bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pervasive hybridizations in the history of wheat relatives
Authors: Glémin Sylvain , Scornavacca Celine , Dainat Jacques , Burgarella Concetta , Viader Véronique , Ardisson Morgane , Sarah Gautier , Santoni Sylvain , David Jacques , Ranwez Vincent 
Published: April 2018

AbstractBread wheat and durum wheat derive from an intricate evolutionary history of three genomes, namely A, B and D, present in both extent diploid and polyploid species. Despite its importance for wheat research, no consensus on the phylogeny of the wheat clade has emerged so far, possibly because of hybridizations and gene flows that make phylogeny reconstruction challenging. Recently, it has been proposed that the D genome originated from an ancient hybridization event between the A and B genomes1. However, the study only relied on four diploid wheat relatives when 13 species are accessible. Using transcriptome data from all diploid species and a new methodological approach, we provide the first comprehensive phylogenomic analysis of this group. Our analysis reveals that most species belong to the D-genome lineage and descend from the previously detected hybridization event, but with a more complex scenario and with a different parent than previously thought. If we confirmed that one parent was the A genome, we found that the second was not the B genome but the ancestor ofAegilops mutica(T genome), an overlooked wild species. We also unravel evidence of other massive gene flow events that could explain long-standing controversies in the classification of wheat relatives. We anticipate that these results will strongly affect future wheat research by providing a robust evolutionary framework and refocusing interest on understudied species. The new method we proposed should also be pivotal for further methodological developments to reconstruct species relationship with multiple hybridizations.
The influence of the supramolecular complex PRE -1 on permeability of membranes of mitochondria
Authors: Mardieva Kamila , Burkhanova Munira 
Published: April 2018

AbstractThe change in the state of the mitochondrial pore of nonspecific conductivity plays a key role in the processes of triggering and regulating apoptosis. Therefore, the study of mechanisms of opening and regulating the state of these pores can have a great importance to find the ways of correcting many mitochondrial dysfunctions, including those which are associated with age-related changes. In our work, we have done a comparative analysis for swelling of brain mitochondria of adult (9 months) and mature rats (12-15 months).
Robust representation of natural images by sparse and variable population of active neurons in visual cortex
Authors: Yoshida Takashi , Ohki Kenichi 
Published: April 2018

AbstractNatural scenes sparsely activate neurons in the primary visual cortex (V1). However, how sparsely active neurons robustly represent natural images and how the information is optimally decoded from the representation have not been revealed. We reconstructed natural images from V1 activity in anaesthetized and awake mice. A single natural image was linearly decodable from a surprisingly small number of highly responsive neurons, and an additional use of remaining neurons even degraded the decoding. This representation was achieved by diverse receptive fields (RFs) of the small number of highly responsive neurons. Furthermore, these neurons reliably represented the image across trials, regardless of trial-to-trial response variability. The reliable representation was supported by multiple neurons with overlapping RFs. Based on our results, the diverse, partially overlapping RFs ensure sparse and reliable representation. We propose a new representation scheme in which information is reliably represented while the representing neuronal patterns change across trials and that collecting only the activity of highly responsive neurons is an optimal decoding strategy for the downstream neurons
Contribution of the endosomal-lysosomal and proteasomal systems in Amyloid-β Precursor Protein derived fragments processing
Authors: Evrard Caroline , Kienlen-Campard Pascal , Opsomer Rémi , Tasiaux Bernadette , Octave Jean-Noël , Buée Luc , Sergeant Nicolas , Vingtdeux Valérie 
Published: April 2018

