bluuebunny/crossref_metadata_2025 huggingface dataset:
The BioScreening Facility at Newcastle University
Authors: Banks Peter
Published: December 2019

The BioScreening facility based within the Medical School at Newcastle University combines robotics, high throughput reagents and expertise to provide a resource to academics throughout the UK. The facility was created in 2011 using technology within the laboratory of Professor David Lydall and has been run since this date by Dr Peter Banks. The facility caters for a range of microbial organisms but yeast screening has for many years been a core part of the BioScreening Facility. The services offered for yeast screening include genomic screening of deletion, over expression and temperature sensitive collections, protein interaction screening and histone mutant collection screening. Compound screening is also offered in collaboration with the life sciences charity LifeArc. The BioScreening facility offers a fully comprehensive yeast screening service from the initial experiment to final data analysis and presentation if required. However, we also welcome requests for training on robotic systems, high throughput experimental design and analysis and advice on large scale data handling.
Drug resistant Candida colonization among ICU patients in a Nigerian teaching hospital
Authors: Abiri Oyekola
Published: December 2019

Introduction:

Colonisation of body surfaces with resistant strains is an initial step in the pathogenesis of drug resistant invasive Candida infections. Nigeria has little data on the species distribution and resistance pattern of colonising Candida species in intensive care unit(ICU) patients. This study set out to investigate the burden of Candida colonisation in the ICU of a tertiary health institution in Ile-Ife, Nigeria.

Methodology:

At admission, 72 hours and 7 days, swabs of skin, oropharynx, perianal region, surgical wounds, tracheal aspirates and urine samples taken from adult ICU patients were cultured on media selective for fungi. Candida species were identified by standard microbiological methods. Sensitivity to fluconazole, voriconazole and caspofungin was determined by disc diffusion according to CLSI guidelines. Strain interrelatedness was investigated by Randomly Amplified Polymorphic DNA (RAPD).

Results:

Of 744 samples from 110 patients, 142 samples (18.3%) yielded Candida. The average colonisation index increased with duration of admission (p=0.001). Most frequently colonized were the oropharynx (39.5%) and the perianal region (22.4%). Species isolated were C. albicans 97 (68.3%), C. tropicalis 20 (14.1%), C. glabrata 12 (8.5%), C. parapsilosis 7 (4.9%) and C. krusei 6 (4.2%). About 1 in every 3 isolates was resistant to fluconazole (42/142; 29.6%). In addition, resistance to voriconazole was 12/142 (8.5%) while 10/142 (7%) were resistant to caspofungin. RAPD showed identical strains across several body sites of many patients.

Conclusion:

Candida species with high rates of resistance to the first line antifungal agent colonise and are transmitted among ICU patients. These can potentially cause difficult to treat invasive infections, underscoring a need for better infection control practices.
Feature selection strategies for drug sensitivity prediction
Authors: Koras Krzysztof , Juraeva Dilafruz , Kreis Julian , Mazur Johanna , Staub Eike , Szczurek Ewa
Published: December 2019

Drug sensitivity prediction constitutes one of the main challenges in personalized medicine. The major difficulty of this problem stems from the fact that the sensitivity of cancer cells to treatment depends on an unknown subset of a large number of biological features. Although feature selection is the key to interpretable results and identification of potential biomarkers, a comprehensive assessment of feature selection methods for drug sensitivity prediction has so far not been performed. We propose feature selection approaches driven by prior knowledge of drug targets, target pathways, and gene expression signatures. We asses these methodologies on Genomics of Drug Sensitivity in Cancer (GDSC) dataset, a panel of around 1000 cell lines screened against multiple anticancer compounds. We compare our results with a baseline model utilizing genome-wide gene expression features and common data-driven feature selection techniques. Together, 2484 unique models were evaluated, providing a comprehensive study of feature selection strategies for the drug response prediction problem. For 23 drugs, the models achieve better predictive performance when the features are selected according to prior knowledge of drug targets and pathways. The best correlation of observed and predicted response using the test set is achieved for Linifanib (r=0.75). Extending the drug-dependent features with gene expression signatures yields models that are most predictive of drug response for 60 drugs, with the best performing example of Dabrafenib. Examples of how pre-selection of features benefits the model interpretability are given for Dabrafenib, Linifanib and Quizartinib. Based on GDSC drug data, we find that feature selection driven by prior knowledge tends to yield better results for drugs targeting specific genes and pathways, while models with the genome-wide features perform better for drugs affecting general mechanisms such as metabolism and DNA replication. For a significant group of the compounds, even a very small number of features based on simple drug properties is often highly predictive of drug sensitivity, can explain the mechanism of drug action and be used as guidelines for their prescription. In general, choosing appropriate feature selection strategies has the potential to develop interpretable models that are indicative for therapy design.
Rough and smooth variant Mycobacterium abscessus infections are differentially controlled by host immunity during chronic infection
Authors: Hortle Elinor , Kam Julia Y , Krogman Elizabeth , Warner Sherridan E , Luo Kaiming , Cheng Tina , Cholan Pradeep Manuneedhi , Kikuchi Kazu , Triccas James A , Britton Warwick J , Johansen Matt D , Kremer Laurent , Oehlers Stefan H
Published: December 2019

