bluuebunny/crossref_metadata_2025 huggingface dataset:
Creating basis for introducing NIPT in the Estonian public health setting
Authors: Žilina Olga , Rekker Kadri , Kaplinski Lauris , Sauk Martin , Paluoja Priit , Teder Hindrek , Ustav Eva-Liina , Tõnisson Neeme , Ridnõi Konstantin , Palta Priit , Krjutškov Kaarel , Kurg Ants , Salumets Andres
Published: October 2018

Objective

The study aimed to validate a whole-genome sequencing-based NIPT method and our newly developed NIPTmer analysis software with the potential to integrate the pipeline into prenatal clinical care in Estonia.

Method

In total, 447 maternal blood samples were included to the study. Analysis pipeline involved whole-genome library preparation and massively parallel sequencing on Illumina NextSeq 500. Aneuploidy status was determined with NIPTmer software, which is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data. To estimate fetal fraction (FF) from total cell-free DNA SeqFF was implemented.

Results

NIPTmer software allowed to identify correctly all samples of non-mosaic T21 (15/15), T18 (9/9) and T13 (4/4) cases. However, one mosaic T18 remained undetected. Six false positive results were observed, including three for T18 (specificity 99.3%) and three for T13 (specificity 99.3%). FF < 4% (2.8-3.99%) was estimated in eight samples, including two samples with T13 and T18. Despite low FF, these two samples were determined as aneuploid with NIPTmer software.

Conclusion

Our NIPT analysis pipeline proved to perform efficiently in detecting common fetal aneuploidies T21, T18 and T13 and is feasible for implementation into clinical service in Estonia.
Cell-type-specific methylome-wide association studies implicate neurodegenerative processes and neuroimmune communication in major depressive disorder
Authors: Chan Robin F. , Turecki Gustavo , Shabalin Andrey A. , Guintivano Jerry , Zhao Min , Xie Lin Y , van Grootheest Gerard , Kaminsky Zachary A. , Dean Brian , Penninx Brenda W.J.H. , Aberg Karolina A. , van den Oord Edwin J.C.G.
Published: October 2018

We studied the methylome in three collections of human postmortem brain (N=206) and blood samples (N=1,132) of subjects with major depressive disorder (MDD) and controls. Using an epigenomic deconvolution approach we performed cell-type-specific methylome-wide association studies (MWAS) within sub-populations of neurons/glia and granulocytes/T-cells/B-cells/monocytes for bulk brain and blood data, respectively. Multiple MWAS findings in neurons/glia replicated across brain collections (ORs=509-538, P-values<1×10−5) and were reproducible in an array-based MWAS of sorted neurons/glia from a fourth brain collection (N=58). Pathway analyses implicated p75NTR/VEGF signaling, neurodegeneration, and blood-brain barrier perturbation. Cell-type-specific analysis in blood identified associations in CD14+ monocytes -- a cell type strongly linked to neuroimmune processes and stress. Top results in neurons/glia/bulk and monocytes were enriched for genes supported by GWAS for MDD (ORs=2.02-2.87, P-values=0.003 to <1×10−5), neurodegeneration and other psychiatric disorders. In summary, we identified novel MDD-methylation associations by using epigenomic deconvolution that provided important mechanistic insights for the disease.
Protein model quality assessment using 3D oriented convolutional neural networks
Authors: Pagès Guillaume , Charmettant Benoit , Grudinin Sergei
Published: October 2018

Protein model quality assessment (QA) is a crucial and yet open problem in structural bioinformatics. The current best methods for single-model QA typically combine results from different approaches, each based on different input features constructed by experts in the field. Then, the prediction model is trained using a machine-learning algorithm. Recently, with the development of convolutional neural networks (CNN), the training paradigm has changed. In computer vision, the expert-developed features have been significantly overpassed by automatically trained convolutional filters. This motivated us to apply a three-dimensional (3D) CNN to the problem of protein model QA.

We developed a novel method for single-model QA called Ornate. Ornate (Oriented Routed Neural network with Automatic Typing) is a residue-wise scoring function that takes as input 3D density maps. It predicts the local (residue-wise) and the global model quality through a deep 3D CNN. Specifically, Ornate aligns the input density map, corresponding to each residue and its neighborhood, with the backbone topology of this residue. This circumvents the problem of ambiguous orientations of the initial models. Also, Ornate includes automatic identification of atom types and dynamic routing of the data in the network. Established benchmarks (CASP 11 and CASP 12) demonstrate the state-of-the-art performance of our approach among singlemodel QA methods.

