bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Authors: Firtina Can , Bar-Joseph Ziv , Alkan Can , Cicek A. Ercument 
Published: December 2017

AbstractMotivationChoosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection. In such cases researchers often combine both technologies and the more erroneous long reads are corrected using the short reads. Current approaches rely on various graph based alignment techniques and do not take the error profile of the underlying technology into account. Memory- and time-efficient machine learning algorithms that address these shortcomings have the potential to achieve better and more accurate integration of these two technologies.ResultsWe designed and developed Hercules, the first machine learning-based long read error correction algorithm. The algorithm models every long read as a profile Hidden Markov Model with respect to the underlying platform’s error profile. The algorithm learns a posterior transition/emission probability distribution for each long read and uses this to correct errors in these reads. Using datasets from two DNA-seq BAC clones (CH17-157L1 and CH17-227A2), and human brain cerebellum polyA RNA-seq, we show that Hercules-corrected reads have the highest mapping rate among all competing algorithms and highest accuracy when most of the basepairs of a long read are covered with short reads.AvailabilityHercules source code is available at https://github.com/BilkentCompGen/Hercules
The impact of HIV-1 within-host evolution on transmission dynamics
Authors: Theys Kristof , Libin Pieter , Pineda-Pena Andrea-Clemencia , Nowe Ann , Vandamme Anne-Mieke , Abecasis Ana B 
Published: December 2017

AbstractThe adaptive potential of HIV-1 is a vital mechanism to evade host immune responses and antiviral treatment. However, high evolutionary rates during persistent infection can impair transmission efficiency and alter disease progression in the new host, resulting in a delicate trade-off between within-host virulence and between-host infectiousness. This trade-off is visible in the disparity in evolutionary rates at within-host and between-host levels, and preferential transmission of ancestral donor viruses. Understanding the impact of within-host evolution for epidemiological studies is essential for the design of preventive and therapeutic measures. Herein, we review recent theoretical and experimental work that generated new insights into the complex link between within-host evolution and between-host fitness, revealing temporal and selective processes underlying the structure and dynamics of HIV-1 transmission.
LTRs activated by Epstein-Barr virus-induced transformation of B cells alter the transcriptome
Authors: Leung Amy , Trac Candi , Kato Hiroyuki , Costello Kevin R , Natarajan Rama , Schones Dustin E 
Published: December 2017

AbstractEndogenous retroviruses (ERVs) are ancient viral elements that have accumulated in the genome through retrotransposition events. Although they have lost their ability to transpose, many of the long terminal repeats (LTRs) that originally flanked full-length ERVs maintain the ability to regulate transcription. While these elements are typically repressed in somatic cells, when this repression is lost, they can function as transcriptional enhancers and promoters. The mechanisms driving LTR activation, however, are not well understood. Epstein-Barr virus (EBV), which transforms primary B cells into continuously proliferating cells, is a tumor virus associated with lymphomas. We report here that transformation of primary B cells by EBV leads to genome-wide activation of LTR enhancers and promoters. The activation of LTRs coincides with local DNA hypomethylation and binding by transcription factors such as RUNX3, EBF1, and EBNA2. The set of EBV-activated LTRs is unique to transformed B cells when compared to other cell lines known to have activated LTRs. Furthermore, we found that EBV-induced LTR activation impacts the B cell transcriptome by upregulating transcripts driven by cryptic LTR promoters. These transcripts include genes important to oncogenesis of Hodgkin lymphoma, as well as those found in other cancers such asHUWE1/HECTH9. These data suggest that the activation of LTRs by EBV may be important to the pathology of EBV-associated cancers. Altogether, our results indicate that EBV-induced transformation of B cells alters endogenous retroviral element activity, thereby impacting host gene regulatory networks and oncogenic potential.
Reanalysis of global proteomic and phosphoproteomic data identified a large number of glycopeptides
Authors: Hu Yingwei , Shah Punit , Clark David J. , Ao Minghui , Zhang Hui 
Published: December 2017

