bluuebunny/crossref_metadata_2025_split huggingface dataset:
A predicted deleterious allele of the essential meiosis geneMND1, present in ~3% of East Asians, does not disrupt reproduction in mice
Authors: Tran Tina N. , Martinez Julianna , Schimenti John C. 
Published: June 2019

AbstractInfertility is a major health problem affecting ~15% of couples worldwide. Except for cases involving readily-detectable chromosome aberrations, confident identification of a causative genetic defect is problematic. Despite the advent of genome sequencing for diagnostic purposes, the preponderance of segregating genetic variants complicates identification of culprit genetic alleles or mutations. Many algorithms have been developed to predict the effects of “variants of unknown significance” (VUS), typically SNPs (single nucleotide polymorphisms), but these predictions are not sufficiently accurate for clinical action. As part of a project to identify population variants that impact fertility, we have been generating CRISPR-Cas9 edited mouse models of suspect SNPs in genes that are known to be required for fertility in mice. Here, we present data on a non-synonymous (amino acid altering) SNP (rs140107488) in the meiosis geneMnd1, which is predicted bioinformatically to be deleterious to protein function. We report that when modeled in mice, this allele (MND1K85M), which is present allele frequency of ~3% in East Asians, has no discernable effect upon fertility, fecundity, or gametogenesis, although it may cause sex skewing of progeny from homozygous males. In sum, this appears to be a benign allele that can be eliminated or de-prioritized in clinical genomic analyses of infertility patients.
High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing
Authors: Ganesamoorthy Devika , Yan Mengjia , Murigneux Valentine , Zhou Chenxi , Cao Minh Duc , Duarte Tania PS , Coin Lachlan JM 
Published: June 2019

ABSTRACTTandem repeats (TRs) are highly prone to variation in copy numbers due to their repetitive and unstable nature, which makes them a major source of genomic variation between individuals. However, population variation of TRs have not been widely explored due to the limitations of existing tools, which are either low-throughput or restricted to a small subset of TRs. Here, we used SureSelect targeted sequencing approach combined with Nanopore sequencing to overcome these limitations. We achieved an average of 3062-fold target enrichment on a panel of 142 TR loci, generating an average of 97X sequence coverage on 7 samples utilizing 2 MinION flow-cells with 200ng of input DNA per sample. We identified a subset of 110 TR loci with length less than 2kb, and GC content greater than 25% for which we achieved an average genotyping rate of 75% and increasing to 91% for the highest-coverage sample. Alleles estimated from targeted long-read sequencing were concordant with gold standard PCR sizing analysis and moreover highly correlated with alleles estimated from whole genome long-read sequencing. We demonstrate a targeted long-read sequencing approach that enables simultaneous analysis of hundreds of TRs and accuracy is comparable to PCR sizing analysis. Our approach is feasible to scale for more targets and more samples facilitating large-scale analysis of TRs.
Subject, session and task effects on power, connectivity and network centrality: a source-based EEG study
Authors: Pani Sara M. , Ciuffi Marta , Demuru Matteo , Bazzano Giovanni , D’aloja Ernesto , Fraschini Matteo 
Published: June 2019

ABSTRACTInter-subjects’ variability in functional brain networks has been extensively investigated in the last few years. In this context, unveiling subject-specific characteristics of EEG features may play an important role for both clinical (e.g., biomarkers) and bio-engineering purposes (e.g., biometric systems and brain computer interfaces). Nevertheless, the effects induced by multi-sessions and task-switching are not completely understood and considered. In this work, we aimed to investigate how the variability due to subject, session and task affects EEG power, connectivity and network features estimated using source-reconstructed EEG time-series. Our results point out a remarkable ability to identify subject-specific EEG traits within a given task together with striking independence from the session. The results also show a relevant effect of task-switching, which is comparable to individual variability. This study suggests that power and connectivity EEG features may be adequate to detect stable (over-time) individual properties within predefined and controlled tasks.
LAVENDER: latent axes discovery from multiple cytometry samples with non-parametric divergence estimation and multidimensional scaling reconstruction
Authors: Nakamura Naotoshi , Okada Daigo , Setoh Kazuya , Kawaguchi Takahisa , Higasa Koichiro , Tabara Yasuharu , Matsuda Fumihiko , Yamada Ryo 
Published: June 2019