The method is available athttps://team.inria.fr/nanod/software/Ornate/. It consists of a C++ executable that transforms molecular structures into volumetric density maps, and a Python code based on the TensorFlow framework for applying the Ornate model to these maps.
Genomic prediction of autotetraploids; influence of relationship matrices, allele dosage, and continuous genotyping calls in the phenotype prediction
Authors: Oliveira Ivone de Bem , Resende Marcio F. R. , Ferrão Luis Felipe V. , Amadeu Rodrigo R. , Endelman Jeffrey B. , Kirst Matias , Coelho Alexandre S. G. , Munoz Patricio R.
Published: October 2018

Estimation of allele dosage in autopolyploids is challenging and current methods often result in the misclassification of genotypes. Here we propose and compare the use of next generation sequencing read depth as continuous parameterization for autotetraploid genomic prediction of breeding values, using blueberry (Vaccinium corybosumspp.) as a model. Additionally, we investigated the influence of different sources of information to build relationship matrices in phenotype prediction; no relationship, pedigree, and genomic information, considering either diploid or tetraploid parameterizations. A real breeding population composed of 1,847 individuals was phenotyped for eight yield and fruit quality traits over two years. Analyses were based on extensive pedigree (since 1908) and high-density marker data (86K markers). Our results show that marker-based matrices can yield significantly better prediction than pedigree for most of the traits, based on model fitting and expected genetic gain. Continuous genotypic based models performed as well as the current best models and presented a significantly better goodness-of-fit for all traits analyzed. This approach also reduces the computational time required for marker calling and avoids problems associated with misclassification of genotypic classes when assigning dosage in polyploid species. Accuracies are encouraging for application of genomic selection (GS) for blueberry breeding. Conservatively, GS could reduce the time for cultivar release by three years. GS could increase the genetic gain per cycle by 86% on average when compared to phenotypic selection, and 32% when compared with pedigree-based selection.
Guiding dose selection of monoclonal antibodies using a new parameter (AFTIR) for characterizing ligand binding systems
Authors: Ahmed Sameed , Ellis Miandra , Li Hongshan , Pallucchini Luca , Stein Andrew M
Published: October 2018

Guiding the dose selection for monoclonal antibody oncology drugs is often done using methods for predicting the receptor occupancy of the drug in the tumor. In this manuscript, previous work on characterizing target inhibition at steady state using the AFIR metric was extended to include a "target-tissue" compartment and the shedding of membrane-bound targets. A new potency metric AFTIR was derived (Averarge Free Tissue target to Initial target ratio at steady state) and it depends on four key quantities: the equilibrium binding constant, the fold-change in target expression at steady state after binding to drug, the biodistribution of target from circulation to target tissue, and the average drug concentration in circulation. The AFTIR metric has been useful for guiding dose selection, for rapidly performing sensitivity analyses, and for building intuition for more complex target mediated drug disposition models. In particular, reducing the complex, physiological model to four key parameters needed to predict target inhibition helps to highlight the particular parameters that are most important to estimate in future experiments and further guide drug development. #ddct #phmx #cpt
Finding structure in multi-armed bandits
Authors: Schulz Eric , Franklin Nicholas T. , Gershman Samuel J.
Published: October 2018

How do humans search for rewards? This question is commonly studied using multi-armed bandit tasks, which require participants to trade off exploration and exploitation. Standard multi-armed bandits assume that each option has an independent reward distribution. However, learning about options independently is unrealistic, since in the real world options often share an underlying structure. We study a class of structured bandit tasks, which we use to probe how generalization guides exploration. In a structured multi-armed bandit, options have a correlation structure dictated by a latent function. We focus on bandits in which rewards are linear functions of an option’s spatial position. Across 5 experiments, we find evidence that participants utilize functional structure to guide their exploration, and also exhibit a learning-to-learn effect across rounds, becoming progressively faster at identifying the latent function. Our experiments rule out several heuristic explanations and show that the same findings obtain with non-linear functions. Comparing several models of learning and decision making, we find that the best model of human behavior in our tasks combines three computational mechanisms: (1) function learning, (2) clustering of reward distributions across rounds, and (3) uncertainty-guided exploration. Our results suggest that human reinforcement learning can utilize latent structure in sophisticated ways to improve efficiency.
dream: Powerful differential expression analysis for repeated measures designs
Authors: Hoffman Gabriel E. , Roussos Panos
Published: October 2018

Large-scale transcriptome studies with multiple samples per individual are widely used to study disease biology. Yet current methods for differential expression are inadequate for cross-individual testing for these repeated measures designs. Most problematic, we observe across multiple datasets that current methods can give reproducible false positive findings that are driven by genetic regulation of gene expression, yet are unrelated to the trait of interest. Here we introduce a statistical software package, dream, that increases power, controls the false positive rate, enables multiple types of hypothesis tests, and integrates with standard workflows. In 12 analyses in 6 independent datasets, dream yields biological insight not found with existing software while addressing the issue of reproducible false positive findings. Dream is available within the variancePartition Bioconductor package (http://bioconductor.org/packages/variancePartition).
Analysis of genomic loci harboring 59,732 human-specific regulatory sequences reveals unique to human regulatory patterns associated with brain development
Authors: Glinsky Gennadi V.
Published: October 2018