Infections caused by Mycobacterium abscessus are increasing in prevalence within patient groups with respiratory comorbidities. Initial colonisation by the smooth colony M. abscessus (S) can be followed by an irreversible genetic switch into a highly inflammatory rough colony M. abscessus (R), often associated with a decline in pulmonary function. Our understanding of the role of adaptive immunity in M. abscessus pathogenesis is largely unknown. Here, we have used intraperitoneal infection of adult zebrafish to model M. abscessus pathogenesis in the context of fully functioning host immunity. We find infection with the R variant penetrates host organs causing an inflammatory immune response leading to necrotic granuloma formation within 2 weeks. The R bacilli are targeted by T cell-mediated immunity and burden is constrained. Strikingly, the S variant colonises host internal surfaces at high loads and is met with a robust innate immune response but little T cell-mediated immunity. Invasive granuloma formation is delayed in S variant infection compared to R variant infection upon which T cell-mediated immunity is required to control infection. In mixed infections, the S variant outcompetes the R variant. We also find the R variant activates host immunity to the detriment of S variant M. abscessus in mixed infections. These findings demonstrate the applicability of the adult zebrafish to model persistent M. abscessus infection and provide insight into the immunopathogenesis of chronic M. abscessus infection.
Theoretical properties of nearest-neighbor distance distributions and novel metrics for high dimensional bioinformatics data
Authors: Dawkins Bryan A. , Le Trang T. , McKinney Brett A.
Published: December 2019

The performance of nearest-neighbor feature selection and prediction methods depends on the metric for computing neighborhoods and the distribution properties of the underlying data. The effects of the distribution and metric, as well as the presence of correlation and interactions, are reflected in the expected moments of the distribution of pairwise distances. We derive general analytical expressions for the mean and variance of pairwise distances for Lq metrics for normal and uniform random data with p attributes and m instances. We use extreme value theory to derive results for metrics that are normalized by the range of each attribute (max – min). In addition to these expressions for continuous data, we derive similar analytical formulas for a new metric for genetic variants (categorical data) in genome-wide association studies (GWAS). The genetic distance distributions account for minor allele frequency and transition/transversion ratio. We introduce a new metric for resting-state functional MRI data (rs-fMRI) and derive its distance properties. This metric is applicable to correlation-based predictors derived from time series data. Derivations assume independent data, but empirically we also consider the effect of correlation. These analytical results and new metrics can be used to inform the optimization of nearest neighbor methods for a broad range of studies including gene expression, GWAS, and fMRI data. The summary of distribution moments and detailed derivations provide a resource for understanding the distance properties for various metrics and data types.
rgenesconverged : An R Package for the Exploration of Molecular Convergent Evolution
Authors: Issakova Dina
Published: December 2019

Sequence convergence is a type of convergent evolution that results in similarity between orthologous genetic sequences. However, this can be difficult to evaluate statistically given classical paradigms for convergent evolution, which rest on the assumption that convergent phenotypes are achieved by unrelated genetic mechanisms. While sophisticated models exist to model this process and to evaluate the probability of this explanation of genetic similarity across two different species, no tool has currently been implemented in R to carry out these analyses. Here we present rgenesconverged, an R package allowing the exploration of sequence convergence hypotheses in a given phylogeny.
High-throughput reclassification ofSCN5Avariants
Authors: Glazer Andrew M. , Wada Yuko , Li Bian , Muhammad Ayesha , Kalash Olivia R. , O’Neill Matthew J. , Shields Tiffany , Hall Lynn , Short Laura , Blair Marcia A. , Kroncke Brett M. , Capra John A. , Roden Dan M.
Published: December 2019

Rationale

Partial or complete loss of function variants inSCN5Aare the most common genetic cause of the arrhythmia disorder Brugada Syndrome (BrS1). However, the pathogenicity ofSCN5Avariants is often unknown or disputed; 80% of the 1,390SCN5Amissense variants observed in at least one individual to date are variants of uncertain significance (VUS). The designation of VUS is a barrier to the use of sequence data in clinical care.

Objective

We selected 83 variants for study: 10 previously studied control variants, 10 suspected benign variants, and 63 suspected Brugada Syndrome-associated variants, selected on the basis of their frequency in the general population and in patients with Brugada Syndrome. We used high-throughput automated patch clamping to study the function of the 83 variants, with the goal of reclassifying variants with functional data.

Methods and Results

Ten previously studied variants had functional properties concordant with published manual patch clamp data. All 10 suspected benign variants had wildtype-like function. 22 suspected BrS variants had loss of channel function (<10% normalized peak current) and 23 variants had partial loss of function (10-50% normalized peak current). The 73 previously unstudied variants were initially classified as likely benign (n=2), likely pathogenic (n=11), or VUS (n=60). After the patch clamp studies, 16 variants were benign/likely benign, 47 were pathogenic/likely pathogenic, and only 10 were still VUS. 8/22 loss of function variants were partially rescuable by incubation at lower temperature or pretreatment with a sodium channel blocker. Structural modeling identified likely mechanisms for loss of function including altered thermostability, and disruptions to alpha helices, disulfide bonds, or the permeation pore.