ABSTRACTProtein glycosylation plays fundamental roles in many cellular processes, and previous reports have shown dysregulation to be associated with several human diseases, including diabetes, cancer, and neurodegenerative disorders. Despite the vital role of glycosylation for proper protein function, the analysis of glycoproteins has been lagged behind to other protein modifications. In this study, we describe the re-analysis of global proteomic data from breast cancer xenograft tissues using recently developed software package GPQuest 2.0, revealing a large number of previously unidentifiedN-linked glycopeptides. More importantly, we found that using immobilized metal affinity chromatography (IMAC) technology for the enrichment of phosphopeptides had co-enriched a substantial number of sialoglycopeptides, allowing for a large-scale analysis of sialoglycopeptides in conjunction with the analysis of phosphopeptides. Collectively, combined MS/MS analyses of global proteomic and phosphoproteomic datasets resulted in the identification of 6,724 N-linked glycopeptides from 617 glycoproteins derived from two breast cancer xenograft tissues. Next, we utilized GPQuest for the re-analysis of global and phosphoproteomic data generated from 108 human breast cancer tissues that were previously analyzed by Clinical Proteomic Analysis Consortium (CPTAC). Reanalysis of the CPTAC dataset resulted in the identification of 2,683 glycopeptides from the global proteomic data set and 4,554 glycopeptides from phosphoproteomic data set, respectively. Together, 11,292 N-linked glycopeptides corresponding to 1,731 N-linked glycosites from 883 human glycoproteins were identified from the two data sets. This analysis revealed an extensive number of glycopeptides hidden in the global and enriched in IMAC-based phosphopeptide-enriched proteomic data, information which would have remained unknown from the original study otherwise. The reanalysis described herein can be readily applied to identify glycopeptides from already existing data sets, providing insight into many important facets of protein glycosylation in different biological, physiological, and pathological processes.
Genomic heritability estimates in sweet cherry reveal non-additive genetic variance is relevant for industry-prioritized traits
Authors: Piaskowski J. , Hardner Craig , Cai Lichun , Zhao Yunyang , Iezzoni Amy , Peace Cameron 
Published: December 2017

ABSTRACTBackgroundSweet cherry is consumed widely across the world and provides substantial economic benefits in regions where it is grown. While cherry breeding has been conducted in the Pacific Northwest for over half a century, little is known about the genetic architecture of important traits. We used a genome-enabled mixed model to predict the genetic performance of 505 individuals for 32 phenological, disease response and fruit quality traits evaluated in the RosBREED sweet cherry crop data set. Genome-wide predictions were estimated using a repeated measures model for phenotypic data across 3 years, incorporating additive, dominance and epistatic variance components. Genomic relationship matrices were constructed with high-density SNP data and were used to estimate relatedness and account for incomplete replication across years.ResultsHigh broad-sense heritabilities of 0.83, 0.77, and 0.75 were observed for days to maturity, firmness, and fruit weight, respectively. Epistatic variance exceeded 40% of the total genetic variance for maturing timing, firmness and powdery mildew response. Dominance variance was the largest for fruit weight and fruit size at 34% and 27%, respectively. Omission of non-additive sources of genetic variance from the genetic mode resulted in inflation of narrow-sense heritability but minimally influenced prediction accuracy of genetic values in validation. Predicted genetic rankings of individuals from single-year models were inconsistent across years, likely due to incomplete sampling of the population genetic variance.ConclusionsPredicted breeding values and genetic values a measure revealed many high-performing individuals for use as parents and the most promising selections to advance for cultivar release consideration, respectively. This study highlights the importance of using the appropriate genetic model for calculating breeding values to avoid inflation of expected parental contribution to genetic gain. The genomic predictions obtained will enable breeders to efficiently leverage the genetic potential of North American sweet cherry germplasm by identifying high quality individuals more rapidly than with phenotypic data alone.
Medaka population genome structure and demographic history described via genotyping-by-sequencing
Authors: Katsumura Takafumi , Oda Shoji , Hiroshi Mitani , Oota Hiroki 
Published: December 2017

AbstractMedaka is a model organism in medicine, genetics, developmental biology and population genetics. Lab stocks composed of more than 100 local wild populations are available for research in these fields. Thus, medaka represents a potentially excellent bioresource for screening disease-risk- and adaptation-related genes in genome-wide association studies. Although the genetic population structure should be known before performing such an analysis, a comprehensive study on the genome-wide diversity of wild medaka populations has not been performed. Here, we performed genotyping-by-sequencing (GBS) for 81 and 12 medakas captured from a bioresource and the wild, respectively. Based on the GBS data, we evaluated the genetic population structure and estimated the demographic parameters using an approximate Bayesian computation (ABC) framework. The autosomal data confirmed that there were substantial differences between local populations and supported our previously proposed hypothesis on medaka dispersal based on mitochondrial genome (mtDNA) data. A new finding was that a local group that was thought to be a hybrid between the northern and the southern Japanese groups was actually a sister group of the northern Japanese group. Thus, this paper presents the first population-genomic study of medaka and reveals its population structure and history based on autosomal diversity.
Archaeal community structure and underlying ecological processes in swine manure slurry
Authors: Kumari Priyanka , Choi Hong L. 
Published: December 2017