Extensive searches for genomic regions harboring various types of candidate human-specific regulatory sequences (HSRS) identified thousands’ HSRS using high-resolution next-generation sequencing technologies and methodologically diverse comparative analyses of human and non-human primates’ reference genomes. Here, a comprehensive catalogue of 59,732 genomic loci harboring candidate HSRS has been assembled to facilitate the systematic analyses of genomic sequences that were either inherited from extinct common ancestors (ECAs) or created de novo in human genomes. Present analyses identified thousands of HSRS that appear inherited from ECAs yet absent in genomes of our closest evolutionary relatives, Chimpanzee and Bonobo, presumably due to the incomplete lineage sorting and/or species-specific loss or regulatory DNA. This pattern is particularly prominent for HSRS that have been putatively associated with human-specific (HS) gene expression changes in cerebral organoid models. Significant fractions of retrotransposon-derived loci transcriptionally-active in human dorsolateral prefrontal cortex (DLPFC) are highly conserved in genomes of Gorilla, Orangutan, Gibbon, and Rhesus (1,688; 1,371; 1,148; and 1,045 loci, respectively), yet they are absent in genomes of both Chimpanzee and Bonobo. A prominent majority of regions harboring HS mutations associated with HS expression changes during brain development is highly conserved in Chimpanzee, Bonobo, and Gorilla genomes. Among non-human primates (NHP), dominant fractions of HSRS associated with HS gene expression in both excitatory neurons (347 loci; 67%) and radial glia (683 loci; 72%) are highly conserved in the Gorilla genome. Analysis of 4,433 genes encoding virus-interacting proteins (VIPs) revealed that 95.9% of human VIPs are components of HS regulatory networks that appear to operate in distinct types of human cells from preimplantation embryos to adult DLPFC. Present analyses demonstrate that Modern Humans captured unique combinations of regulatory sequences, divergent subsets of which are highly conserved in distinct species of six NHP separated by 30 million years of evolution. Concurrently, this unique-to-human mosaic of genomic regulatory patterns inherited from ECAs was supplemented with 12,486 created de novo HSRS. Present analyses of HSRS support the model of complex continuous speciation process during evolution of the human lineage that is not likely to occur as an instantaneous event. Genes encoding VIPs may represent a principal genomic target of HS regulatory networks, thus affecting a functionally diverse spectrum of biological processes controlled by VIP-containing liquid-liquid phase separated condensates.
Unsupervised integration of multimodal dataset identifies novel signatures of health and disease
Authors: Shomorony Ilan , Cirulli Elizabeth T. , Huang Lei , Napier Lori A. , Heister Robyn R. , Hicks Michael , Cohen Isaac V. , Yu Hung-Chun , Swisher Christine Leon , Schenker-Ahmed Natalie M. , Li Weizhong , Kahn Andrew M. , Spector Timothy D. , Caskey C. Thomas , Venter J. Craig , Karow David S. , Kirkness Ewen F. , Shah Naisha
Published: October 2018

Modern medicine is rapidly moving towards a data-driven paradigm based on comprehensive multimodal health assessments. We collected 1,385 data features from diverse modalities, including metabolome, microbiome, genetics and advanced imaging, from 1,253 individuals and from a longitudinal validation cohort of 1,083 individuals. We utilized an ensemble of unsupervised machine learning techniques to identify multimodal biomarker signatures of health and disease risk. In particular, our method identified a set of cardiometabolic biomarkers that goes beyond standard clinical biomarkers, which were used to cluster individuals into distinct health profiles. Cluster membership was a better predictor for diabetes than established clinical biomarkers such as glucose, insulin resistance, and BMI. The novel biomarkers in the diabetes signature included 1-stearoyl-2-dihomo-linolenoyl-GPC and 1-(1-enyl-palmitoyl)-2-oleoyl-GPC. Another metabolite, cinnamoylglycine, was identified as a potential biomarker for both gut microbiome health and lean mass percentage. We also identified an early disease signature for hypertension, and individuals at-risk for a poor metabolic health outcome. We found novel associations between an uremic toxin, p-cresol sulfate, and the abundance of the microbiome genera Intestinimonas and an unclassified genus in the Erysipelotrichaceae family. Our methodology and results demonstrate the potential of multimodal data integration, from the identification of novel biomarker signatures to a data-driven stratification of individuals into disease subtypes and stages -- an essential step towards personalized, preventative health risk assessment.
Right hemisphere superiority for executive control of attention
Authors: Spagna Alfredo , Kim Tae Hyeong , Wu Tingting , Fan Jin
Published: October 2018

Over forty years have passed since the first evidence showing the unbalanced attentional allocation of humans across the two visual fields, and since then, a wealth of behavioral, neurophysiological, and clinical data increasingly showed a right hemisphere dominance for orienting of attention. However, inconsistent evidence exists regarding the right-hemisphere dominance for executive control of attention, possibly due to a lack of consideration of its dynamics with the alerting and orienting functions. In this study, we used a version of the Attentional Network Test with lateralized presentation of the stimuli to the left visual field (processed by the right hemisphere, RH) and right visual field (processed by the left hemisphere, LH) to examine visual field differences in executive control of attention under conditions of alerting or orienting. Analyses of behavioral performance (reaction time and error rate) showed a more efficient executive control (reduced conflict effect) in the RH compared to the LH for the reaction time, under conditions of increased alerting and of informative spatial orienting. These results demonstrate the right-hemisphere superiority for executive control, and that this effect depends on the activation of the alerting and orienting functions.
Expression of a recombinant high affinity IgG Fc receptor by engineered NK cells as a docking platform for therapeutic mAbs to target cancer cells
Authors: Snyder Kristin M. , Hullsiek Robert , Mishra Hemant K , Mendez Daniel C. , Li Yunfang , Rogich Allison , Kaufman Dan S. , Wu Jianming , Walcheck Bruce
Published: October 2018

