Deletion of the 262 kb plasmid boosted growth rate (>3‐fold) and growth efficiency (yields for carbon, O2 and CO2), which was not observed for the 65 or 78 kb plasmid. Carriage of the 262 kb plasmid was most costly for the wild type, i.e. contributing ∼50% to its energetic (dissimilatory) expenditures. Cost–benefit analysis of plasmid carriage reflects the high value of plasmids for niche specialization of P. inhibens DSM 17395 and most likely also for related Phaeobacter species.
Microbial dinitrogen fixation in coral holobionts exposed to thermal stress and bleaching
Authors: Cardini Ulisse , van Hoytema Nanne , Bednarz Vanessa N. , Rix Laura , Foster Rachel A. , Al‐Rshaidat Mamoon M. D. , Wild Christian
Published: May 2016

Coral holobionts (i.e., coral‐algal‐prokaryote symbioses) exhibit dissimilar thermal sensitivities that may determine which coral species will adapt to global warming. Nonetheless, studies simultaneously investigating the effects of warming on all holobiont members are lacking. Here we show that exposure to increased temperature affects key physiological traits of all members (herein: animal host, zooxanthellae and diazotrophs) of both Stylophora pistillata and Acropora hemprichii during and after thermal stress. S. pistillata experienced severe loss of zooxanthellae (i.e., bleaching) with no net photosynthesis at the end of the experiment. Conversely, A. hemprichii was more resilient to thermal stress. Exposure to increased temperature (+ 6°C) resulted in a drastic increase in daylight dinitrogen (N2) fixation, particularly in A. hemprichii (threefold compared with controls). After the temperature was reduced again to in situ levels, diazotrophs exhibited a reversed diel pattern of activity, with increased N2 fixation rates recorded only in the dark, particularly in bleached S. pistillata (twofold compared to controls). Concurrently, both animal hosts, but particularly bleached S. pistillata, reduced both organic matter release and heterotrophic feeding on picoplankton. Our findings indicate that physiological plasticity by coral‐associated diazotrophs may play an important role in determining the response of coral holobionts to ocean warming.
A transposon present in specific strains of Bacillus subtilis negatively affects nutrient‐ and dodecylamine‐induced spore germination
Authors: Krawczyk Antonina O. , Berendsen Erwin M. , de Jong Anne , Boekhorst Jos , Wells‐Bennik Marjon H. J. , Kuipers Oscar P. , Eijlander Robyn T.
Published: May 2016

Spore germination shows a large inter‐strain variability. Spores of certain Bacillus subtilis strains, including isolates from spoiled food products, exhibit different germination behavior from spores of the well‐studied model organism Bacillus subtilis 168, often for unknown reasons. In this study, we analyzed spore germination efficiencies and kinetics of seventeen B. subtilis strains with previously sequenced genomes. A subsequent gene‐trait matching analysis revealed a correlation between a slow germination phenotype and the presence of a mobile genetic element, i.e., a Tn1546‐like transposon. A detailed investigation of the transposon elements showed an essential role of a specific operon (spoVA2mob) in inhibiting spore germination with nutrients and with the cationic surfactant dodecylamine. Our results indicate that this operon negatively influences release of Ca‐DPA by the SpoVA channel and may additionally alter earlier germination events, potentially by affecting proteins in the spore inner membrane. The spoVA2mob operon is an important factor that contributes to inter‐strain differences in spore germination. Screening for its genomic presence can be applied for identification of spores that exhibit specific properties that impede spore eradication by industrial processes.
Anaerobic microbial Fe(II) oxidation and Fe(III) reduction in coastal marine sediments controlled by organic carbon content
Authors: Laufer Katja , Byrne James M. , Glombitza Clemens , Schmidt Caroline , Jørgensen Bo Barker , Kappler Andreas
Published: May 2016

