bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the relationship between pollinator behavior and plant reproductive isolation
Authors: Hopkins Robin 
Published: December 2016

ABSTRACTPollinator behavior is an important contributor to reproductive isolation in plants. Despite hundreds of years of empirical research, we lack a quantitative framework for evaluating how variation in pollinator behavior causes variation in reproductive isolation in plants. Here I present a model describing how two aspects of pollinator behavior – constancy and preference – lead to reproductive isolation in plants. This model is motivated by two empirical observations: most co-occurring plants vary in frequency over space and time and most plants have multiple pollinators that differ in behavior. These two observations suggest a need to understand how plant frequency and pollinator frequency influence reproductive isolation between co-occurring plants. My model predicts how the proportion of heterospecific matings varies over plant frequencies given pollinator preference and constancy. I find that the shape of this relationship is dependent on the strength of pollinator behavior. Additionally, my model incorporates multiple pollinators with different behaviors to predict the proportion of heterospecific matings across pollinator frequencies. I find that when two pollinators display different strength constancy the total proportion of heterospecific matings is simply the average proportion of heterospecific matings predicted for each pollinator. When pollinators vary in their preference the pollinator with the stronger preference disproportionally contributes to the predicted proportion of total heterospecific matings. I apply this model to examples of pollinator-mediated reproductive isolation inPhloxand inMimulusto predict relationships between plant and pollinator frequency and reproductive isolation in natural systems.
Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks
Authors: Baryshnikova Anastasia 
Published: December 2016

Summary/AbstractSpatial Analysis of Functional Enrichment (SAFE) is a systematic quantitative approach for annotating large biological networks. SAFE detects network regions that are statistically overrepresented for functional groups or quantitative phenotypes of interest, and provides an intuitive visual representation of their relative positioning within the network. In doing so, SAFE determines which functions are represented in a network, which parts of the network they are associated with and how they are potentially related to one another.Here, I provide a detailed stepwise description of how to perform a SAFE analysis. As an example, I use SAFE to annotate the genome-scale genetic interaction similarity network fromSaccharomyces cerevisiaewith Gene Ontology (GO) biological process terms. In addition, I show how integrating GO with chemical genomic data in SAFE can recapitulate known modes-of-action of chemical compounds and potentially identify novel drug mechanisms.
An Integrated Risk Predictor for Pulmonary Nodules
Authors: Kearney Paul , Li Xiao-Jun , Porter Alex , Springmeyer Steve , Mazzone Peter 
Published: December 2016

AbstractIt is estimated that over 1.5 million lung nodules are detected annually in the United States. Most of these are benign but frequently undergo invasive and costly procedures to rule out malignancy. A risk predictor that can accurately differentiate benign and malignant lung nodules could be used to more efficiently route benign lung nodules to non-invasive observation by CT surveillance and route malignant lung nodules to invasive procedures. The majority of risk predictors developed to date are based exclusively on clinical risk factors, imaging technology or molecular markers. Assessed here are the relative performances of previously reported clinical risk factors and proteomic molecular markers for assessing cancer risk in lung nodules. From this analysis an integrated model incorporating clinical risk factors and proteomic molecular markers is developed and its performance assessed on a previously reported prospective collection of lung nodules that enrolled 475 patients from 12 sites with lung nodules between 8 and 30mm in diameter. In this analysis it is found that the molecular marker is most predictive. However, the integration of clinical and molecular markers is superior to both clinical and molecular markers separately.Clinical Trial Registration: Registered at ClinicalTrials.gov (NCT01752101).
Cohesin dependent compaction of mitotic chromosomes
Authors: Schalbetter Stephanie A. , Goloborodko Anton , Fudenberg Geoffrey , Belton Jon M. , Miles Catrina , Yu Miao , Dekker Job , Mirny Leonid , Baxter Jon 
Published: December 2016