Anti-tumor mAbs are the most widely used and characterized cancer immunotherapy agents. Despite having a significant impact on some malignancies, most cancer patients respond poorly or develop resistance to this therapy. A known mechanism of action of these therapeutic mAbs is antibody-dependent cell-mediated cytotoxicity (ADCC), which is a primarily effector function of NK cells. CD16A on human NK cells has an exclusive role in binding to tumor-bound IgG antibodies. Though CD16A is a potent activating receptor, it is a low affinity FcγR and its cell surface levels can be rapidly downregulated by a proteolytic process involving ADAM17 upon NK cell activation, which are likely to limit the efficacy of tumor-targeting therapeutic mAbs in the tumor environment. We sought to enhance NK cell binding to anti-tumor mAbs by engineering these cells with a recombinant FcγR consisting of the extracellular region of CD64, the highest affinity IgG Fc receptor expressed by leukocytes, and the transmembrane and cytoplasmic regions of CD16A. This novel recombinant FcγR (CD64/16A) was expressed in the human NK cell line NK92 and in induced pluripotent stem cells from which primary NK cells were derived. CD64/16A also lacked the ADAM17 cleavage region in CD16A and it was not rapidly downregulated in expression following NK cell activation during ADCC. CD64/16A on NK cells facilitated conjugation to antibody-treated tumor cells, ADCC, and cytokine production, demonstrating functional activity by its two components. Unlike NK cells expressing CD16A, CD64/16A captured soluble therapeutic mAbs and the modified NK cells mediated tumor cell killing. Hence, CD64/16A could potentially be used as a docking platform on engineered NK cells for therapeutic mAbs and IgG Fc chimeric proteins, allowing for switchable targeting elements, and a novel cancer cellular therapy.
Light-based tuning of ligand half-life supports kinetic proofreading model of T cell activation
Authors: Tischer Doug , Weiner Orion D.
Published: October 2018

T cells are thought to discriminate stimulatory versus non-stimulatory ligands by converting small changes in ligand binding half-life to large changes in cell activation. Such a kinetic proofreading model has been difficult to test directly, as existing methods of altering ligand binding half-life also change other potentially important biophysical parameters, most notably the stability of the receptor-ligand interaction under load. Here we develop an optogenetic approach to specifically tune the binding half-life of a light-responsive ligand to a chimeric antigen receptor without changing other binding parameters. By simultaneously manipulating binding half-life while controlling for receptor occupancy, we find that signaling is strongly gated by ligand binding half-life. Our results provide direct evidence of kinetic proofreading in ligand discrimination by T cells.

One Sentence Summary

Direct control of ligand binding half-life with light shows that lifetime, not occupancy, dominates T cell activation.
Study of the action of lactic acid bacteria on acrylamide in food products
Authors: Surana Pallavi , Singh Shruti , Manokaran Sumathra , Reddy A.H. Manjunatha
Published: October 2018

The aim of this study is to extract Lactic acid bacteria (LAB) and test its effect on starchy food products. We extracted LAB as it is GRAS (Generally Recognised As Safe) and is abundantly present in probiotics like curd. After extraction of LAB colonies and were tested for its effect on foods rich in acrylamide content. Acrylamide formation is studied by the maillard reaction. Acrylamide is found in food products which have been subjected to very high temperatures. The application of LAB to remove many mutagens, by using the binding mechanism was assessed for acrylamide. When this acrylamide degrades it produces toxic gases like ammonia, hydrogen and carbon monoxide. Asparagine is an important precursor to acrylamide formation. So in foods containing free asparagine group with reducing sugars will form acrylamide. We used liquid chromatography to determine the presence of acrylamide in the food product. Acrylamide content in the body is responsible for various mutations at the genomic level thereby, leading to cancers like colon, breast. It also leads to neural damages and is directly linked to Alzhimers disease. This study concludes the beneficial effects of consuming probiotics and suggests a way to reduce the acrylamide formation in food products.
INSTRAL: Discordance-aware Phylogenetic Placement using Quartet Scores
Authors: Rabiee Maryam , Mirarab Siavash
Published: October 2018

Phylogenomic analyses have increasingly adopted species tree reconstruction using methods that account for gene tree discordance using pipelines that require both human effort and computational resources. As the number of available genomes continues to increase, a new problem is facing researchers. Once more species become available, they have to repeat the whole process from the beginning because updating species trees is currently not possible. However, thede novoinference can be prohibitively costly in human effort or machine time. In this paper, we introduce INSTRAL, a method that extends ASTRAL to enable phylogenetic placement. INSTRAL is designed to place a new species on an existing species tree after sequences from the new species have already been added to gene trees; thus, INSTRAL is complementary to existing placement methods that update gene trees.
Structural and biochemical characterization on the cognate and heterologous interactions of the MazEF-mt9 TA system
Authors: Chen Ran , Tu Jie , Tan Yaoju , Cai Xingshan , Yang Chengwen , Deng Xiangyu , Su Biyi , Ma Shangming , Liu Xin , Ma Pinyun , Du Chaochao , Xie Wei
Published: October 2018

The toxin-antitoxin (TA) modules widely exist in bacteria, and their activities are associated with the persister phenotype of the pathogen Mycobacterium tuberculosis (M. tb). M. tb causes Tuberculosis, a contagious and severe airborne disease. There are ten MazEF TA systems in M. tb, which play important roles in stress adaptation. How the antitoxins antagonize toxins in M. tb or how the ten TA systems crosstalk to each other are of interests, but the detailed molecular mechanisms are largely unclear. MazEF-mt9 is a unique member among the MazEF families due to its tRNase activity, which is usually carried out by the VapC family toxins. Here we present the cocrystal structure of the MazEF-mt9 complex at 2.7 Å. By characterizing the association mode between the TA pairs through various characterization techniques, we found that MazF-mt9 not only bound its cognate antitoxin, but also the non-cognate antitoxin MazE-mt1, a phenomenon that could be also observed in vivo. Based on our structural and biochemical work, we proposed that the cognate and heterologous interactions among different TA systems work together to relieve MazF-mt9’s toxicity to M. tb cells, which may facilitate their adaptation to the stressful conditions encountered during host infection.