Conclusions

High-throughput automated patch clamping enabled the reclassification of the majority of tested VUS’s inSCN5A.
Diverse and complex muscle spindle afferent firing properties emerge from multiscale muscle mechanics
Authors: Blum Kyle P. , Campbell Kenneth S. , Horslen Brian C. , Nardelli Paul , Housley Stephen N. , Cope Timothy C. , Ting Lena H.
Published: December 2019

Abstract

Despite decades of research, we lack a mechanistic framework capable of predicting how movement-related signals are transformed into the diversity of muscle spindle afferent firing patterns observed experimentally, particularly in naturalistic behaviors. Here, a biophysical model demonstrates that well-known firing characteristics of muscle spindle Ia afferents – including dependence on movement history, and nonlinear scaling with muscle stretch velocity – emerge from first principles of muscle contractile mechanics. Further, mechanical interactions of the muscle spindle with muscle-tendon dynamics reveal how motor commands to the muscle (alpha drive) versus muscle spindle (gamma drive) can cause highly variable and complex activity during active muscle contraction and muscle stretch that defy simple explanation. Depending on the neuromechanical conditions, the muscle spindle model output appears to “encode” aspects of muscle force, yank, length, stiffness, velocity, and/or acceleration, providing an extendable, multiscale, biophysical framework for understanding and predicting proprioceptive sensory signals in health and disease.
The effect of single-task training on learning transfer to a novel bimanual task
Authors: Hadi Zaeem , Shakeel Aqsa , Ahmad Hafsa , Anwar Muhammad Nabeel , Navid Muhammad Samran
Published: December 2019

Background

The contextual interference effect suggests that the random practice of multiple-tasks is more beneficial for the retention and transfer of the learning as compared to blocked practice. Therefore, the transfer of learning is usually attributed to the contextual interference effect and is studied in a multi-task setting.

Objective

The goals of this study were to evaluate whether the transfer of learning (i) can occur when a single bimanual task is practiced, (ii) is affected by the knowledge of results (feedback), and (iii) sustains over an extended number of trials.

Methods

Fifty-two healthy subjects were equally divided into four groups. Before the transfer test, two groups practiced a bimanual finger-tapping task with feedback (EF) and without feedback (ENF). The third group (IM) practiced the same task using the kinesthetic motor imagery, whereas the last group acted as a control (CTRL) and performed only a bimanual button-pressing task used for the transfer test.

Results

Linear mixed-model showed that in the transfer test, groups EF, ENF and IM had similar performance but significantly higher scores compared to the CTRL group. Compared to the CTRL, the EF and IM groups showed significantly improved performance in most of the sessions but group ENF had similar results.

Conclusion

This study suggests that the single-task practice of a discrete bimanual task can facilitate the learning transfer to a novel task and knowledge of results (feedback) have no significant impact on the transfer of learning. Moreover, the transfer of learning effect does not disappear in extended trials.

Highlights

Single-task practice of a discrete bimanual task can facilitate the learning of a novel bimanual task

Knowledge of results (feedback) does not improve learning transfer in single-task setting

Transfer of learning effect does not disappear in extended trials
A common pattern of influenza A virus single cell gene expression heterogeneity governs the innate antiviral response to infection
Authors: Vera J. Cristobal , Sun Jiayi , Lin Yen Ting , Drnevich Jenny , Ke Ruian , Brooke Christopher B.
Published: December 2019

Viral infection outcomes are governed by the complex and dynamic interplay between the infecting virus population and the host response. It is increasingly clear that both viral and host cell populations are highly heterogeneous, but little is known about how this heterogeneity influences infection dynamics or viral pathogenicity. To dissect the interactions between influenza A virus (IAV) and host cell heterogeneity, we examined the combined host and viral transcriptomes of thousands of individual, single virion-infected cells. We observed complex patterns of viral gene expression and the existence of multiple distinct host transcriptional responses to infection at the single cell level. Our analyses reveal that viral NS segment gene expression diverges from that of the rest of the viral genome within a subset of infected cells, and that this unique pattern of NS segment expression can play a dominant role in shaping the host cell response to infection. Finally, we show that seasonal human H1N1 and H3N2 strains differ significantly in patterns of host anti-viral gene transcriptional heterogeneity at the single cell level. Altogether, these data reveal a common pattern of viral gene expression heterogeneity across human IAV subtypes that can serve as a major determinant of antiviral gene activation.
An Epigenetic LTR-retrotransposon insertion in the upstream region ofBnSHP1.A9controls quantitative pod shattering resistance inBrassica napus
Authors: Liu Jia , Zhou Rijin , Wang Wenxiang , Wang Hui , Qiu Yu , Rosy Raman , Mei Desheng , Harsh Raman , Hu Qiong
Published: December 2019