AbstractComputational cytometry methods are now frequently used in flow and mass cytometric data analyses. However, systematic bias-free methodologies to assess inter-sample variability have been lacking, thereby hampering efficient data mining from a large set of samples. Here, we devised a computational method termed LAVENDER (latent axes discovery from multiple cytometry samples with nonparametric divergence estimation and multidimensional scaling reconstruction). It measures the Jensen-Shannon distances between samples using the k-nearest neighbor density estimation and reconstructs samples in a new coordinate space, called the LAVENDER space. The axes of this space can then be compared against other omics measurements to obtain biological information. Application of LAVENDER to multidimensional flow cytometry datasets of 301 Japanese individuals immunized with a seasonal influenza vaccine revealed an axis related to baseline immunological characteristics of each individual. This axis correlated with the proportion of plasma cells and the neutrophil-to-lymphocyte ratio, a clinical marker of the systemic inflammatory response. The same method was also applicable to mass cytometry data with more molecular markers. These results demonstrate that LAVENDER is a useful tool for identifying critical heterogeneity among similar, yet different, single-cell datasets.
Highly Accelerated Vessel-Selective Arterial Spin Labelling Angiography using Sparsity and Smoothness Constraints
Authors: Schauman Sophie , Chiew Mark , Okell Thomas W. 
Published: June 2019

AbstractPurposeTo demonstrate that vessel-selectivity in arterial spin labeling angiography can be achieved without any scan time penalty or noticeable loss of image quality compared to conventional arterial spin labeling angiography.MethodsSimulations on a numerical phantom were used to assess whether the increased sparsity of vessel-encoded angiograms compared to non-vessel-encoded angiograms alone can improve reconstruction results in a compressed sensing framework. Further simulations were performed to study whether the difference in relative sparsity between non-selective and vessel-selective dynamic angiograms were sufficient to achieve similar image quality at matched scan times in the presence of noise. Finally, data were acquired from 5 healthy volunteers to validate the technique in vivo. All data, both simulated and in vivo, were sampled in 2D using a golden angle radial trajectory and reconstructed by enforcing both image domain sparsity and temporal smoothness on the angiograms in a parallel imaging and compressed sensing framework.ResultsRelative sparsity was established as a primary factor governing the reconstruction fidelity. Using the proposed reconstruction scheme, differences between vessel-selective and non-selective angiography were negligible compared to the dominant factor of total scan time in both simulations and in vivo experiments at acceleration factors up to R = 34. The reconstruction quality was not heavily dependent on hand-tuning the parameters of the reconstruction.ConclusionThe increase in relative sparsity of vessel-selective angiograms compared to non-selective angiograms can be leveraged to achieve higher acceleration without loss of image quality, resulting in the acquisition of vessel-selective information at no scan time cost.
Body size but not age influences phototaxis in bumble bee (Bombus terrestris, L.) workers
Authors: Merling Michal , Eisenmann Shmuel , Bloch Guy 
Published: June 2019

AbstractWe studied phototaxis, the directional movement relative to light, in the bumble bee Bombus terrestris. We first developed and validated a MATLAB based system enabling reliable high-resolution tracking of a bee and a measurement of her distance relative to a changing LED light source. Using this system we found in all our experiments that workers show positive phototaxis. The strength of the phototactic response was influenced by body size but not age, and this effect was significant when the light source was weak. In a separate experiment, foragers showed stronger phototactic response compared to nurses only in one of two trials in which they were larger and tested with weak light intensity. The evidence that phototaxis is associated with size-based division of labor in the bumble bee and with age-related division of labor in the honey bee, lends credence to response threshold models implicating the response to light in the organization of division of labor in cavity dwelling social insects.
A microtubule RELION-based pipeline for cryo-EM image processing
Authors: Cook Alexander D. , Manka Szymon W. , Wang Su , Moores Carolyn A. , Atherton Joseph 
Published: June 2019

AbstractMicrotubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views owing to the high structural similarity of α- and β-tubulin. The determination of the αβ-tubulin register and seam location during image processing is essential for alignment accuracy that enables determination of biologically relevant structures. Here we present a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing near-atomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins.AbbreviationsMiRP, Microtubule RELION-based Pipeline; cryo-EM, cryo-electron microscopy; MT, microtubule; CTF, contrast transfer function; PF, protofilament.
FOXC1 negatively regulates BMP-SMAD activity and Id1 expression during osteoblast differentiation
Authors: Caddy Jordan. C. , Luoma Leiah. M. , Berry Fred. B. 
Published: June 2019