IMPORTANCE

Tuberculosis (TB) is one of the most severe contagious diseases. Caused by Mycobacterium tuberculosis (M. tb), it poses a serious threat to human health. Additionally, TB is difficult to cure because of the multipledrug-resistant (MDR) and extensively drug-resistant (XDR) M. tb strains. Toxin-antitoxin (TA) systems have been discovered to widely exist in prokaryotic organisms with diverse roles, normally composed of a pair of molecules that antagonize each other. M. tb has ten MazEF systems, and some of them have been proved to be directly associated with the genesis of persisters and drug-resistance of M. tb. We here report the MazEF-mt9 complex structure, and thoroughly characterized the interactions between MazF-mt9 with MazEs within or outside the MazEF-mt9 family. Our study not only revealed the crosstalks between TA families and its significance to M. tb survival but also offers insights into potential anti-TB drug design.
Bazam: A rapid method for read extraction and realignment of high throughput sequencing data
Authors: Sadedin Simon P , Oshlack Alicia
Published: October 2018

Background

As costs of high throughput sequencing have fallen, we are seeing vast quantities of short read genomic data being generated. Often, the data is exchanged and stored as aligned reads, which provides high compression and convenient access for many analyses. However, aligned data becomes outdated as new reference genomes and alignment methods become available. Moreover, some applications cannot utilise pre-aligned reads at all, necessitating conversion back to raw format (FASTQ) before they can be used. In both cases, the process of extraction and realignment is expensive and time consuming.

Findings

We describe Bazam, a tool that efficiently extracts the original paired FASTQ from reads stored in aligned form (BAM or CRAM format). Bazam extracts reads in a format that directly allows realignment with popular aligners with high concurrency. Through eliminating steps and increasing the accessible concurrency, Bazam facilitates up to a 90% reduction in the time required for realignment compared to standard methods. Bazam can support selective extraction of read pairs from focused genomic regions, further increasing efficiency for targeted analyses. Bazam is additionally suitable as a base for other applications that require efficient paired read information, such as quality control, structural variant calling and alignment comparison.

Conclusions

Bazam offers significant improvements for users needing to realign genomic data.
scRNA-seq mixology: towards better benchmarking of single cell RNA-seq analysis methods
Authors: Tian Luyi , Dong Xueyi , Freytag Saskia , Lê Cao Kim-Anh , Su Shian , JalalAbadi Abolfazl , Amann-Zalcenstein Daniela , Weber Tom S. , Seidi Azadeh , Jabbari Jafar S. , Naik Shalin H. , Ritchie Matthew E.
Published: October 2018

Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years, bringing with new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq data to address various biological questions. However, the current lack of gold-standard benchmark datasets makes it difficult for researchers to systematically evaluate the performance of the many methods available. Here, we designed and carried out a realistic benchmark experiment that included mixtures of single cells or ‘pseudo cells’ created by sampling admixtures of cells or RNA from up to 5 distinct cancer cell lines. Altogether we generated 14 datasets using droplet and plate-based scRNA-seq protocols, compared multiple data analysis methods in combination for tasks ranging from normalization and imputation, to clustering, trajectory analysis and data integration. Evaluation across 3,913 analyses (methods × benchmark dataset combinations) revealed pipelines suited to different types of data for different tasks. Our dataset and analysis present a comprehensive comparison framework for benchmarking most common scRNA-seq analysis tasks.
Synchronised spiking activity underlies phase amplitude coupling in the subthalamic nucleus of Parkinson’s disease patients
Authors: Meidahl Anders Christian , Moll Christian K.E. , van Wijk Bernadette , Gulberti Alessandro , Tinkhauser Gerd , Westphal Manfred , Engel Andreas K. , Hamel Wolfgang , Brown Peter , Sharott Andrew
Published: October 2018

Both phase-amplitude coupling (PAC) and beta-bursts in the subthalamic nucleus have been significantly linked to symptom severity in Parkinson’s disease (PD) in humans and emerged independently as competing biomarkers for closed-loop deep brain stimulation (DBS). However, the underlying nature of subthalamic PAC is poorly understood and its relationship with transient beta burst-events has not been investigated. To address this, we studied macro- and micro electrode recordings of local field potentials (LFPs) and single unit activity from 15 hemispheres in 10 PD patients undergoing DBS surgery. PAC between beta phase and high frequency oscillation (HFO) amplitude was compared to single unit firing rates, spike triggered averages, power spectral densities and phase-spike locking, and was studied in periods of beta-bursting. We found a significant synchronisation of spiking to HFOs and correlation of mean firing rates with HFO-amplitude when the latter was coupled to beta phase (i.e. in the presence of PAC). In the presence of PAC, single unit power spectra displayed peaks in the beta and HFO frequency range and the HFO frequency was correlated with that in the LFP. Finally, PAC significantly increased with beta burst-duration. Our findings offer new insight in the pathology of Parkinson’s disease by providing evidence that subthalamic PAC reflects the locking of spiking activity to network beta oscillations and that this coupling progressively increases with beta-burst duration. These findings suggest that beta-bursts capture periods of increased subthalamic input/output synchronisation in the beta frequency range and have important implications for therapeutic closed-loop DBS.