Seed loss resulting from pod shattering is a major problem in oilseed rape (Brassica napusL.) production worldwide. However, the molecular mechanisms underlying pod shatter resistance are not well understood. Here we show that the pod shatter resistance at quantitative trait locus, qSRI.A9.1 is controlled by aSHATTERPROOF1(SHP1) paralog inB. napus(BnSHP1.A9). Expression analysis by quantitative RT-PCR showed that BnSHP1.A9was specifically expressed in flower buds, flowers and developing siliques in the oilseed rape line (R1) carrying the qSRI.A9.1 allele with negative effect, but not expressed in any tissue of the line (R2) carrying the positive effect qSRI.A9.1 allele. Transgenic plants constitutively expressing BnSHP1.A9alleles from pod resistant and pod shattering parental lines showed that both alleles are responsible for pod shattering via promoting lignification of enblayer, which indicated allelic difference of BnSHP1.A9geneper seis not the causal factor of the QTL. The upstream sequence of BnSHP1.A9in the promotor region harboring highly methylated long terminal repeat retrotransposon insertion (LTR, 4803bp) in R2 repressed the expression of BnSHP.A9,and thus contributed to the positive effect on pod shatter resistance. Genetic and association analysis revealed that thecopiaLTR retrotransposon based markerBnSHP1.A9-R2can be used for breeding for pod shatter resistant varieties and reducing the loss of seed yield in oilseed rape.
Localizing components of shared transethnic genetic architecture of complex traits from GWAS summary data
Authors: Shi Huwenbo , Burch Kathryn S. , Johnson Ruth , Freund Malika K. , Kichaev Gleb , Mancuso Nicholas , Manuel Astrid M. , Dong Natalie , Pasaniuc Bogdan
Published: December 2019

Despite strong transethnic genetic correlations reported in the literature for many complex traits, the non-transferability of polygenic risk scores across populations suggests the presence of population-specific components of genetic architecture. We propose an approach that models GWAS summary data for one trait in two populations to estimate genome-wide proportions of population-specific/shared causal SNPs. In simulations across various genetic architectures, we show that our approach yields approximately unbiased estimates with in-sample LD and slight upward-bias with out-of-sample LD. We analyze 9 complex traits in individuals of East Asian and European ancestry, restricting to common SNPs (MAF > 5%), and find that most common causal SNPs are shared by both populations. Using the genome-wide estimates as priors in an empirical Bayes framework, we perform fine-mapping and observe that high-posterior SNPs (for both the population-specific and shared causal configurations) have highly correlated effects in East Asians and Europeans. In population-specific GWAS risk regions, we observe a 2.8x enrichment of shared high-posterior SNPs, suggesting that population-specific GWAS risk regions harbor shared causal SNPs that are undetected in the other GWAS due to differences in LD, allele frequencies, and/or sample size. Finally, we report enrichments of shared high-posterior SNPs in 53 tissue-specific functional categories and find evidence that SNP-heritability enrichments are driven largely by many low-effect common SNPs.
Comparative evaluation ofAspergillus nigerstrains for endogenous pectin depolymerization capacity and suitability for D-galacturonic acid production
Authors: Schäfer Dominik , Schmitz Kevin , Weuster-Botz Dirk , Benz J. Philipp
Published: December 2019

Pectinaceous agricultural residues rich ind-galacturonic acid (d-GalA), such as sugar beet pulp, are considered as promising feedstocks for waste-to-value conversions.Aspergillus nigeris known for its strong pectinolytic activity. However, while specialized strains for production of citric acid or proteins are openly available, this is not the case for the production of pectinases. We therefore systematically compared the pectinolytic capabilities of sixA. nigerstrains (ATCC 1015, ATCC 11414, NRRL 3122, CBS 513.88, NRRL 3, N402) using controlled batch cultivations in stirred-tank bioreactors.A. nigerATCC 11414 showed the highest polygalacturonase activity, specific protein secretion and a suitable morphology. Furthermore,d-GalA release from sugar beet pulp was 75% higher compared to the standard lab strainA. nigerN402. Our study therefore presents a robust initial strain selection to guide future process improvement ofd-GalA production from agricultural residues and identifies the most suitable base strain for further genetic optimizations.
Checkpoint defects require WRNIP1 to counteract R-loop-associated genomic instability
Authors: Marabitti Veronica , Lillo Giorgia , Malacaria Eva , Palermo Valentina , Pichierri Pietro , Franchitto Annapaola
Published: December 2019

Conflicts between replication and transcription are common source of genome instability and many factors participate in prevention or removal of harmful R-loops. Here, we demonstrate that a WRNIP1-mediated response plays an important role in counteracting accumulation of aberrant R-loops. Using human cellular models with compromised ATR-dependent checkpoint activation, we show that WRNIP1 is stabilised in chromatin and is needed for maintaining genome integrity by mediating the ATM-dependent phosphorylation of CHK1. Furthermore, we show that loss of WRN or ATR signalling leads to accumulation of R-loop-dependent parental ssDNA, which is covered by RAD51. We demonstrate that WRNIP1 chromatin retention is also required to stabilise the association of RAD51 with ssDNA in proximity of R-loops. Therefore, in these pathological contexts, ATM inhibition or WRNIP1 abrogation is accompanied by increased levels of genomic instability. Overall our findings reveal a novel function of WRNIP1 in preventing R-loop-driven genome instability, providing new clues to understand the way replication-transcription conflicts are resolved.
Cancer Associated Fibroblasts Mediate Cancer Progression and Remodel the Tumouroid Stroma
Authors: Pape Judith , Magdeldin Tarig , Stamati Katerina , Nyga Agata , Loizidou Marilena , Emberton Mark , Cheema Umber
Published: December 2019

Objective

Cancer associated fibroblasts (CAFs) are highly differentiated and heterogenous cancer stromal cells that promote tumour growth, angiogenesis and matrix remodelling.

