bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of corticospinal motor control during overground and treadmill walking in humans
Authors: Roeder Luisa , Boonstra Tjeerd W , Smith Simon S , Kerr Graham K 
Published: August 2017

AbstractIncreasing evidence suggests cortical involvement in the control of human gait. However, the nature of corticospinal interactions remains poorly understood. We performed time-frequency analysis of electrophysiological activity acquired during treadmill and overground walking in 22 healthy, young adults. Participants walked at their preferred speed (4.2, SD 0.4 km h−1), which was matched across both gait conditions. Event-related power, corticomuscular coherence (CMC) and inter-trial coherence (ITC) were assessed for EEG from bilateral sensorimotor cortices and EMG from the bilateral tibialis anterior (TA) muscles. Cortical power, CMC and ITC at theta, alpha, beta and gamma frequencies (4-45 Hz) increased during the double support phase of the gait cycle for both overground and treadmill walking. High beta (21-30 Hz) CMC and ITC of EMG was significantly increased during overground compared to treadmill walking, as well as EEG power in theta band (4-7 Hz). The phase spectra revealed positive time lags at alpha, beta and gamma frequencies, indicating that the EEG response preceded the EMG response. The parallel increases in power, CMC and ITC during double support suggest evoked responses at spinal and cortical populations rather than a modulation of ongoing corticospinal oscillatory interactions. The evoked responses are not consistent with the idea of synchronization of ongoing corticospinal oscillations, but instead suggest coordinated cortical and spinal inputs during the double support phase. Frequency-band dependent differences in power, CMC and ITC between overground and treadmill walking suggest differing neural control for the two gait modalities, emphasizing the task-dependent nature of neural processes during human walking.New & NoteworthyWe investigated cortical and spinal activity during overground and treadmill walking in healthy adults. Parallel increases in power, CMC and ITC during double support suggest evoked responses at spinal and cortical populations rather than a modulation of ongoing corticospinal oscillatory interactions. These findings identify neurophysiological mechanisms that are important for understanding cortical control of human gait in health and disease.
GIC: A computational method for predicting the essentiality of long noncoding lncRNAs
Authors: Zeng Pan , Chen Ji , Zhou Yuan , Yang Jichun , Cui Qinghua 
Published: August 2017

ABSTRACTMeasuring the essentiality of genes is critically important in biology and medicine. Some bioinformatic methods have been developed for this issue but none of them can be applied to long noncoding RNAs (lncRNAs), one big class of biological molecules. Here we developed a computational method, GIC (Gene Importance Calculator), which can predict the essentiality of both protein-coding genes and lncRNAs based on RNA sequence information. For identifying the essentiality of protein-coding genes, GIC is competitive with well-established computational scores. More important, GIC showed a high performance for predicting the essentiality of lncRNAs. In an independent mouse lncRNA dataset, GIC achieved an exciting performance (AUC=0.918). In contrast, the traditional computational methods are not applicable to lncRNAs. As a public web server, GIC is freely available at http://www.cuilab.cn/gic/.
SFMetaDB: A Comprehensive Annotation of Mouse RNA Splicing Factor RNA-Seq Datasets
Authors: Li Jin , Tseng Ching-San , Federico Antonio , Ivankovic Franjo , Huang Yi-Shuian , Ciccodicola Alfredo , Swanson Maurice S. , Yu Peng 
Published: August 2017

AbstractAlthough the number of RNA-Seq datasets deposited publicly has increased over the past few years, incomplete annotation of the associated metadata limits their potential use. Because of the importance of RNA splicing in diseases and biological processes, we constructed a database called SFMetaDB by curating datasets related with RNA splicing factors. Our effort focused on the RNA-Seq datasets in which splicing factors were knocked-down, knocked-out or over-expressed, leading to 75 datasets corresponding to 56 splicing factors. These datasets can be used in differential alternative splicing analysis for the identification of the potential targets of these splicing factors and other functional studies. Surprisingly, only ∼15% of all the splicing factors have been studied by loss- or gain-of-function experiments using RNA-Seq. In particular, splicing factors with domains from a few dominant Pfam domain families have not been studied. This suggests a significant gap that needs to be addressed to fully elucidate the splicing regulatory landscape. Indeed, there are already mouse models available for ∼20 of the unstudied splicing factors, and it can be a fruitful research direction to study these splicing factors in vitro and in vivo using RNA-Seq.Database URLhttp://sfmetadb.ece.tamu.edu/
The small non-coding vault RNA1-1 acts as a riboregulator of autophagy
Authors: Horos Rastislav , Alleaume Anne-Marie , Kleinendorst Roos , Tarafder Abul K. , Schwarzl Thomas , Zielonka Elisabeth M. , Adak Asli , Castello Alfredo , Huber Wolfgang , Sachse Carsten , Hentze Matthias W. 
Published: August 2017