Significance statement

Identifying biomarkers for closed-loop deep brain stimulation (DBS) has become an increasingly important issue in Parkinson’s Disease (PD) research. Two such biomarkers, phase–amplitude coupling (PAC) and beta-bursts, recorded from the implanted electrodes in subthalamic nucleus in PD patients, correlate with motor impairment. However, the physiological basis of PAC, and it relationship to beta bursts, is unclear. We provide multiple lines of evidence that PAC in the human STN reflects the locking of spiking activity to network beta oscillations and that this coupling progressively increases with the duration of beta-bursts. This suggests that beta-bursts capture increased subthalamic input/output synchronisation and provides new insights in PD pathology with direct implications for closed-loop DBS therapy strategies.
MiniScrub: de novo long read scrubbing using approximate alignment and deep learning
Authors: LaPierre Nathan , Egan Rob , Wang Wei , Wang Zhong
Published: October 2018

Long read sequencing technologies such as Oxford Nanopore can greatly de-crease the complexity of de novo genome assembly and large structural variation iden-tification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. Many methods for resolving these errors require access to reference genomes, high-fidelity short reads, or reference genomes, which are often not available. De novo error correction modules are available, often as part of assembly tools, but large-scale errors still remain in resulting assemblies, motivating further innovation in this area. We developed a novel Convolutional Neu-ral Network (CNN) based method, called MiniScrub, for de novo identification and subsequent “scrubbing” (removal) of low-quality Nanopore read segments. MiniScrub first generates read-to-read alignments by MiniMap, then encodes the alignments into images, and finally builds CNN models to predict low-quality segments that could be scrubbed based on a customized quality cutoff. Applying MiniScrub to real world con-trol datasets under several different parameters, we show that it robustly improves read quality. Compared to raw reads, de novo genome assembly with scrubbed reads pro-duces many fewer mis-assemblies and large indel errors. We propose MiniScrub as a tool for preprocessing Nanopore reads for downstream analyses. MiniScrub is open-source software and is available at https://bitbucket.org/berkeleylab/jgi-miniscrub
G-Protein signaling accelerates stem cell divisions in Drosophila males
Authors: Malpe Manashree , McSwain Leon F. , Kudyba Karl , Ng Chun L. , Nicholson Jennie , Brady Maximilian , Qian Yue , Choksi Vinay , Hudson Alicia G. , Parrott Benjamin B. , Schulz Cordula
Published: October 2018

Adult stem cells divide to renew the stem cell pool and replenish specialized cells that are lost due to death or usage. However, little is known about the mechanisms regulating how stem cells adjust to a demand for specialized cells. A failure of the stem cells to respond to this demand can have serious consequences, such as tissue loss, or prolonged recovery post injury.

Here, we challenge the male germline stem cells (GSCs) of Drosophila melanogaster for the production of specialized cells using mating experiments. We show that repeated mating reduced the sperm pool and accelerated germline stem cell (GSC) divisions. The increase in GSC divisions depended on the activity of the highly conserved G-proteins. Germline expression of RNA-Interference (RNA-i) constructs against G-proteins or a dominant negative G-protein eliminated the increase in GSC divisions in mated males. Consistent with a role for the G-proteins in the regulation of GSC divisions, RNA-i against seven out of 35 G-protein coupled receptors (GPCRs) within the germline cells also eliminated the capability of males to accelerate their GSC divisions in response to mating. Our data show that GSCs are receptive to GPCR stimulus, potentially through a network of interactions among multiple signaling pathways.
The effect of X-linked dosage compensation on complex trait variation
Authors: Sidorenko Julia , Kassam Irfahan , Kemper Kathryn , Zeng Jian , Lloyd-Jones Luke , Montgomery Grant W. , Gibson Greg , Metspalu Andres , Esko Tonu , Yang Jian , McRae Allan F. , Visscher Peter M.
Published: October 2018

Quantitative genetics theory predicts that X-chromosome dosage compensation between sexes will have a detectable effect on the amount of genetic and therefore phenotypic trait variances at associated loci in males and females. Here, we systematically examine the role of dosage compensation in complex trait variation in humans in 20 complex traits in a sample of more than 450,000 individuals from the UK Biobank and in 1,600 gene expression traits from a sample of 2,000 individuals as well as across-tissue gene expression from the GTEx resource. We find, on average, twice as much genetic variation for complex traits due to X-linked loci in males compared to females, consistent with a negligible effect of predicted escape from X-inactivation on complex trait variation across traits and also detect biologically relevant X-linked heterogeneity between the sexes for a number of complex traits.
Elevated trace elements in Posidonia oceanica and Cymodocea nodosa at six Mediterranean volcanic seeps
Authors: Mishra A.K. , Santos R. , Hall-Spencer J.M.
Published: October 2018