Design

We utilised a novel 3D in vitro model of colorectal cancer, composed of a cancer mass and surrounding stromal compartment. We compared cancer invasion with an acellular stromal surround, a ‘healthy’ or normal cellular stroma and a cancerous stroma. For the cancerous stroma we incorporated six patient-derived CAF samples to study their differential effects on cancer growth, vascular network formation, and remodelling.

Results

CAFs enhanced the distance and surface area of the invasive cancer mass whilst inhibiting vascular-like network formation. These processes were driven by the upregulation of hepatocyte growth factor (HFG), metallopeptidase inhibitor 1 (TIMP1) and fibulin 5 (FBLN5).

Remodelling appeared to occur through the process of disruption of complex networks and was associated with the up upregulation of vascular endothelial growth factor (VEGFA) and down-regulation in vascular endothelial cadherin (VE-Cadherin).

Conclusion

These results support, within a biomimetic 3D, in vitro framework, the direct role of CAFs in promoting cancer invasion and that CAFs are also key components in driving vasculogenesis and angiogenesis.
Structural basis of RNA polymerase III transcription repression by Maf1
Authors: Vorländer Matthias K. , Baudin Florence , Moir Robyn D. , Wetzel René , Hagen Wim J. H. , Willis Ian M. , Müller Christoph W.
Published: December 2019

Maf1 is a highly conserved central regulator of transcription by RNA polymerase III (Pol III), and Maf1 activity influences a wide range of phenotypes from metabolic efficiency to lifespan. Here, we present a 3.3 Å cryo-EM structure of yeast Maf1 bound to Pol III, which establishes how Maf1 achieves transcription repression. In the Maf1-bound state, Pol III elements that are involved in transcription initiation are sequestered, and the active site is sealed off due to ordering of the mobile C34 winged helix 2 domain. Specifically, the Maf1 binding site overlaps with the binding site of the Pol III transcription factor TFIIIB and DNA in the pre-initiation complex, rationalizing that binding of Maf1 and TFIIIB to Pol III are mutually exclusive. We validate our structure using variants of Maf1 with impaired transcription-inhibition activity. These results reveal the exact mechanism of Pol III inhibition by Maf1, and rationalize previous biochemical data.
DeepSleep: Fast and Accurate Delineation of Sleep Arousals at Millisecond Resolution by Deep Learning
Authors: Li Hongyang , Guan Yuanfang
Published: December 2019

Sleep arousals are transient periods of wakefulness punctuated into sleep. Excessive sleep arousals are associated with many negative effects including daytime sleepiness and sleep disorders. High-quality annotation of polysomnographic recordings is crucial for the diagnosis of sleep arousal disorders. Currently, sleep arousals are mainly annotated by human experts through looking at millions of data points manually, which requires considerable time and effort. Here we present a deep learning approach, DeepSleep, which ranked first in the 2018 PhysioNet Challenge for automatically segmenting sleep arousal regions based on polysomnographic recordings. DeepSleep features accurate (area under receiver operating characteristic curve of 0.93), high-resolution (5-millisecond resolution), and fast (10 seconds per sleep record) delineation of sleep arousals.
Dissecting chronic myeloid leukaemia overlapping transcriptome with TIF-Seq2
Authors: Wang Jingwen , Li Bingnan , Marques Sueli , Steinmetz Lars M. , Wei Wu , Pelechano Vicent
Published: December 2019

Eukaryotic transcriptomes are complex involving thousands of overlapping transcripts. The interleaved nature of the transcriptome limits our ability to identify regulatory regions and, in some cases, can lead to misinterpretation of gene expression. To improve the understanding of the overlapping transcriptome, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5’ and 3’ ends of individual RNA molecules at single-nucleotide resolution. We investigated the transcriptome of a well characterized human cell line (K562) and identify thousands of unannotated transcript isoforms. By focusing on transcripts which are challenging to be investigated with RNA-seq, we accurately defined boundaries of lowly expressed unannotated and read-though transcripts putatively encoding fusion genes. We validated our results by targeted long-read sequencing and standard RNA-Seq for chronic myeloid leukaemia patient samples. Taking the advantage of TIF-Seq2, we explore transcription regulation among the overlapping units and investigate their crosstalk. We show that most overlapping upstream transcripts use poly(A) sites within the first 2 kb of the downstream transcription unit. Our work shows that, by paring the 5’ and 3’ end of each RNA, TIF-Seq2 can improve the annotation of complex genomes, facilitates accurate assignment of promoters to genes and easily identify transcriptionally fused genes.