AbstractAβ peptides, the major components of amyloid deposits of Alzheimer’s disease, are released following sequential cleavages by secretases of its precursor named the amyloid precursor protein (APP). In addition to secretases, degradation pathways, in particular the endosomal/lysosomal and proteasomal systems have also been reported to contribute to APP processing. However, the respective role of each of these pathways towards APP metabolism remains to be established. To address this, we used HEK 293 cells and primary neurons expressing full-length APPWTor the β-secretase-derived C99 fragments (β-CTFs) in which degradation pathways were selectively blocked using pharmacological drugs. APP metabolites, including carboxy-terminal fragments (CTFs), soluble APP (sAPP) and Aβ peptides were studied. In this report, we show that APP-CTFs produced from endogenous or overexpressed full-length APP are mainly processed by γ-secretase and the endosomal/lysosomal pathway, while in sharp contrast, overexpressed C99 alone is mainly degraded by the proteasome and to a lesser extent by γ-secretase.
B cell receptor crosslinking can augment T cell help-mediated germinal center B cell selection
Authors: Turner Jackson S. , Ke Fang , Grigorova Irina L. 
Published: April 2018

AbstractSelection of germinal center (GC) B cells with B cell receptors (BCR) possessing high affinity to foreign antigen (Ag) and their differentiation into antibody-secreting long-lived plasma cells is critical for potent long-term humoral immunity. Ag-dependent engagement of GC B cell BCR triggers Ag internalization and loading of antigenic peptides on MHCII molecules for presentation to follicular helper T cells (Tfh) and acquisition of T cell help. However, whether it also provides signals that are critical or synergistic with T cell help for GC B cell selection and differentiationin vivois not known. Here we show that T cell help is sufficient to induce GC B cell expansion and plasmablast (PB) formation in the absence of recurrent BCR engagement with Ag. Ag-mediated BCR crosslinking on the other hand is not sufficient to promote GC B cell selection, but can synergize with T cell help to enhance the GC B cell and PB responses when T cell help is limiting.
Complementary information on single nucleotide variants, INDELs and functional translocations can be obtained with RNAseq using different library preparations
Authors: Panero Riccardo , Arigoni Maddalena , Olivero Martina , Cordero Francesca , Weisz Alessandro , Beccuti Marco , Renzo Mariaflavia Di , Calogero Raffaele A. 
Published: April 2018

AbstractBackgroundRNA-seq represents an attractive methodology for the detection of functional genomic variants because it allows the integration of variant frequency and their expression. However, although specific statistic frameworks have been designed to detect SNVs/INDELS/gene fusions in RNA-seq data, very little has been done to understand the effect of library preparation protocols on transcript variant detection in RNA-seq data.ResultsHere, we compared RNA-seq results obtained on short reads sequencing platform with two protocols: one based on polyA+ RNA selection protocol (POLYA) and the other based on exonic regions capturing protocol (ACCESS). Our data indicate that ACCESS detects 10% more coding SNV/INDELs with respect to POLYA, making this protocol more suitable for this goal. Furthermore, ACCESS requires less reads for coding SNV detection with respect to POLYA. On the other hand, if the analysis aims at identifying SNV/INDELs also in the 5’and 3’ UTRs, POLYA is definitively the preferred method. No particular advantage comes from the usage of ACCESS or POLYA in the detection of fusion transcripts.ConclusionData show that a careful selection of the “wet” protocol adds specific features that cannot be obtained with bioinformatics alone.
The Use of Visual Cues in Gravity Judgements on Parabolic Motion
Authors: Jörges Björn , Slupinski Lena , López-Moliner Joan 
Published: April 2018

AbstractEvidence suggests that humans rely on an earth gravity prior for sensory-motor tasks like catching or reaching. Even under earth-discrepant conditions, this prior biases perception and action towards assuming a gravitational downwards acceleration of 9.81 m/s2. This can be particularly detrimental in interactions with virtual environments employing earth-discrepant gravity conditions for their visual presentation. The present study thus investigates how well humans discriminate visually presented gravities and which cues they use to extract gravity from the visual scene. To this end, we employed a Two-Interval Forced-Choice Design. In Experiment 1, participants had to judge which of two presented parabolas had the higher underlying gravity. We used two initial vertical velocities, two horizontal velocities and a constant target size. Experiment 2 added a manipulation of the reliability of the target size. Experiment 1 shows that participants have generally high discrimination thresholds for visually presented gravities, with weber fractions of 13 to beyond 30 %. We identified the rate of change of the elevation angle (ẏ) and the visual angle (θ) as major cues. Experiment 2 suggests furthermore that size variability has a small influence on discrimination thresholds, while at the same time larger size variability increases reliance on ẏ and decreases reliance on θ. All in all, even though we use all available information, humans display low precision when extracting the governing gravity from a visual scene, which might further impact our capabilities of adapting to earth-discrepant gravity conditions with visual information alone.
E proteins differentially co-operate with proneural bHLH transcription factors to sharpen neurogenesis
Authors: Dréau Gwenvael Le , Escalona René , Fueyo Raquel , Herrera Antonio , Martínez Juan D. , Usieto Susana , Menendez Anghara , Pons Sebastián , Martínez-Balbás Marian A. , Martí Elisa 
Published: April 2018