Coastal marine sediments contain varying concentrations of iron, oxygen, nitrate and organic carbon. It is unknown how organic carbon content influences the activity of nitrate‐reducing and phototrophic Fe(II)‐oxidizers and microbial Fe‐redox cycling in such sediments. Therefore, microcosms were prepared with two coastal marine sediments (Kalø Vig and Norsminde Fjord at Aarhus Bay, Denmark) varying in TOC from 0.4 to 3.0 wt%. The microcosms were incubated under light/dark conditions with/without addition of nitrate and/or Fe(II). Although most probable number (MPN) counts of phototrophic Fe(II)‐oxidizers were five times lower in the low‐TOC sediment, phototrophic Fe(II) oxidation rates were higher compared with the high‐TOC sediment. Fe(III)‐amended microcosms showed that this lower net Fe(II) oxidation in the high‐TOC sediment is caused by concurrent bacterial Fe(III) reduction. In contrast, MPN counts of nitrate‐reducing Fe(II)‐oxidizers and net rates of nitrate‐reducing Fe(II) oxidation were comparable in low‐ and high‐TOC sediments. However, the ratio of nitratereduced:iron(II)oxidized was higher in the high‐TOC sediment, suggesting that a part of the nitrate was reduced by mixotrophic nitrate‐reducing Fe(II)‐oxidizers and chemoorganoheterotrophic nitrate‐reducers. Our results demonstrate that dynamic microbial Fe cycling occurs in these sediments and that the extent of Fe cycling is dependent on organic carbon content.
Prediction of bacterial associations with plants using a supervised machine‐learning approach
Authors: Martínez‐García Pedro Manuel , López‐Solanilla Emilia , Ramos Cayo , Rodríguez‐Palenzuela Pablo
Published: May 2016

Recent scenarios of fresh produce contamination by human enteric pathogens have resulted in severe food‐borne outbreaks, and a new paradigm has emerged stating that some human‐associated bacteria can use plants as secondary hosts. As a consequence, there has been growing concern in the scientific community about these interactions that have not yet been elucidated. Since this is a relatively new area, there is a lack of strategies to address the problem of food‐borne illnesses due to the ingestion of fruits and vegetables. In the present study, we performed specific genome annotations to train a supervised machine‐learning model that allows for the identification of plant‐associated bacteria with a precision of ∼93%. The application of our method to approximately 9500 genomes predicted several unknown interactions between well‐known human pathogens and plants, and it also confirmed several cases for which evidence has been reported. We observed that factors involved in adhesion, the deconstruction of the plant cell wall and detoxifying activities were highlighted as the most predictive features. The application of our strategy to sequenced strains that are involved in food poisoning can be used as a primary screening tool to determine the possible causes of contaminations.
Large‐scale maps of variable infection efficiencies in aquatic Bacteroidetes phage‐host model systems
Authors: Holmfeldt Karin , Solonenko Natalie , Howard‐Varona Cristina , Moreno Mario , Malmstrom Rex R. , Blow Matthew J. , Sullivan Matthew B.
Published: May 2016

Microbes drive ecosystem functioning and their viruses modulate these impacts through mortality, gene transfer and metabolic reprogramming. Despite the importance of virus‐host interactions and likely variable infection efficiencies of individual phages across hosts, such variability is seldom quantified. Here, we quantify infection efficiencies of 38 phages against 19 host strains in aquatic Cellulophaga (Bacteroidetes) phage‐host model systems. Binary data revealed that some phages infected only one strain while others infected 17, whereas quantitative data revealed that efficiency of infection could vary 10 orders of magnitude, even among phages within one population. This provides a baseline for understanding and modeling intrapopulation host range variation. Genera specific host ranges were also informative. For example, the Cellulophaga Microviridae, showed a markedly broader intra‐species host range than previously observed in Escherichia coli systems. Further, one phage genus, Cba41, was examined to investigate nonheritable changes in plating efficiency and burst size that depended on which host strain it most recently infected. While consistent with host modification of phage DNA, no differences in nucleotide sequence or DNA modifications were detected, leaving the observation repeatable, but the mechanism unresolved. Overall, this study highlights the importance of quantitatively considering replication variations in studies of phage–host interactions.