AbstractBone morphogenetic proteins regulate a diverse range of biological processes through their activation of SMAD1, 5, or 8 proteins that in turn regulate gene expression. These SMAD transcription factors achieve a layer of functional specificity in different cells types largely through actions with additional transcriptional regulatory molecules. In this report we demonstrate that the Forkhead Box C1 (FOXC1) transcription factor can modulate BMP signalling to impair expression of BMP4-responsive genes and prevent efficient osteoblast differentiation. We demonstrate that repression occurs downstream of BMP signalling and impacts the ability SMAD1 or 5 to activate gene expression. Repression of SMAD activity requires FOXC1 DNA-binding capacity and the transcriptional inhibitory domain of FOXC1. We report that FOXC1 inhibits BMP4 induction of Id1 expression and identify a motif in the regulatory region of mouse Id1 gene that FOXC1 binds. We determine that this inhibition by FOXC1 binding does not affect SMAD1, 5, or 8 binding to its target sequence in the Id1 gene. Finally we determine that elevated expression of FOXC1 can reduces expression osteogenic differentiation genes in mouse embryonic stems directed to the osteoblast lineage through BMP4 treatment. Together, these findings indicate that FOXC1 can negative regulate certain aspects of BMP4 signalling required for osteoblast differentiation. We propose that FOXC1 acts to attenuate the initial BMP-activated pathways that establishes osteoblast differentiation and allow for terminal osteoblast differentiation to conclude.
Plasmodium condensin core subunits (SMC2/SMC4) mediate atypical mitosis and are essential for parasite proliferation and transmission
Authors: Pandey Rajan , Abel Steven , Boucher Matthew , Wall Richard J. , Zeeshan Mohammad , Rea Edward , Freville Aline , Lu Xueqing Maggie , Brady Declan , Daniel Emilie , Stanway Rebecca R. , Wheatley Sally , Batugedara Gayani , Hollin Thomas , Bottrill Andrew R. , Gupta Dinesh , Holder Anthony A. , Le Roch Karine G. , Tewari Rita 
Published: June 2019

SummaryCondensin is a multi-subunit protein complex regulating chromosome condensation and segregation during cell division. In Plasmodium spp., the causative agent of malaria, cell division is atypical and the role of condensin is unclear. Here we examine the role of SMC2 and SMC4, the core subunits of condensin, during endomitosis in schizogony and endoreduplication in male gametogenesis. During early schizogony SMC2/SMC4 localize to a distinct focus, identified as the centromeres by NDC80 fluorescence and ChIP-seq analyses, but do not form condensin I or II complexes. In mature schizonts and during male gametogenesis, there is a diffuse SMC2/SMC4 distribution on chromosomes and in the nucleus, and both condensin I and II complexes form at these stages. Knockdown of smc2 and smc4 gene expression revealed essential roles in parasite proliferation and transmission. The condensin core subunits (SMC2/SMC4) form different complexes and may have distinct functions at various stages of the parasite life cycle.
yacrd and fpa: upstream tools for long-read genome assembly
Authors: Marijon Pierre , Chikhi Rayan , Varré Jean-Stéphane 
Published: June 2019

AbstractMotivationGenome assembly is increasingly performed on long, uncorrected reads. Assembly quality may be degraded due to unfiltered chimeric reads; also, the storage of all read overlaps can take up to terabytes of disk space.ResultsWe introduce two tools, yacrd and fpa, preform respectively chimera removal, read scrubbing, and filter out spurious overlaps. We show that yacrd results in higher-quality assemblies and is one hundred times faster than the best available alternative.Availabilityhttps://github.com/natir/yacrd and https://github.com/natir/fpaContactpierre.marijon@inria.frSupplementary informationSupplementary data are available online.
Simultaneous integration of gene expression and nutrient availability for studying metabolism of hepatocellular carcinoma
Authors: Weglarz-Tomczak Ewelina , Mondeel Thierry D.G.A. , Piebes Diewertje G.E. , Westerhoff Hans V. 
Published: June 2019

AbstractHow cancer cells utilize nutrients to support their growth and proliferation in complex nutritional systems is still an open question. However, it is certainly determined by both genetics and an environmental-specific context. The interactions between them lead to profound metabolic specialization, such as consuming glucose and glutamine and producing lactate at prodigious rates. To investigate whether and how glucose and glutamine availability impact metabolic specialization, we integrated computational modeling on the genome-scale metabolic reconstruction with an experimental study on cell lines. We used the most comprehensive human metabolic network model to date, Recon3D, to build cell line-specific models. RNA-Seq data was used to specify the activity of genes in each cell line and the uptake rates were quantitatively constrained according to nutrient availability. To integrated both constraints we applied a novel method, named GENSI (Gene Expression and Nutrients Simultaneous Integration), that translates the relative importance of gene expression and nutrient availability data into the metabolic fluxes based on an observed experimental feature(s). We applied GENSI to study hepatocellular carcinoma addiction to glucose/glutamine. We were able to identify that proliferation, and lactate production is associated with the presence of glucose but does not necessarily increase with its concentration when the latter exceeds the physiological concentration. There was no such association with glutamine. We show that the integration of gene expression and nutrient availability data into genome-wide models improves the prediction of metabolic phenotypes.
Successful forecasting of harmful cyanobacteria blooms with high frequency lake data
Authors: Kehoe M.J. , Ingalls B.P. , Venkiteswaran J.J. , Baulch H.M. 
Published: June 2019