Seagrasses form important habitats around shallow marine CO2 seeps, providing opportunities to assess trace element (TE) accumulation along gradients in seawater pH. Here we assessed Cd, Cu, Hg, Ni, Pb and Zn levels in sediment and seagrasses at six CO2 seeps and reference sites off Italy and Greece. Some seep sediments had much higher concentrations of TEs, the extreme example being Cd at 43-fold above reference levels. Sediment Quality Guideline (SQG) scores indicated that three seeps had sediment TEs levels likely to have “Adverse impacts” on marine biota; namely Vulcano (for Hg), Ischia (for Cu) and Paleochori (for Cd and Ni). SQG indicated seep sediments of Italian seeps were adversely affected by Cu and Hg, whereas Greek CO2 seeps were affected by Cd and Ni. An increase in sediment TEs levels positively corelated with higher levels of TEs in seagrass roots of Posidonia oceanica (Zn and Ni) and Cymodocea nodosa (Zn). Differences in the bioavailability and possible toxicity of TEs helps explain why seagrasses were abundant at some CO2 seeps but not others.
Central carbon metabolism is an intrinsic factor for optimal replication of a norovirus
Authors: Passalacqua Karla D. , Lu Jia , Goodfellow Ian , Kolawole Abimbola O. , Arche Jacob R. , Maddox Robert J. , O’Riordan Mary X.D. , Wobus Christiane E.
Published: October 2018

The metabolic pathways of central carbon metabolism, glycolysis and oxidative phosphorylation (OXPHOS), are important host factors that determine the outcome of viral infections and can therefore be manipulated by some viruses to favor infection. However, mechanisms of metabolic modulation and their effects on viral replication vary widely. Herein, we present the first metabolomics profile of norovirus-infected cells, which revealed increases in glycolysis, OXPHOS, and the pentose phosphate pathway (PPP) during murine norovirus infection. Inhibiting glycolysis with 2-deoxyglucose (2DG) in transformed and primary macrophages revealed that host cell metabolism is an important factor for optimal murine norovirus (MNV) infection. 2DG affected an early stage in the viral life cycle after viral uptake and capsid uncoating, leading to decreased levels of viral protein translation and viral RNA replication. The requirement of central carbon metabolism was specific for MNV (but not astrovirus) infection, independent of the Type I interferon antiviral response, and unlikely to be due to a lack of host cell nucleotide synthesis. MNV infection increased activation of the protein kinase Akt, but not AMPK, two master regulators of cellular metabolism, suggesting Akt signaling may play a role in upregulating central carbon metabolism during norovirus infection. In conclusion, our findings suggest that the metabolic state of target cells is an intrinsic host factor that determines the extent of norovirus replication and implicates metabolism as a virulence determinant. They further implicate cellular metabolism as a novel therapeutic target for norovirus infections and improvements of current human norovirus culture systems.

IMPORTANCE

Viruses depend on the host cells they infect to provide the machinery and substrates for replication. Host cells are highly dynamic systems that can alter their intracellular environment and metabolic behavior, which may be helpful or inhibitory for an infecting virus. In this study, we show that macrophages, a target cell of murine norovirus (MNV), increase central carbon metabolism upon viral infection, which is important for early steps in MNV infection. Human noroviruses (hNoV) are a major cause of gastroenteritis globally, causing enormous morbidity and economic burden. Currently, no effective antivirals or vaccines exist for hNoV, mainly due to the lack of high efficiencyin vitroculture models for their study. Thus, insights gained from the MNV model may reveal aspects of host cell metabolism that can be targeted for improving hNoV cell culture systems and for developing effective antiviral therapies.
Innate Immune Priming by cGAS as a Preparatory Countermeasure Against RNA Virus Infection
Authors: Parker Michael T. , Gopinath Smita , Perez Corey E. , Linehan Melissa M. , Crawford Jason M. , Iwasaki Akiko , Lindenbach Brett D.
Published: October 2018

The detection of nucleic acids by pattern recognition receptors is an ancient and conserved component of the innate immune system. Notably, RNA virus genomes are sensed by mammalian cytosolic RIG-I–like receptors, thereby activating interferon-stimulated gene (ISG) expression to restrict viral replication. However, recent evidence indicates that the cGAS-STING DNA sensing pathway also protects against RNA viruses. So far, the mechanisms responsible for DNA sensing of RNA viruses, which replicate without known DNA intermediates, remain unclear. By using cGAS gene knockout and reconstitution in human and mouse cell cultures, we discovered that DNA sensing and cGAMP synthase activities are required for cGAS-mediated restriction of vesicular stomatitis virus and Sindbis virus. The level of cGAMP produced in response to RNA virus infection was below the threshold of detection, suggesting that only transient and/or low levels of cGAMP are produced during RNA virus infections. To clarify the DNA ligands that activate cGAS activity, we confirmed that cGAS binds mitochondrial DNA in the cytosol of both uninfected and infected cells; however, the amount of cGAS-associated mitochondrial DNA did not change in response to virus infection. Rather, a variety of pre-existing cytosolic DNAs, including mitochondrial DNA and endogenous cDNAs, may serve as stimuli for basal cGAS activation. Importantly, cGAS knockout and reconstitution experiments demonstrated that cGAS drives low-level ISG expression at steady state. We propose that cGAS-STING restricts RNA viruses by promoting a preparatory immune activation state within cells, likely primed by endogenous cellular DNA ligands.