AbstractVault RNAs (vtRNA) are small, 88-100nt non-coding RNAs found in many eukaryotes. Although they have been linked to drug resistance, apoptosis and nuclear transport, their function remains unclear. Here we show that a human vtRNA, RNA1-1, specifically binds to the autophagy receptor sequestosome-1/p62. Antisense-mediated depletion of vault RNA1-1 augments, whereas increased vault RNA1-1 expression restricts, autophagic flux in a p62-dependent manner. Bulk autophagy induced by starvation reduces the levels of vault RNA1-1 and the fraction of RNA-bound p62. These findings show that RNAs can act as riboregulators of biological processes by interacting with proteins, and assign a function to a vault RNA.
microRNA tissue atlas of the malaria mosquitoAnopheles gambiae
Authors: Lampe Lena , Levashina Elena A. 
Published: August 2017

ABSTRACTAnopheles gambiaemosquitoes transmit the human malaria parasitePlasmodium falciparum, which causes the majority of fatal malaria cases worldwide. The hematophagous life style defines the mosquito reproductive biology and is exploited byP. falciparumfor its own sexual reproduction and transmission. The two main phases of the mosquito reproductive cycle, pre-vitellogenic (PV) and post-blood meal (PBM) shape its capacity to transmit malaria. Transition between these phases is tightly coordinated to ensure homeostasis between mosquito tissues and successful reproduction. One layer of control is provided by microRNAs, well known regulators of blood meal digestion and egg development inAedesmosquitoes. Here, we report a global overview of tissue-specific miRNA expression during the PV and PBM phases and identify miRNAs regulated during PV to PBM transition. The observed coordinated changes in the expression levels of a set of miRNAs in the energy-storing tissues suggest a role in the regulation of blood meal-induced metabolic changes.
The RS Domain of Human CFIm68 Plays a Key Role in Selection Between Alternative Sites of Pre-mRNA Cleavage and Polyadenylation
Authors: Hardy Jessica G. , Tellier Michael , Murphy Shona , Norbury Chris J. 
Published: August 2017

AbstractMany eukaryotic protein-coding genes give rise to alternative mRNA isoforms with identical protein-coding capacities but which differ in the extents of their 3´ untranslated regions (3´UTRs), due to the usage of alternative sites of pre-mRNA cleavage and polyadenylation. By governing the presence of regulatory 3´UTR sequences, this type of alternative polyadenylation (APA) can significantly influence the stability, localisation and translation efficiency of mRNA. Though a variety of molecular mechanisms for APA have been proposed, previous studies have identified a pivotal role for the multi-subunit cleavage factor I (CFIm) in this process in mammals. Here we show that, in line with previous reports, depletion of the CFIm 68 kDa subunit (CFIm68) by CRISPR/Cas9-mediated gene disruption in HEK293 cells leads to a shift towards the use of promoter-proximal poly(A) sites. Using these cells as the basis for a complementation assay, we show that CFIm68 lacking its arginine/serine-rich (RS) domain retains the ability to form a nuclear complex with other CFIm subunits, but selectively lacks the capacity to restore polyadenylation at promoter-distal sites. In addition, nanoparticle-mediated analysis indicates that the RS domain is extensively phosphorylated in vivo. Overall, these results suggest that the CFIm68 RS domain makes a key regulatory contribution to APA.
Expression of lamina proteins Lamin Dm0 and Kugelkern suppresses stem cell proliferation
Authors: Petrovsky Roman , Großhans Jörg 
Published: August 2017