AbstractThe ecological processes underlying the observed patterns in community composition of archaea in swine manure slurry are poorly understood. We studied the archaeal communities from six swine manure slurry storage tanks using paired-end Illumina sequencing of the v3 hypervariable region of 16S rRNA gene. Across all samples, the archaeal community was dominated by methanogens related toThermoplasmata, Methanomicrobia, andMethanobacteriaclasses. At the genus level, the archaeal community was dominated by a single uncultured lineage of archaea,vadinCA11, followed by methanogenic generaMethanobrevibacter,Methanosarcina,Methanosphaera,Methanogenium,Methanocorpusculum,Methanoculleus, andMethanomicrococcus. Significant phylogenetic signals were detected across relatively short phylogenetic distances, indicating that closely related archaeal operational taxonomic units (OTUs) tend to have similar niches. The standardized effect sizes of mean nearest taxon distance (SES.MNTD) showed that archaeal community was phylogenetically clustered, suggesting that environmental filtering deterministically influence the within-community composition of archaea. However, between-community analysis based onβ-nearest taxon index (βNTI) revealed that both deterministic selection and stochastic processes operate simultaneously to govern the assembly of archaeal communities. These findings significantly enhance our understanding of archaeal community assembly and underlying ecological processes is swine manure slurry.
The assessment of fishery status depends on the condition of fish habitats
Authors: Brown Christopher J. , Broadley Andrew , Adame Fernanda , Branch Trevor A. , Turschwell Mischa , Connolly Rod M. 
Published: December 2017

AbstractAt the crux of the debate over the global sustainability of fisheries is what society must do prevent overexploitation of fisheries and aid recovery of fisheries that have historically been overexploited. The focus of debates has been on controlling fishing pressure and assessments have not considered that stock production may be affected by changes in fish habitat. Fish habitats are being modified by climate change, built infrastructure, destructive fishing practices and pollution. We conceptualise how the classification of stock status can be biased by habitat change. Habitat loss can result in either overly optimistic or overly conservative assessment of stock status. The classification of stock status depends on how habitat affects fish demography and what reference points management uses to assess status. Nearly half of the 418 stocks in a global stock assessment database use seagrass, mangroves, coral reefs and macroalgae, habitats that have well documented trends. There is also considerable circumstantial evidence that habitat change has contributed to overexploitation or enhanced production of data-poor fisheries, like inland and subsistence fisheries. Globally many habitats are in decline, so the role of habitat should be considered when assessing the global status of fisheries. New methods and global databases of habitat trends, and use of habitats by fishery species are required to properly attribute the causes of decline in fisheries, and are likely to raise the profile of habitat protection as an important complementary aim for fisheries management.
Ultrafast glutamate sensors resolve high-frequency release at Schaffer collateral synapses
Authors: Helassa Nordine , Dürst Céline D. , Coates Catherine , Kerruth Silke , Arif Urwa , Schulze Christian , Wiegert J. Simon , Geeves Michael , Oertner Thomas G. , Török Katalin 
Published: December 2017

ABSTRACTGlutamatergic synapses display a rich repertoire of plasticity mechanisms on many different time scales, involving dynamic changes in the efficacy of transmitter release as well as changes in the number and function of postsynaptic glutamate receptors. The genetically encoded glutamate sensor iGluSnFR enables visualization of glutamate release from presynaptic terminals at frequencies up to ∼10 Hz. However, to resolve glutamate dynamics during high frequency bursts, faster indicators are required. Here we report the development of fast (iGluf) and ultrafast (iGluu) variants with comparable brightness, but increased Kd for glutamate (137 μM and 600 μM, respectively). Compared to iGluSnFR, iGluu has a 6-fold faster dissociation rate in vitro and 5-fold faster kinetics in synapses. Fitting a three-state model to kinetic data, we identify the large conformational change after glutamate binding as the rate-limiting step. In rat hippocampal slice culture stimulated at 100 Hz, we find that iGluu is sufficiently fast to resolve individual glutamate release events, revealing that glutamate is rapidly cleared from the synaptic cleft. Depression of iGluu responses during 100 Hz trains correlates with depression of postsynaptic EPSPs, indicating that depression during high frequency stimulation is purely presynaptic in origin. At individual boutons, the recovery from depression could be predicted from the amount of glutamate released on the second pulse (paired pulse facilitation/depression), demonstrating differential frequency-dependent filtering of spike trains at Schaffer collateral boutons.Significance StatementExcitatory synapses convert presynaptic action potentials into chemical signals that are sensed by postsynaptic glutamate receptors. To eavesdrop on synaptic transmission, genetically encoded fluorescent sensors for glutamate have been developed. However, even the best available sensors lag behind the very fast glutamate dynamics in the synaptic cleft. Here we report the development of an ultrafast genetically encoded glutamate sensor, iGluu, which allowed us to image glutamate clearance and synaptic depression during 100 Hz spike trains. We found that only boutons showing paired-pulse facilitation were able to rapidly recover from depression. Thus, presynaptic boutons act as frequency-specific filters to transmit select features of the spike train to specific postsynaptic cells.
Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago
Authors: Cabrera Vicente M. , Marrero Patricia , Abu-Amero Khaled K. , Larruga Jose M. 
Published: December 2017