Structural Maintenance of Chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply-conserved SMC complexes, organize chromosomes in budding yeast. The canonical role of cohesins is to co-align sister chromatids whilst condensins generally compact mitotic chromosomes. We find strikingly different roles in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosomes arms, independent of and in addition to its role in sister-chromatid cohesion. Cohesin dependent mitotic chromosome compaction can be fully accounted for throughcis-looping of chromatin by loop extrusion. Second, condensin is dispensable for compaction along chromosomal arms and instead plays a specialized role, structuring rDNA and peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that SMC-dependent looping is readily deployed in a range of contexts to functionally organize chromosomes.HighlightsCohesin compacts mitotic chromosomes independently of sister chromatid cohesion.Formation ofcis-loops by loop extrusion fully accounts for cohesin-mediated compaction.Condensin is not required for mitotic chromosome compaction of yeast chromosome armsCondensin has a focused pre-anaphase role at centromeres and rDNA in yeast
In culture cross-linking of bacterial cells reveals proteome scale dynamic protein-protein interactions at the peptide level
Authors: de Jong Luitzen , de Koning Edward A. , Roseboom Winfried , Buncherd Hansuk , Wanner Martin J. , Dapic Irena , Jansen Petra J. , van Maarseveen Jan H. , Corthals Garry L. , Lewis Peter J. , Hamoen Leendert W. , de Koster Chris G. 
Published: December 2016

AbstractIdentification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram positive model bacteriumBacillus subtilisas an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species,Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG. We were able to identify 82 unique inter-protein cross-linked peptides with less than a 1% false discovery rate by mass spectrometry and genome-wide data base searching. Nearly 60% of the inter-protein cross-links occur in assemblies involved in transcription and translation. Several of these interactions are new, and we identified a binding site between the δ and β′ subunit of RNA polymerase close to the downstream DNA channel, providing a clue into how δ might regulate promoter selectivity and promote RNA polymerase recycling. Our methodology opens new avenues to investigate the functional dynamic organization of complex protein assemblies involved in bacterial growth.
poRe GUIs for parallel and real-time processing of MinION sequence data
Authors: Stewart Robert , Watson Mick 
Published: December 2016

AbstractMotivationOxford Nanopore’s MinION device has matured rapidly and is now capable of producing over one million reads and several gigabases of sequence data per run. The nature of the MinION output requires new tools that are easy to use by scientists with a range of computational skills and which enable quick and simple QC and data extraction from MinION runs.ResultsWe have developed two GUIs for the R package poRe that allow parallel and real-time processing of MinION datasets. Both GUIs are capable of extracting sequence- and meta- data from large MinION datasets via a friendly point-and-click interface using commodity hardware.AvailabilityThe GUIs are packaged within poRe which is available on SourceForge:https://source-forge.net/projects/rpore/files/. Documentation is available on GitHub:https://github.com/mw55309/poRe_docs
Bacterial communities affected by experimental disturbances to canopy soils of a temperate rainforest
Authors: Dangerfield Cody R. , Nadkarni Nalini M. , Brazelton William J. 
Published: December 2016

ABSTRACTTrees of temperate rainforests host a large biomass of epiphytes, living plants associated with soils formed in the forest canopy. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different species-level operational taxonomic units. A field experiment was conducted to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, connection to the living tree is an important factor in the ecology of canopy soil bacteria. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.IMPORTANCETemperate rainforests host large accumulations of epiphytes, plants that live on the branches of trees. This study provides a first look at the unique nature of bacterial communities in soil that is formed by the decomposition of epiphytes in the canopy of a temperate rainforest. Falling of epiphytic material results in the transfer of significant amounts of carbon and nutrients from the canopy to the forest floor. This study also experimentally documented how soil bacterial communities are affected by their movement from the canopy to the forest floor. The bacterial composition of canopy soil was altered by the severing of the epiphytic material from the living tree, even when the epiphytes remained in the canopy. Therefore, the unique nature of canopy soil bacteria is determined in part by the living host tree and not only by the physical environmental conditions associated with the canopy.
Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean
Authors: Chen Minmin , Fontaine Michael C. , Ben Chehida Yacine , Zheng Jinsong , Labbe Frédéric , Mei Zhigang , Hao Yujiang , Wang Kexiong , Wu Min , Zhao Qingzhong , Wang Ding 
Published: December 2016

AbstractUnderstanding demographic trends and patterns of gene flow in an endangered species is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). By analysing genetic variation at the mitochondrial and nuclear microsatellite loci for 148 individuals, we identified three populations along the Yangtze River, each one connected to a group of admixed ancestry. Each population displayed extremely low genetic diversity, consistent with extremely small effective size (≤92 individuals). Habitat degradation and distribution gaps correlated with highly asymmetric gene-flow that was inefficient in maintaining connectivity between populations. Genetic inferences of historical demography revealed that the populations in the Yangtze descended from a small number of founders colonizing the river from the sea during the last Ice Age. The colonization was followed by a rapid population split during the last millennium predating the Chinese Modern Economy Development. However, genetic diversity showed a clear footprint of population contraction over the last 50 years leaving only ~2% of the pre-collapsed size, consistent with the population collapses reported from field studies. This genetic perspective provides background information for devising mitigation strategies to prevent this species from extinction.
Universal scaling of maximum speed with body mass - Why the largest animals are not the fastest
Authors: Hirt Myriam R. , Jetz Walter , Rall Bjöern C. , Brose Ulrich 
Published: December 2016