AbstractThe nuclear lamina is involved in numerous cellular functions, such as gene expression, nuclear organization, nuclear stability, and cell proliferation. The mechanism underlying the involvement of lamina is often not clear, especially in physiological contexts. Here we investigate how the farnesylated lamina proteins Lamin Dm0 and Kugelkern are linked to proliferation control of intestinal stem cells (ISCs) in adultDrosophilaflies by loss-of-function and gain-of-function experiments. We found that ISCs mutant for Lamin Dm0 or Kugelkern proliferate, whereas overexpression of Lamin Dm0 or Kugelkern strongly suppressed proliferation. The anti-proliferative activity is, at least in part, due to suppression of Jak/Stat but not Delta/Notch signalling. Lamin Dm0 expression suppresses Jak/Stat signalling by normalization of about 50% of the Stat target genes in ISCs.Author summaryThe nuclear lamina is a protein meshwork that lies beneath the inner side of the nuclear membrane and interacts with nuclear pores, chromatin and the cytoskeleton. Changes in proteins of the nuclear lamina cause a wide range of diseases which are often not well understood. It is hypothesized that impairment of stem cell function, as a result of lamina changes, might play a key role in some of those diseases. Here we use the well characterizedDrosophilamidgut as a system to investigate the role of lamina proteins Lamin Dm0 and Kugelkern on stem cell proliferation.
Bioinformatics analysis for L polymerase homology of arenaviruses
Authors: Alrashedi Hasan , Jones Ian , Mulley Geraldine , Neuman Benjamin W 
Published: August 2017

AbstractMany pathogenic viruses can transmit between humans and animals as zoonotic infectious often to cause dangerous disease with obvious clinical signs, sometimes globally. However, these outbreaks are generally only dealt with seriously when the viruses concerned have been confirmed and classified as zoonotic. Arenavirus haemorrhagic fever viruses can cause epidemics in some areas of the world. To assess the potential of similar viruses to become zoonotic in the future, bioinformatics of relatively conserved virus proteins, such as the L polymerase of arenaviruses, can be used to identify homology with viruses that might give future outbreaks. In this paper, new and archival metazoan transcriptome sequence data was used as a resource to identify similar sequences to known arenavirus sequences for the purpose of risk prediction. In essence, bioinformatics was utilized to provide a better understanding of the potential evolution and natural history of uncharacterized virus sequences in the GenBank database. Several matches were identified which, along with a reasoned approach to their phyla, was used to provide a likelihood score of their zoonotic potential.
A gut pathobiont synergizes with the microbiota to instigate inflammatory disease marked by immunoreactivity against other symbionts but not itself
Authors: Gomes-Neto João Carlos , Kittana Hatem , Mantz Sara , Segura Munoz Rafael R. , Schmaltz Robert J. , Bindels Laure B. , Clarke Jennifer , Hostetter Jesse M. , Benson Andrew K. , Walter Jens , Ramer-Tait Amanda E. 
Published: August 2017

AbstractInflammatory bowel diseases (IBD) are likely driven by aberrant immune responses directed against the resident microbiota. Although IBD is commonly associated with a dysbiotic microbiota enriched in putative pathobionts, the etiological agents of IBD remain unknown. Using a pathobiont-induced intestinal inflammation model and a defined bacterial community, we provide new insights into the immune-microbiota interactions during disease. In our model system, the pathobiontHelicobacter bilisinstigates disease following sub-pathological dextran sulfate sodium treatment. We show thatH. biliscauses mild inflammation in mono-associated mice, but severe disease in the presence of a microbiota, demonstrating synergy between the pathobiont and microbiota in exacerbating pathology. Remarkably, inflammation depends on the presence ofH. bilis, but is marked by a predominant Th17 response against specific members of the microbiota and not the pathobiont, even upon the removal of the most immune-dominant taxa. Neither increases in pathobiont burden nor unique changes in immune-targeted microbiota member abundances are observed during disease. Collectively, our findings demonstrate that a pathobiont instigates inflammation without being the primary target of a Th17 response or by altering the microbiota community structure. Moreover, our findings point toward monitoring pathobiont-induced changes in microbiota immune targeting as a new concept in IBD diagnotics.
LhrandHmrare required for sister chromatid detachment during anaphase but not for centromere function
Authors: Blum Jacob A. , Bonaccorsi Silvia , Marzullo Marta , Palumbo Valeria , Yamashita Yukiko M. , Barbash Daniel A. , Gatti Maurizio 
Published: August 2017