AbstractBasic HLH proteins heterodimerize with class I HLH/E proteins to promote transcription. Here we show that E proteins differentially co-operate with proneural bHLH transcription factors sharpening their neurogeneic activity. We find that inhibiting BMP signaling or its target ID2, in the chick embryo spinal cord, impairs the neuronal production from progenitors expressing ATOH1/ASCL1, but less severely that from progenitors expressing NEUROG1/2/PTF1a. We define the mechanisms of this differential response as a dual co-operation of E proteins with proneural proteins. E proteins synergize with bHLH proteins when acting on CAGSTG motifs, thereby facilitating the neurogenic activity of ASCL1/ATOH1 which preferentially bind to such motifs. Conversely, E proteins restrict the strong neurogenic potential of NEUROG1/2 by directly inhibiting their preferential binding to CADATG motifs. Since we find this mechanism to be conserved in corticogenesis, we propose this dual co-operation of E proteins with bHLH proteins as a novel though general feature of their mechanism of action.
Epigenetic regulation of the circadian genePer1in the hippocampus mediates age-related changes in memory and synaptic plasticity
Authors: Kwapis Janine L. , Alaghband Yasaman , Kramár Enikö A. , López Alberto J. , Ciernia Annie Vogel , White André O. , Shu Guanhua , Rhee Diane , Michael Christina M. , Montellier Emilie , Liu Yu , Magnan Christophe N. , Sassone-Corsi Paolo , Baldi Pierre , Matheos Dina P. , Wood Marcelo A. 
Published: April 2018

AbstractAging is accompanied by impairments in both circadian rhythmicity and long-term memory. Although it is clear that memory performance is affected by circadian cycling, it is unknown whether age-related disruption of the circadian clock causes impaired hippocampal memory. Here, we show that the repressive histone deacetylase HDAC3 restricts long-term memory, synaptic plasticity, and learning-induced expression of the circadian genePer1in the aging hippocampus without affecting rhythmic circadian activity patterns. We also demonstrate that hippocampalPer1is critical for long-term memory formation. Together, our data challenge the traditional idea that alterations in the core circadian clock drive circadian-related changes in memory formation and instead argue for a more autonomous role for circadian clock gene function in hippocampal cells to gate the likelihood of long-term memory formation.
npphen: an R-package for non-parametric reconstruction of vegetation phenology and anomaly detection using remote sensing
Authors: Estay Sergio A. , Chávez Roberto O. 
Published: April 2018

AbstractFor ecologists, the challenge at using remote sensing tools is to convert spectral data into ecologically relevant information like abundance, productivity or traits distribution. Among these features, plant phenology is one of the most used variables in any study applying remote sensing to plant ecology and it has formally considered as one of the Essential Biodiversity Variables. Currently, satellite imagery make possible cost-efficient monitoring of land surface phenology (LSP), but methods applicable to different ecosystems are not available. Here, we introduce the ‘npphen’ R-package developed for remote sensing LSP reconstruction and anomaly detection using non-parametric techniques. The package implements basic and high-level functions for manipulating vector and raster data to obtain high resolution spatial and temporal LSP reconstructions. Advantages of ‘npphen’ are: its flexibility to describe any LSP pattern (suitable for any ecosystem), it handles time series or raster stacks with and without gaps, and it provides confidence interval for the expected LSP at yearly basis, useful to judge anomaly magnitudes. We present two study cases to show how ‘npphen’ can successfully reconstruct and map LSP and anomalies for contrasting ecosystems.
Searching Algorithm for Type IV Effector proteins (S4TE) 2.0: improved tools for type IV effector prediction, analysis and comparison
Authors: Noroy Christophe , Lefrançois Thierry , Meyer Damien F. 
Published: April 2018