AbstractSpeed is the fundamental constraint on animal movement, yet there is no general consensus on the determinants of maximum speed itself. Here, we provide a universal scaling model of maximum speed with body mass, which holds across locomotion modes, ecosystem types and taxonomic groups. In contrast to traditional power-law scaling, we predict a hump-shaped relationship due to a finite acceleration time for animals. This model is strongly supported by extensive empirical data (470 species with body masses ranging from 5.7×10−8to 108,000 kg) from terrestrial as well as aquatic ecosystems. Our approach offers a novel concept of what determines the upper limit of animal movement, thus enabling a better understanding of realized movement patterns in nature and their multifold ecological consequences.
Helical reconstruction in RELION
Authors: He Shaoda , Scheres Sjors H.W. 
Published: December 2016

AbstractWe describe a new implementation for the reconstruction of helical assemblies in the empirical Bayesian framework of RELION. Our approach calculates optimal linear filters for the 3D reconstruction by embedding helical symmetry operators in Fourier-space, and deals with deviations from perfect helical symmetry through Gaussian-shaped priors on the orientations of individual segments. By incorporating our approach into the standard pipeline for single-particle analysis in RELION, our implementation aims to be easily accessible for non-experienced users. Although our implementation does not solve the problem that grossly incorrect structures can be obtained when the wrong helical symmetry is imposed, we show for four different test cases that it is capable of reconstructing structures to near-atomic resolution.AbbreviationsCARDCaspase Activation and Recruitment DomainEMElectron MicroscopyFSCFourier Shell CorrelationIHRSRIterative Helical Real-Space ReconstructionMAVSMitochondrial Antiviral Signaling ProteinTMVTobacco Mosaic Virus
Computational Pharmacogenetics of P-Glycoprotein Mediated Antiepileptic Drug Resistance
Authors: Palaniappan Ashok , Varghese Sindhu 
Published: December 2016

AbstractThe treatment of epilepsy using antiepileptogenic drugs is complicated by drug re-sistance, resulting in treatment failure in more than one-third of cases. Human P-glycoprotein (hPGP;MDR1) is a known epileptogenic mediator. Given that experimental investigations have suggested a role for pharmacogenetics in this treatment failure, it would be of interest to study hPGP polymorphisms that might contribute to the emergence of drug resistance. Changes in protein functional activity could result from point mutations as well as altered abundance. Bioinformatics approaches were used to assess and rank the functional impact of 20 missense MDR1 polymorphisms and the top five were selected. The structures of the wildtype and mutant hPGP were modelled based on the mouse PGP structure. Docking studies of the wildtype and mutant hPGP with four standard anti-epileptic drugs were carried out. Our results revealed that the drug binding site with respect to the wildtype protein was uniform. However the mutant hPGP proteins displayed a repertoire of binding sites with stronger binding affinities towards the drug. Our studies indicated that specific polymorphisms in MDR1 could drive conformational changes of PGP structure, facilitating altered contacts with drug-substrates and resulting in drug extrusion. This suggests that MDR1 polymorphisms could play an active role in modifying drug bioavailability, leading to pharmacoresistance in antiepileptic chemotherapy.
Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease
Authors: Patrick Ellis , Rajagopal Sathyapriya , Wong Hon-Kit Andus , McCabe Cristin , Xu Jishu , Tang Anna , Imboywa Selina H. , Schneider Julie A. , Pochet Nathalie , Krichevsky Anna M. , Chibnik Lori B. , Bennett David A. , De Jager Philip L. 
Published: December 2016