AbstractCrosses betweenDrosophila melanogasterfemales andDrosophila simulansmales produce hybrid sons that die at the larval stage. This hybrid lethality is suppressed by loss-of-function mutations in theD. melanogaster Hybrid male rescue(Hmr) or in theD. simulans Lethal hybrid rescue(Lhr)genes. Previous studies have shown that Hmr and Lhr interact with heterochromatin proteins and suppress expression of transposable elements withinD. melanogaster. It also has been proposed that Hmr and Lhr function at the centromere. We examined mitotic divisions in larval brains fromHmrandLhrsingle mutants andHmr; Lhrdouble mutants inD. melanogaster. In none of the mutants did we observe defects in metaphase chromosome alignment or hyperploid cells, which are hallmarks of centromere or kinetochore dysfunction. In addition, we found that Hmr-HA and Lhr-HA do not localize to centromeres either during interphase or mitotic division. However, all mutants displayed anaphase bridges and chromosome aberrations resulting from the breakage of these bridges, predominantly at the euchromatin-heterochromatin junction. The few dividing cells present in hybrid males showed irregularly condensed chromosomes with fuzzy and often closely apposed sister chromatids. Despite this defect in condensation, chromosomes in hybrids managed to align on the metaphase plate and undergo anaphase. We conclude that there is no evidence for a centromeric function of Hmr and Lhr withinD. melanogasternor for a centromere defect causing hybrid lethality. Instead we find thatHmrandLhrare required inD. melanogasterfor detachment of sister chromatids during anaphase.
Predictive coding over the lifespan: Increased reliance on perceptual priors in older adults – a magnetoencephalography and dynamic causal modelling study
Authors: Chan Jason S. , Wibral Michael , Wollstadt Patricia , Stawowsky Cerisa , Brandl Mareike , Helbling Saskia , Naumer Marcus , Kaiser Jochen 
Published: August 2017

AbstractAging is accompanied by unisensory decline; but to compensate for this, two complementary strategies are potentially relied upon increasingly: first, older adults integrate more information from different sensory organs. Second, according to predictive coding (PC) we form ‘templates’ (internal models or ‘priors’) of the environment through our experiences. It is through increased life experience that older adults may rely more on these templates compared to younger adults. Multisensory integration and predictive coding would be effective strategies for the perception of near-threshold stimuli, but they come at the cost of integrating irrelevant information. Their role can be studied in multisensory illusions because these require the integration of different sensory information, as well as an internal model of the world that can take precedence over sensory input. Here, we elicited a classic multisensory illusion, the sound-induced flash illusion, in younger (mean: 27 yrs) and older (mean: 67 yrs) adult participants while recording the magnetoencephalogram. Older adults perceived more illusions than younger adults. Older adults had increased pre-stimulus beta(β)-band activity compared to younger adults as predicted by microcircuit theories of predictive coding, which suggest priors and predictions are linked to β-band activity. In line with our hypothesis, transfer entropy analysis and dynamic causal models of pre-stimulus MEG data revealed a stronger illusion-related modulation of cross-modal connectivity from auditory to visual cortices in older compared to younger adults. We interpret this as the neural correlate of increased reliance on a cross-modal predictive template in older adults that is leading to the illusory percept.
npInv: accurate detection and genotyping of inversions mediated by non-allelic homologous recombination using long read sub-alignment
Authors: Shao Haojing , Ganesamoorthy Devika , Duarte Tania , Cao Minh Duc , Hoggart Clive , Coin Lachlan J.M. 
Published: August 2017