ABSTRACTBacterial pathogens have evolved numerous strategies to corrupt, hijack or mimic cellular processes in order to survive and proliferate. Among those strategies, Type IV effectors (T4Es) are proteins secreted by pathogenic bacteria to manipulate host cell processes during infection. They are delivered into eukaryotic cells in an ATP-dependent manner via the type IV secretion system, a specialized multiprotein complex. T4Es contain a wide spectrum of features including eukaryotic-like domains, localization signals or a C-terminal translocation signal. A combination of these features enables prediction of T4Es in a given bacterial genome. In this study, we developed a web-based comprehensive suite of tools with a user-friendly graphical interface. This version 2.0 of S4TE (Searching Algorithm for Type IV Effector Proteins; http://sate.cirad.fr) enables accurate prediction and comparison of T4Es. Search parameters and threshold can be customized by the user to work with any genome sequence, whether publicly available or not. Applications range from characterizing effector features and identifying potential T4Es to analyzing the effectors based on the genome G+C composition and local gene density. S4TE 2.0 allows the comparison of putative T4E repertoires of up to four bacterial strains at the same time. The software identifies T4E orthologs among strains and provides a Venn diagram and lists of genes for each intersection. New interactive features offer the best visualization of the location of candidate T4Es and hyperlinks to NCBI and Pfam databases. S4TE 2.0 is designed to evolve rapidly with the publication of new experimentally validated T4Es, which will reinforce the predictive power of the algorithm. The computational methodology can be used to identify a wide spectrum of candidate bacterial effectors that lack sequence conservation but have similar amino acid characteristics. This approach will provide very valuable information about bacterial host-specificity and virulence factors, and help identify host targets for the development of new anti-bacterial molecules.
Schizophrenia-related cognitive dysfunction in the Cyclin-D2 knockout mouse model of ventral hippocampal hyperactivity
Authors: Grimm Christina M. , Aksamaz Sonat , Schulz Stefanie , Teutsch Jasper , Sicinski Piotr , Liss Birgit , Kätzel Dennis 
Published: April 2018

ABSTRACTElevated activity at the output stage of the anterior hippocampus has been described as a physiological endophenotype of schizophrenia, and its development maps onto the transition from its prodromal to its psychotic state. Interventions that halt the spreading glutamatergic over-activity in this region and thereby the development of overt schizophrenia could be promising therapies. However, animal models with high construct validity to support such pre-clinical development are scarce. The Cyclin-D2 knockout (CD2-KO) mouse model shows a hippocampal Parvalbumin-interneuron dysfunction and its pattern of hippocampal over-activity shares similarities with that seen in prodromal patients. In a comprehensive phenotyping of CD2-KO mice, we found that they displayed novelty-induced hyperlocomotion (a correlate in the positive symptom domain), that was largely resistant against D1- and D2-dopamine receptor antagonism, but responsive to the mGluR2/3-agonist LY379268. In the negative symptom domain, CD2-KO mice showed transiently reduced sucrose-preference (anhedonia), but enhanced interaction with novel mice and objects, as well as normal nest building and incentive motivation. Also, unconditioned anxiety, perseveration, and motor impulsivity were unaltered. However, in the cognitive domain, CD2-knockouts showed reduced executive function in assays of rule-shift and rule-reversal learning, but also an impairment in working memory, that was resistant against LY379268. In contrast, sustained attention and forms of spatial and object-related memory that are mediated by short-term habituation of stimulus-specific attention were intact. Our results suggest, that CD2-KO mice are a valuable model in translational research targeted at the pharmacoresistant cognitive symptom domain in causal relation to hippocampal over-activity in the prodrome-to-psychosis transition.
Intrinsic cooperativity potentiates parallel cis-regulatory evolution
Authors: Sorrells Trevor R , Johnson Amanda N , Howard Conor J , Britton Candace S , Fowler Kyle R , Feigerle Jordan T , Weil P Anthony , Johnson Alexander D 
Published: April 2018