AbstractBackgroundGiven multiple studies of brain microRNA (miRNA) in relation to Alzheimer’s disease (AD) with few consistent results and the heterogeneity of this disease, the objective of this study was to explore their mechanism by evaluating their relation to different elements of Alzheimer’s disease pathology, confounding factors and mRNA expression data from the same subjects in the same brain region.ResultsWe report analyses of expression profiling of miRNA (n=700 subjects) and lincRNA (n=540 subjects) from the dorsolateral prefrontal cortex of individuals participating in two longitudinal cohort studies of aging. Evaluating well-established (miR-132, miR-129), we confirm their association with pathologic AD in our dataset, and then characterize their in disease role in terms of neuritic β-amyloid plaques and neurofibrillary tangle pathology. Additionally, we identify one new miRNA (miR-99) and four lincRNA that are associated with these traits. Many other previously reported associations of microRNA with AD are associated with the confounders quantified in our longitudinal cohort. Finally, by performing analyses integrating both miRNA and RNA sequence data from the same individuals (525 samples), we characterize the impact of AD associated miRNA on human brain expression: we show that the effects of miR-132 and miR-129-5b converge on certain genes such as EP300 and find a role for miR200 and its target genes in AD using an integrated miRNA/mRNA analysis.ConclusionsOverall, miRNAs play a modest role in human AD, but we observe robust evidence that a small number of miRNAs are responsible for specific alterations in the cortical transcriptome that are associated with AD.
Benchmarking BarraCUDA on Epigenetic DNA and nVidia Pascal GPUs
Authors: Langdon W. B. 
Published: December 2016

AbstractTypically BarraCUDA uses CUDA graphics cards to map DNA reads to the human genome. Previously its software source code was genetically miproved for short paired end next generation sequences. On longer, 150 base paired end noisy Cambridge Epigsnetix’s data, a Pascal GTX 1080 proc esses about 10000 strings per second, comparable with twin nVidia Tesla K40.
Loss of the homologous recombination generad51leads to Fanconi anemia-like symptoms in zebrafish
Authors: Botthof Jan Gregor , Bielczyk-Maczyńska Ewa , Ferreira Lauren , Cvejic Ana 
Published: December 2016

AbstractRAD51is an indispensable homologous recombination protein, necessary for strand invasion and crossing over. It has recently been designated as a Fanconi anemia (FA) gene, following the discovery of two patients carrying dominant negative mutations. FA is a hereditary DNA repair disorder characterized by various congenital abnormalities, progressive bone marrow failure and cancer predisposition. In this paper, we describe the first viable vertebrate model ofRAD51loss. Zebrafishrad51loss-of-function mutants developed key features of FA, including hypocellular kidney marrow, sensitivity to crosslinking agents and decreased size. We show that some of these symptoms stem from both decreased proliferation and increased apoptosis of embryonic hematopoietic stem and progenitor cells. Co-mutation ofp53was able to rescue the hematopoietic defects seen in the single mutants, but led to tumor development. We further demonstrate that prolonged inflammatory stress can exacerbate the hematological impairment, leading to an additional decrease in kidney marrow cell numbers. These findings strengthen the assignment ofRAD51as a Fanconi gene and provide more evidence for the notion that aberrant p53 signaling during embryogenesis leads to the hematological defects seen later in life in FA. Further research on this novel zebrafish FA model will lead to a deeper understanding of the molecular basis of bone marrow failure in FA and the cellular role of RAD51.Significance statementThe homologous recombination protein RAD51 has been extensively studied in prokaryotes and lower eukaryotes. However, there is a significant lack of knowledge of the role of this protein and its regulation in anin-vivocontext in vertebrates. Here we report the first viable vertebrate mutant model ofrad51in zebrafish. These mutant fish enabled us to confirm for the first time the recently discovered role ofRAD51in Fanconi anemia pathogenesis. We report that p53 linked embryonic stem cell defects directly lead to hematological impairments later in life. Co-mutation ofrad51withp53rescues the observed hematological defects, but predisposes the fish to early tumor development. The application of this model opens new possibilities to advance Fanconi anemia drug discovery.
Researching fractured (information) landscapes
Authors: Lloyd Annemaree 
Published: December 2016

Purpose
The purpose of this paper is to introduce a range of sensitising themes that may help to frame the emerging concept of fractured landscapes.

Design/methodology/approach
Key concepts are drawn from the forced migration field, from social theory and from Library and information science research to frame the concept of fractured landscape research. Methodological and ethical aspects that influence research are also introduced.

Findings
The importance of nomenclature is identified in relation to designations of refugee and migrant. The concept of a fractured landscape provides a suitable way of describing the disruption that is caused to refugees’ information landscapes in the process of transition and resettlement. The sensitising themes such as the exilic journey, liminality, integration, bonding and bridging capital are introduced to provide a way of framing a deeper analysis of the information experience of people who must reconcile previously established ways of knowing with the new landscapes related to transition and resettlement.

Originality/value
Original paper that introduces an emerging conceptual framework and a range of questions that may be useful to library and information science researchers who wish to pursue research that contributes to the humanitarian area or library services.