ABSTRACTDetection of genomic inversions remains challenging. Many existing methods primarily target inversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombination (NAHR) inversions largely unexplored. We present npInv, a novel tool specifically for detecting and genotyping NAHR inversion using long read sub-alignment of long read sequencing data. We use npInv to generate a whole-genome inversion map for NA12878 consisting of 30 NAHR inversions (of which 15 are novel), including all previously known NAHR mediated inversions in NA12878 with flanking IR less than 7kb. Our genotyping accuracy on this dataset was 94%. We used PCR to confirm presence of two of these novel NAHR inversions. We show that there is a near linear relationship between the length of flanking IR and the size of the NAHR inversion.
Evolutionary history of New World monkeys revealed by molecular and fossil data
Authors: Silvestro Daniele , Tejedor Marcelo F. , Serrano-Serrano Martha L. , Loiseau Oriane , Rossier Victor , Rolland Jonathan , Zizka Alexander , Antonelli Alexandre , Salamin Nicolas 
Published: August 2017

AbstractNew World monkeys (parvorder Platyrrhini) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, the ancestral morphology, and the evolution of the distribution of the clade. Here we integrate paleontological and molecular evidence to investigate the evolutionary dynamics of extinct and extant platyrrhines. We develop an analytical framework to infer ancestral states, the evolution of body mass, and changes in latitudinal ranges through time. Our results show that extant platyrrhines originated some 5–10 million years earlier than previously assumed, likely dating back to the Middle Eocene (∼ 43 million years ago, Ma). The estimated ancestral platyrrhine was strikingly small – weighing ∼ 0.4 kg, as compared to the largest modern species over 10 kg – matching the size of their presumed Eocene North African ancestors. Small-sized callitrichines (marmosets and tamarins) retained a small body mass throughout their evolutionary history, thus challenging the hypothesis of phyletic dwarfism as an explanation to their adaptive traits. In contrast, a rapid change in body mass range took place as the three families diverged between the Late Oligocene and the Early Miocene. That period also marks a peak in diversity of fossil platyrrhines and is associated with their widest latitudinal range, expanding as far to the South as Patagonia. This geographic expansion is temporally coincident with a significant increase in platyrrhine population size inferred from genomic data, and with warm and humid climatic conditions linked to the Miocene Climatic Optimum and the lower elevation of the Andes. These results unveil the early evolution of an iconic group of monkeys and showcase the advantages of integrating fossil and molecular data for estimating evolutionary rates and trends.
CHIC: a short read aligner for pan-genomic references
Authors: Valenzuela Daniel , Mäkinen Veli 
Published: August 2017

AbstractRecently the topic of computational pan-genomics has gained increasing attention, and particularly the problem of moving from a single-reference paradigm to a pan-genomic one. Perhaps the simplest way to represent a pan-genome is to represent it as a set of sequences. While indexing highly repetitive collections has been intensively studied in the computer science community, the research has focused on efficient indexing and exact pattern patching, making most solutions not yet suitable to be used in bioinformatic analysis pipelines.Results:We present CHIC, a short-read aligner that indexes very large and repetitive references using a hybrid technique that combines Lempel-Ziv compression with Burrows-Wheeler read aligners.Availability:Our tool is open source and available online athttps://gitlab.com/dvalenzu/CHIC
Regulatory divergence of flowering time genes in the allopolyploidBrassica napus
Authors: Marc Jones D. , Wells Rachel , Pullen Nick , Trick Martin , Irwin Judith A. , Morris Richard J. 
Published: August 2017

AbstractPolyploidy is a recurrent feature of eukaryotic evolution and has been linked to increases in complexity, adaptive radiation and speciation. Within angiosperms, such events occur repeatedly in many plant lineages. We investigated the role of duplicated genes in the regulation of flowering inBrassica napus. This relatively young allotetraploid represents a snapshot of evolution and artificial selection in progress. In line with the gene balance hypothesis, we find preferential retention of expressed flowering time genes relative to the whole genome. Furthermore, gene expression dynamics across development reveal diverged regulation of many flowering time gene copies. This finding supports the concept of responsive backup circuits being key for the retention of duplicated genes. A case study ofBnaTFL1reveals differences in cis-regulatory elements downstream of these genes that could explain this divergence. Such differences in the regulatory dynamics of duplicated genes highlight the challenges for translating gene networks from model to more complex polyploid crop species.