AbstractCyanobacterial blooms are causing increasing issues across the globe. Bloom forecasting can facilitate adaptation to blooms. Most bloom forecasting models depend on weekly or fortnightly sampling, but these sparse measurements can miss important dynamics. Here we develop forecasting models from five years of high frequency summer monitoring in a shallow lake (which serves as an important regional water supply). A suite of models were calibrated to predict cyanobacterial fluorescence (a biomass proxy) using measurements of: cyanobacterial fluorescence, water temperature, light, and wind speed. High temporal autocorrelation contributed to relatively strong predictive power over 1, 4 and 7 day intervals. Higher order derivatives of water temperature helped improve forecasting accuracy. While traditional monitoring and modelling have supported forecasting on longer timescales, we show high frequency monitoring combined with telemetry allows forecasting over timescales of 1 day to 1 week, supporting early warning, enhanced monitoring, and adaptation of water treatment processes.
Efficient and Modular CRISPR-Cas9 Vector System for Physcomitrella patens
Authors: Mallett Darren R. , Chang Mingqin , Cheng Xiaohang , Bezanilla Magdalena 
Published: June 2019

ABSTRACTCRISPR-Cas9 has been shown to be a valuable tool in recent years, allowing researchers to precisely edit the genome using an RNA-guided nuclease to initiate double-strand breaks. Until recently, classical RAD51-mediated homologous recombination has been a powerful tool for gene targeting in the moss Physcomitrella patens. However, CRISPR-Cas9 mediated genome editing in P. patens was shown to be more efficient than traditional homologous recombination (Collonnier et al. 2017). CRISPR-Cas9 provides the opportunity to efficiently edit the genome at multiple loci as well as integrate sequences at precise locations in the genome using a simple transient transformation. To fully take advantage of CRISPR-Cas9 genome editing in P. patens, here we describe the generation and use of a flexible and modular CRISPR-Cas9 vector system. Without the need for gene synthesis, this vector system enables editing of up to 12 loci simultaneously. Using this system, we generated multiple lines that had null alleles at four distant loci. We also found that targeting multiple sites within a single locus can produce larger deletions, but the success of this depends on individual protospacers. To take advantage of homology-directed repair, we developed modular vectors to rapidly generate DNA donor plasmids to efficiently introduce DNA sequences encoding for fluorescent proteins at the 5’ and 3’ ends of gene coding regions. With regards to homology-directed repair experiments, we found that if the protospacer sequence remains on the DNA donor plasmid, then Cas9 cleaves the plasmid target as well as the genomic target. This can reduce the efficiency of introducing sequences into the genome. Furthermore, to ensure the generation of a null allele near the Cas9 cleavage site, we generated a homology plasmid harboring a “stop codon cassette” with down-stream near-effortless genotyping.
High throughput imaging identifies a spatially localized response of primary fetal pulmonary artery endothelial cells to insulin-like growth factor 1 treatment
Authors: Kim Christina , Seedorf Gregory J , Abman Steven H , Shepherd Douglas P 
Published: June 2019

AbstractA common strategy to measure the efficacy of drug treatment is the in vitro comparison of ensemble readouts with and without treatment, such as proliferation and cell death. A fundamental assumption underlying this approach is there is minimal cell to cell variability in the response to drug. Here, we demonstrate that ensemble and non-spatial single cell readouts applied to primary cells lead to incomplete conclusions due to cell to cell variability. We exposed primary fetal pulmonary artery endothelial cells (PAEC) isolated from healthy newborn healthy and persistent pulmonary hypertension of the newborn (PPHN) sheep to the growth hormone insulin-like growth factor 1 (IGF-1). We found that IGF-1 increased proliferation and branch points in tube formation assays but not angiogenic signaling proteins at the population level for both cell types. We hypothesized that this molecular ambiguity was due to the presence of cellular subpopulations with variable responses to IGF-1. Using high throughput single cell imaging, we discovered a spatially localized response to IGF-1. This suggests localized signaling or heritable cell response to external stimuli may ultimately be responsible for our observations. Discovering and further exploring these rare cells is critical to finding new molecular targets to restore cellular function.