Key points

Study of TSS-PAS co-occurrence allows dissecting complex overlapping transcription units.

Partially overlapping transcription units in human commonly use PAS within the first 2Kb.

TIF-Seq2 facilitates the identification of lowly expressed and transcriptionally fused genes.
Cascading Epigenomic Analysis for Identifying Disease Genes from the Regulatory Landscape of GWAS Variants
Authors: Ng Bernard , Casazza William , Kim Nam Hee , Wang Chendi , Farhadi Farnush , Tasaki Shinya , Bennett David A. , De Jager Philip L. , Gaiteri Christopher , Mostafavi Sara
Published: December 2019

The majority of genetic variants detected in genome wide association studies (GWAS) exert their effects on phenotypes through gene regulation. Motivated by this observation, we propose a multi-omic integration method that models the cascading effects of genetic variants from epigenome to transcriptome and eventually to the phenome in identifying target genes influenced by risk alleles. This cascading epigenomic analysis for GWAS, which we refer to as CEWAS, comprises two types of models: one for linkingcisgenetic effects to epigenomic variation and another for linkingcisepigenomic variation to gene expression. Applying these models in cascade to GWAS summary statistics generates gene level statistics that reflect genetically-driven epigenomic effects. We show on sixteen brain-related GWAS that CEWAS provides higher gene detection rate than related methods, and finds disease relevant genes and gene sets that point toward less explored biological processes. CEWAS thus presents a novel means for exploring the regulatory landscape of GWAS variants in uncovering disease mechanisms.

The majority of genetic variants detected in genome wide association studies (GWAS) exert their effects on phenotypes through gene regulation. Motivated by this observation, we propose a multi-omic integration method that models the cascading effects of genetic variants from epigenome to transcriptome and eventually to the phenome in identifying target genes influenced by risk alleles. This cascading epigenomic analysis for GWAS, which we refer to as CEWAS, combines the effect of genetic variants on DNA methylation as well as gene expression. We show on sixteen brain-related GWAS that CEWAS provides higher gene detection rate than related methods, and finds disease relevant genes and gene sets that point toward less explored biological processes.
SUSD4 Controls Activity-Dependent Degradation of AMPA Receptor GLUA2 and Synaptic Plasticity
Authors: González-Calvo I. , Iyer K. , Carquin M. , Khayachi A. , Giuliani F.A. , Vincent J. , Séveno M. , Sigoillot S.M. , Veleanu M. , Tahraoui S. , Albert M. , Vigy O. , Nadjar Y. , Dumoulin A. , Triller A. , Bessereau J.-L. , Rondi-Reig L. , Isope P. , Selimi F.
Published: December 2019

At excitatory synapses, the choice between recycling or degradation of glutamate AMPA receptors controls the direction of synaptic plasticity. In this context, how the degradation machinery is targeted to specific synaptic substrates in an activity-dependent manner is not understood. Here we show that SUSD4, a complement-related transmembrane protein, is a tether for HECT ubiquitin ligases of the NEDD4 subfamily, which promote the degradation of a large number of cellular substrates. SUSD4 is expressed by many neuronal populations starting at the time of synapse formation. Loss-of-function ofSusd4in the mouse prevents activity-dependent degradation of the GLUA2 AMPA receptor subunit and long-term depression at cerebellar synapses, and leads to impairment in motor coordination adaptation and learning. SUSD4 could thus act as an adaptor targeting NEDD4 ubiquitin ligases to AMPA receptors during long-term synaptic plasticity. These findings shed light on the potential contribution ofSUSD4mutations to the etiology of neurodevelopmental diseases.
Methylphenidate boosts choices of mental labor over leisure depending on baseline striatal dopamine
Authors: Hofmans Lieke , Papadopetraki Danae , van den Bosch Ruben , Määttä Jessica I. , Froböse Monja I. , Zandbelt Bram. B. , Westbrook Andrew , Verkes Robbert-Jan , Cools Roshan
Published: December 2019

The cognitive enhancing effects of methylphenidate are well established, but the mechanisms remain unclear. We recently demonstrated that methylphenidate boosts cognitive motivation by enhancing the weight on the benefits of a cognitive task in a manner that depended on striatal dopamine. Here we considered the complementary hypothesis that methylphenidate might also act by changing the weight on the opportunity cost of a cognitive task. To this end, fifty healthy participants (25 women) completed a novel cognitive effort discounting task that was sensitive to opportunity cost, and required choices between task and leisure. They were tested on methylphenidate, sulpiride or placebo and also underwent an [18F]DOPA PET scan to quantify baseline dopamine synthesis capacity. Methylphenidate boosted choices of cognitive effort over leisure across the group, and this effect was greatest in participants with more striatal dopamine at baseline. The effects of sulpiride did not reach significance. This study strengthens the motivational account of methylphenidate’s effects on cognition and suggests that methylphenidate reduces the cost of mental labor by increasing striatal dopamine.
Topologically Dependent Abundance of Spontaneous DNA Damage in Single Human Cells
Authors: Zhu Qiangyuan , Niu Yichi , Gundry Michael , Sheng Kuanwei , Niu Muchun , Zong Chenghang
Published: December 2019