Importance

Many medically important RNA viruses are restricted by the cGAS-STING DNA-sensing pathway of innate immune activation. Since these viruses replicate without DNA intermediates, it is unclear what DNA ligand(s) are responsible for triggering this pathway. We show here that cGAS’s DNA binding and signaling activities are required for RNA virus restriction, similar to the mechanisms by which it restricts DNA viruses. Furthermore, we confirmed that cGAS continuously binds host DNA, which was unaffected by RNA virus infection. Finally, cGAS expression correlated with the low-level expression of interferon-stimulated genes in uninfected cells, bothin vitroandin vivo. We propose that cGAS-mediated sensing of endogenous DNA ligands contributes to RNA virus restriction by establishing a baseline of innate immune activation.
An E3 ubiquitin ligase fromNicotiana benthamianatargets the replicase ofBamboo mosaic virusand restricts its replication
Authors: Chen I-Hsuan , Chang Jui-En , Wu Chen-Yu , Huang Ying-Ping , Hsu Yau-Huei , Tsai Ching-Hsiu
Published: October 2018

One upregulated host gene identified previously was found involved in the infection process ofBamboo mosaic virus(BaMV). The full-length cDNA of this gene was cloned by 5′- and 3′-rapid amplification of cDNA ends and found to encode a polypeptide containing a conserved RING-domain and a transmembrane domain. The gene might function as an E3 ubiquitin ligase. We designated this protein inNicotiana benthamianaas ubiquitin E3 ligase containing RING-domain 1 (NbUbE3R1). Further characterization by usingTobacco rattle virus-based virus-induced gene silencing revealed an increased BaMV accumulation in both knockdown plants and protoplasts. To further inspect the functional role of NbUbE3R1 in BaMV accumulation, NbUbE3R1 was expressed inN. benthamianaplants. The wild-type NbUbE3R1-orange fluorescent protein (NbUbE3R1-OFP), NbUbE3R1/△TM-OFP (removal of the transmembrane domain) and NbUbE3R1/mRING-OFP (mutation at the RING domain, the E2 interaction site) were transiently expressed in plants. NbUbE3R1 and its derivatives all functioned in restricting BaMV accumulation. The common feature of these constructs was the intact substrate-interacting domain. Yeast two-hybrid and co-immunoprecipitation experiments used to determine the possible viral-encoded substrate of NbUbE3R1 revealed the replicase of BaMV as the possible substrate. In conclusion, we identified an upregulated gene, NbUbE3R1, that plays a role in BaMV replication.
Purkinje cell number-correlated cerebrocerebellar circuit anomaly in the valproate model of autism
Authors: Spisák Tamás , Román Viktor , Papp Edit , Kedves Rita , Sághy Katalin , Csölle Cecília Katalin , Varga Anita , Gajári Dávid , Nyitrai Gabriella Éva , Spisák Zsófia , Kincses Zsigmond Tamás , Lévay György , Lendvai Balázs , Czurkó András
Published: October 2018

While cerebellar alterations may play a crucial role in the development of core autism spectrum disorder (ASD) symptoms, their pathophysiology on the function of cerebrocerebellar circuit loops is largely unknown. We combined multimodal MRI (9.4 T) brain assessment of the prenatal rat valproate (VPA) model and correlated immunohistological analysis of the cerebellar Purkinje cell number to address this question. We hypothesized that a suitable functional MRI (fMRI) paradigm might show some altered activity related to disrupted cerebrocerebellar information processing. Two doses of maternal VPA (400 and 600 mg/kg, s.c.) were used, and while the higher VPA dose induced a global decrease in whole brain volume, the lower dose induced a focal gray matter density decrease in the cerebellum and brainstem. Increased cortical BOLD responses to whisker stimulation were detected in both VPA groups, but it was more pronounced and extended to cerebellar regions in the 400 mg/kg VPA group. Immunohistological analysis revealed a decreased number of Purkinje cells in both VPA groups. In a detailed analysis, we revealed that the Purkinje cell number interacts with the cerebral BOLD response distinctively in the two VPA groups that highlights atypical function of the cerebrocerebellar circuit loops with potential translational value as an ASD biomarker.
Plasmid transfer is biased towards close kin in bacteria from natural populations
Authors: Dimitriu Tatiana , Marchant Lauren , Buckling Angus , Raymond Ben
Published: October 2018

Plasmids play a key role in microbial ecology and evolution, yet the determinants of plasmid transfer rates are poorly understood. Here we investigate the importance of genetic similarity between naturally co-occurringEscherichia coliisolates in the transfer of two plasmids (narrow-host-range R1 and broad-host-range RP4). We uncovered extensive variability, spanning over five orders of magnitude, in the ability of isolates to donate and receive plasmids. Overall, transfer was strongly biased towards clone-mates, but not correlated to genetic distance between donors and recipients. Transfer was limited by the presence of a functional restriction-modification system in recipients, thus bias towards kin might be explained by sharing of identical restriction systems. Such conjugation within lineages sets the stage for longer-term pair-wise coevolutionary interactions between plasmids and bacterial hosts.