AbstractConvergent evolutionary events in independent lineages provide an opportunity to understand why evolution favors certain outcomes over others. We studied such a case, where a large set of genes—those coding for the ribosomal proteins—gained cis-regulatory sequences for a particular transcription regulator (Mcm1) in independent fungal lineages. We present evidence that these gains occurred because Mcm1 shares a mechanism of transcriptional activation with an ancestral regulator of the ribosomal protein genes, Rap1. Specifically, we show that Mcm1 and Rap1 have the inherent ability to cooperatively activate transcription through contacts with the general transcription factor TFIID. Because the two regulatory proteins share a common interaction partner, the presence of one ancestral cis-regulatory sequence can “channel” random mutations into functional sites for the second regulator. At a genomic scale, this type of intrinsic cooperativity can account for a pattern of parallel evolution involving the fixation of hundreds of substitutions.
Learning and Imputation for Mass-spec Bias Reduction (LIMBR)
Authors: Crowell Alexander M , Greene Casey S , Loros Jennifer J. , Dunlap Jay C 
Published: April 2018

AbstractMotivationDecreasing costs are making it feasible to perform time series proteomics and genomics experiments with more replicates and higher resolution than ever before. With more replicates and time points, proteome and genome-wide patterns of expression are more readily discernible. These larger experiments require more batches exacerbating batch effects and increasing the number of bias trends. In the case of proteomics, where methods frequently result in missing data this increasing scale is also decreasing the number of peptides observed in all samples. The sources of batch effects and missing data are incompletely understood necessitating novel techniques.ResultsHere we show that by exploiting the structure of time series experiments, it is possible to accurately and reproducibly model and remove batch effects. We implement Learning and Imputation for Mass-spec Bias Reduction (LIMBR) software, which builds on previous block based models of batch effects and includes features specific to time series and circadian studies. To aid in the analysis of time series proteomics experiments, which are often plagued with missing data points, we also integrate an imputation system. By building LIMBR for imputation and time series tailored bias modeling into one straightforward software package, we expect that the quality and ease of large-scale proteomics and genomics time series experiments will be significantly increased.Contactalexander.m.crowell@gmail.com, jay.c.dunlap@dartmouth.edu
Effects of duplicated mapped read PCR artifacts on RNA-seq differential expression analysis based on qRNA-seq
Authors: Salzberg Anna C. , Hu Jiafen , Conroy Elizabeth J. , Cladel Nancy M. , Brucklacher Robert M. , Bixler Georgina V. , Kawasawa Yuka Imamura 
Published: April 2018

AbstractBest practices to handling duplicated mapped reads in RNA-seq analyses has long been discussed but a gold standard method has yet to be established, as such duplicates could originate from valid biological transcripts or they could be PCR-related artifacts. Here we used the NEXTflex™qRNA-SeqTM(aka Molecular Indexing™) technology to identify PCR duplicates via the random attachment of unique molecular labels to each cDNA molecule prior to PCR amplification. We found that up to 64.3% of the single end and 19.3% of the mouse paired end duplicates originated from valid biological transcripts rather than PCR artifacts. For single end reads, either removing or retaining all duplicates resulted in a substantial number of false positives (up to 47.0%) and false negatives (up to 12.1%) in the sets of significantly differentially expressed genes. For paired end reads, only the alignment retaining all duplicates resulted in a substantial number of false positives. This is the first effort to evaluate the performance of qRNA-seq using ‘real-world’ biomedical samples, and we found that PCR duplicate identification provided minor benefits for paired end reads but greatly improved the sensitivity and specificity in the determination of the significantly differentially expressed genes for single end reads.