ABSTRACTBackgroundAfter three decades of mtDNA studies on human evolution the only incontrovertible main result is the African origin of all extant modern humans. In addition, a southern coastal route has been relentlessly imposed to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, that out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion. Consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basic L3 lineages around 70 kya.ResultsThe coalescence ages of all Eurasian (M,N) and African L3 lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. A Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. It seems better to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.ConclusionsThese results are congruent with a model proposing an out-of-Africa of early anatomically modern humans around 125 kya. A return to Africa of Eurasian fully modern humans around 70 kya, and a second Eurasian global expansion by 60 kya. Climatic conditions and the presence of Neanderthals played key roles in these human movements.
Pre-mature senescence in the oldest leaves of low nitrate-grown Atxdh1 mutant uncovers a role for purine catabolism in plant nitrogen metabolism
Authors: Soltabayeva Aigerim , Srivastava Sudhakar , Kurmanbayeva Assylay , Bekturova Aizat , Fluhr Robert , Sagi Moshe 
Published: December 2017

ABSTRACTThe nitrogen rich ureides allantoin and allantoate, are known to play a role in nitrogen delivery in Leguminosae, in addition to their role as reactive oxygen species scavengers. However, their role as a nitrogen source in non-legume plants has not been shown. Xanthine dehydrogenase1 (AtXDH1) activity is a catalytic bottleneck step in purine catabolism. Atxdh1 mutant exhibited early leaf senescence, lower soluble protein and organic-N levels as compared to wild-type (WT) older leaves when grown with 1 mM nitrate, whereas under 5mM, mutant plants were comparable to WT. Similar nitrate-dependent senescence phenotypes were evident in the older leaves of allantoinase (Ataln) and allantoate amidohydrolase (Ataah) mutants, impaired in further downstream steps of purine catabolism. Importantly, under low nitrate conditions, xanthine was accumulated in older leaves of Atxdh1, whereas allantoin in both older and younger leaves of Ataln but not in WT leaves, indicating remobilization of xanthine degraded products from older to younger leaves. Supporting this notion, ureide transporters UPS1, UPS2 and UPS5 were enhanced in older leaves of 1 mM nitrate-fed WT as compared to 5 mM. Enhanced AtXDH, AtAAH and purine catabolic transcripts, were detected in WT grown in low nitrate, indicating regulation at protein and transcript levels. Higher nitrate reductase activity in Atxdh1 than WT leaves, indicates their need for nitrate assimilation products. It is further demonstrated that the absence of remobilized purine-degraded N from older leaves is the cause for senescence symptoms, a result of higher chloroplastic protein degradation in older leaves of nitrate starved Atxdh1 plants.SummaryThe absence of remobilized purine-degraded N from older to the young growing leaves is the cause for senescence symptoms, a result of higher chloroplastic protein degradation in older leaves of nitrate starved Atxdh1 plants.
Cryptic, extensive and non-random chromosome reorganization revealed by a butterfly chromonome
Authors: Hill Jason , Rastas Pasi , Hornett Emil A. , Neethiraj Ramprasad , Clark Nathan , Morehouse Nathan , Paz Celorio-Mancera Maria de la , Cols Jofre Carnicer , Dircksen Heinrich , Meslin Camille , Keehnen Naomi , Pruisscher Peter , Sikkink Kristin , Vives Maria , Vogel Heiko , Wiklund Christer , Woronik Alyssa , Boggs Carol L. , Nylin Sören , Wheat Christopher 
Published: December 2017

AbstractChromosome evolution, an important component of mico- and macroevolutionary dynamics 1–5, presents an enigma in the mega-diverse Lepidoptera6. While most species exhibit constrained chromosome evolution, with nearly identical haploid chromosome counts and chromosome-level shared gene content and collinearity among species despite more than 140 Million years of divergence7, a small fraction of species independently exhibit dramatic changes in chromosomal count due to extensive fission and fusion events that are facilitated by their holocentric chromosomes7–9. Here we address this enigma of simultaneous conservation and dynamism in chromosome evolution in our analysis of the chromonome (chromosome level assembly10) of the green-veined white butterfly, Pieris napi (Pieridae, Linnaeus, 1758). We report an unprecedented reorganization of the standard Lepidopteran chromosome structure via more than 90 fission and fusion events that are cryptic at other scales, as the haploid chromosome number is identical to related genera and gene collinearity within the large rearranged segments matches other Lepidoptera. Furthermore, these rearranged segments are significantly enriched for clusters of functionally related genes and the maintenance of ancient telomeric ends. These results suggest an unexpected role for selection in shaping chromosomal evolution when the structural constraints of monocentricq chromosomes are relaxed.