In the studies of single-cell genomics, the large endeavor has been focused on the detection of the permanent changes in the genome. On the other hand, spontaneous DNA damage frequently occurs and results in transient single-stranded changes to the genome until they are repaired. So far, successful profiling of these dynamic changes has not been demonstrated by single-cell whole-genome amplification methods. Here we reported a novel single-cell WGA method: Linearly Produced Semiamplicon based Split Amplification Reaction (LPSSAR), which allows, for the first time, the genome-wide detection of the DNA damage associated single nucleotide variants (dSNVs) in single human cells. The sequence-based detection of dSNVs allows the direct characterization of the major damage signature that occurred in human cells. In the analysis of the abundance of dSNVs along the genome, we observed two modules of dSNV abundance, instead of a homogeneous abundance of dSNVs. Interestingly, we found that the two modules are associated with the A/B topological compartments of the genome. This result suggests that the genome topology directly influences genome stability. Furthermore, with the detection of a large number of dSNVs in single cells, we showed that only under a stringent filtering condition, can we distinguish the de novo mutations from the dSNVs and achieve a reliable estimation of the total level of de novo mutations in a single cell.
Characterization of transcription activation domain of EcaICE1 and its interaction with EcaSIZ1 in Eucalyptus camaldulensis
Authors: Zhang Ziyang , Cheng Ling , Zhang Weihua , Hu Jianlin , Liu Yan , Lin Yuanzhen
Published: December 2019

SUMOylation in plants is associated with biotic and abiotic stress responses, flowering and other aspects of development, and ICE1 protein SUMOylation by SUMO E3 ligase SIZ1 plays important roles in plant cold tolerance. Here, we reported the subcellular localization of EcaICE1 and its interaction with EcaSIZ1 in Eucalyptus camaldulensis. The genes EcaICE1 and EcaSIZ1 were isolated by homologous cloning. The subcellular localization analysis showed that EcaICE1 was located in nucleus. Bimolecular fluorescence complementation (BiFC) analysis revealed that EcaICE1 could interact with EcaSIZ1 in the nucleus of Nicotiana benthamiana leaves. Moreover, yeast two-hybrid assay confirmed that the amino acid region from position 84 to 126 in EcaICE1 was critical for the strong transactivation activity of EcaICE1 and that the C terminal region from position 361 to 557 in EcaICE1 was the key region for its interaction with EcaSIZ1 by using different truncated lengths of non-transactivation activity of EcaICE1 as the bait protein. Collectively, our results showed that EcaICE1 may have a SUMOylation pathway similar to Arabidopsis thaliana.
Functional magnetic resonance imaging of regional impaired cerebrovascular reactivity for migraineurs in the interictal state
Authors: Chan Suk-tak , Evans Karleyton C. , Song Tian-yue , Gupta Rajiv , Rosen Bruce R. , Singhal Aneesh , Kwong Kenneth K.
Published: December 2019

There is still an unmet need of mapping the potential impairment of cerebrovascular reactivity (CVR) in episodic migraineurs in the interictal state. We mapped CVR of 6 episodic migraineurs and 5 headache-free controls (HC) with blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) under carbon dioxide (CO2) challenge of 30-second epochs with elevated end-tidal partial pressure of CO2 (PETCO2) by 4-8mmHg. Three migraineurs have migraine without aura (MOA) and the other three have migraine with aura (MA). We found that only MOA subjects showed a reduced or negative BOLD response to CO2 at the red nucleus. All 3 MOA subjects were characterized by bilateral posterior communicating artery hypoplasia (bPCAH) identified by MR angiography (MRA). MOA and HC subjects did not show any significant difference in BOLD responses to CO2 challenge in cortical and white matter while MA subjects showed poor positive association between BOLD responses and PETCO2 in large territories of the cortex and white matter tracts. The combined use of fMRI under CO2 challenge and MRA presented a unique approach to investigate the mechanisms of episodic migraine in the interictal state demonstrating for the first time negative CVR at the red nucleus of the midbrain in patients with MOA. CVR maps obtained from both the midbrain and cortical regions provided various signatures to explore the differences between migraineurs and HC and between MOA and MA.
Task rule and choice are reflected by layer-specific processing in rodent auditory cortical microcircuits
Authors: Zempeltzi Marina M. , Kisse Martin , Brunk Michael G. K. , Glemser Claudia , Aksit Sümeyra , Deane Katrina E. , Maurya Shivam , Schneider Lina , Ohl Frank W. , Deliano Matthias , Happel Max F. K.
Published: December 2019

The primary auditory cortex (A1) is an essential node in the integrative brain network that encodes the behavioral relevance of acoustic stimuli, predictions, and auditory-guided decision making. Previous studies have revealed task-related information being present at both the single-unit and population activity. However, its realization with respect to the cortical microcircuitry is less well understood. In this study, we used chronic, laminar current source density (CSD) analysis from the A1 of behaving Mongolian gerbils (Meriones unguiculatus) in order to characterize layer-specific, spatiotemporal synaptic population activity. Animals were trained to first detect and subsequently to discriminate two pure tone frequencies in consecutive training phases in a Go/NoGo shuttle-box task. We demonstrate that not only sensory but also task- and choice-related information is represented in the mesoscopic neuronal population code distributed across cortical layers. Based on a single-trial analysis using generalized linear-mixed effect models (GLMM), we found infragranular layers to be involved in auditory-guided action initiation during tone detection. Supragranular layers, particularly, are involved in the coding of choice options during tone discrimination. Further, we found that the overall columnar synaptic network activity represents the accuracy of the opted choice. Our study thereby suggests a multiplexed representation of stimulus features in dependence of the task, action selection, and the behavioral options of the animal in preparation of correct choices. The findings expand our understanding of how individual layers contribute to the integrative circuit of the A1 in order to code task-relevant information and guide sensory-based decision making.
LiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes
Authors: Piazza Ilaria , Beaton Nigel , Bruderer Roland , Knobloch Thomas , Barbisan Crystel , Siepe Isabella , Rinner Oliver , de Souza Natalie , Picotti Paola , Reiter Lukas
Published: December 2019

Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in developing optimized small-molecule compounds. Current unbiased approaches cannot directly pinpoint the interaction surfaces between ligands and protein targets. To address his limitation we have developed a new drug target deconvolution approach based on limited proteolysis coupled with mass spectrometry that works across species including human cells (LiP-Quant). LiP-Quant features an automated data analysis pipeline and peptide-level resolution for the identification of any small-molecule binding sites, Here we demonstrate drug target identification by LiP-Quant across compound classes, including compounds targeting kinases and phosphatases. We demonstrate that LiP-Quant estimates the half maximal effective concentration (EC50) of compound binding sites in whole cell lysates. LiP-Quant identifies targets of both selective and promiscuous drugs and correctly discriminates drug binding to homologous proteins. We finally show that the LiP-Quant technology identifies targets of a novel research compound of biotechnological interest.
Mass-spectrometry based proteomics reveals mitochondrial supercomplexome plasticity
Authors: Gonzalez-Franquesa Alba , Stocks Ben , Chubanava Sabina , Hattel Helle Baltzer , Moreno-Justicia Roger , Treebak Jonas T. , Zierath Juleen R. , Deshmukh Atul S.
Published: December 2019

Mitochondrial respiratory complex subunits assemble in supercomplexes. Studies of supercomplexes have typically relied upon antibody-based protein quantification, often limited to the analysis of a single subunit per respiratory complex. To provide a deeper insight into mitochondrial and supercomplex plasticity, we combined Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) and mass spectrometry to determine the supercomplexome of skeletal muscle from sedentary and exercise-trained mice. We quantified 422 mitochondrial proteins within ten supercomplex bands, in which we showed the debated presence of complex II and V. Upon exercise-induced mitochondrial biogenesis, non-stoichiometric changes in subunits and incorporation into supercomplexes was apparent. We uncovered the dynamics of supercomplex-related assembly proteins and mtDNA-encoded subunits within supercomplexes, as well as the complexes of ubiquinone biosynthesis enzymes and Lactb, a mitochondrial-localized protein implicated in obesity. Our approach can be applied to broad biological systems. In this instance, comprehensively analyzing respiratory supercomplexes illuminates previously undetectable complexity in mitochondrial plasticity.

Highlights

Comprehensive quantification of respiratory subunits within supercomplexes

Complex II and V assemble within supercomplexes

Mitochondrial-encoded subunits display elevated upregulation upon exercise training

Exercise increases ubiquinone biosynthesis enzyme complexes
Lateral mechanical impedance rather than frontal, promotes cortical expansion of roots
Authors: Feng Xuanjun , Xiong Jing , Hu Yue , Pan Liteng , Liao Zhengqiao , Zhang Xuemei , Guo Wei , Wu Fengkai , Xu Jie , Hu Erliang , Lan Hai , Lu Yanli
Published: December 2019

It has long been considered that mechanical impedance on root will restrict root elongation and consequently promote radial growth. However, we did observe radial expansion but not elongation restriction in maize seedlings after short growth in sands. Mechanical impedance of soil can be classified into frontal- and lateral-type based on the interaction site of root. Therefore, we suspected that radial expansion might be mainly stimulated by lateral rather than frontal impedance. To verify our speculation, frontal and lateral impedance was provided separately. Small plastic caps were used to provide unique frontal impedance on root tip and cylindrical plastic containers were used to provide lateral impedance. Plastic caps could reduce root length remarkably. However, the radial expansion of plastic-cap-fitted roots was significantly inferior to that of the sand-cultured roots. Microstructural analysis revealed that sand-condition thickened root largely dependents on cortical expansion, whereas plastic cap did it mainly by thickening stele. In cylindrical plastic containers, mechanical impedance came only from the lateral direction and promoted the expansion of cortex just as sand-condition. Thus, we proposed that the expansion of the cortex and the consequent radial growth is mainly due to lateral impedance when growing in sands.