bluuebunny/crossref_metadata_2025 huggingface dataset:
Variants in ACE2 and TMPRSS2 genes are not major determinants of COVID-19 severity in UK Biobank subjects
Authors: Curtis David
Published: May 2020

It is plausible that variants in the ACE2 and TMPRSS2 genes might contribute to variation in COVID-19 severity and that these could explain why some people become very unwell whereas most do not. Exome sequence data was obtained for 49,953 UK Biobank subjects of whom 74 had tested positive for SARS-CoV-2 and could be presumed to have severe disease. A weighted burden analysis was carried out using SCOREASSOC to determine whether there were differences between these cases and the other sequenced subjects in the overall burden of rare, damaging variants in ACE2 or TMPRSS2. There were no statistically significant differences in weighted burden scores between cases and controls for either gene. There were no individual DNA sequence variants with a markedly different frequency between cases and controls. Whether there are small effects on severity, or whether there might be rare variants with major effect sizes, would require studies in much larger samples. Genetic variants affecting the structure and function of the ACE2 and TMPRSS2 proteins are not a major determinant of whether infection with SARS-CoV-2 results in severe symptoms. This research has been conducted using the UK Biobank Resource.
Sleep Deficits and Cannabis Use Behaviors: An Analysis of Shared Genetics Using Linkage Disequilibrium Score Regression and Polygenic Risk Prediction
Authors: Winiger Evan A. , Ellingson Jarrod M. , Morrison Claire L. , Corley Robin P. , Pasman Joëlle A. , Wall Tamara L. , Hopfer Christian J. , Hewitt John K.
Published: May 2020

Study Objectives

Estimate the genetic relationship of cannabis use with sleep deficits and eveningness chronotype.

Methods

We used linkage disequilibrium score regression (LDSC) to analyze genetic correlations between sleep deficits and cannabis use behaviors. Secondly, we generated sleep deficit polygenic risk scores (PRSs) and estimated their ability to predict cannabis use behaviors using logistic regression. Summary statistics came from existing genome wide association studies (GWASs) of European ancestry that were focused on sleep duration, insomnia, chronotype, lifetime cannabis use, and cannabis use disorder (CUD). A target sample for PRS prediction consisted of high-risk participants and participants from twin/family community-based studies (n = 796, male = 66%; mean age = 26.81). Target data consisted of self-reported sleep (sleep duration, feeling tired, and taking naps) and cannabis use behaviors (lifetime use, number of lifetime uses, past 180-day use, age of first use, and lifetime CUD symptoms).

Results

Significant genetic correlation between lifetime cannabis use and eveningness chronotype (rG = 0.24,p< 0.01), as well as between CUD and both short sleep duration (<7 h) (rG = 0.23,p= 0.02) and insomnia (rG = 0.20,p= 0.02). Insomnia PRS predicted earlier age of first cannabis use (β= −0.09,p= 0.02) and increased lifetime CUD symptom count use (β= 0.07,p= 0.03).

Conclusion

Cannabis use is genetically associated with both sleep deficits and an eveningness chronotype, suggesting that there are genes that predispose individuals to both cannabis use and sleep deficits.
Clarithromycin Exerts an Antibiofilm Effect againstSalmonella typhimuriumrdar Biofilm Formation, and Transforms the Physiology towards an Apparent Oxygen-depleted Energy and Carbon Metabolism
Authors: Zafar Munira , Jahan Humera , Shafeeq Sulman , Nimtz Manfred , Jänsch Lothar , Römling Ute , Choudhary M. Iqbal
Published: May 2020

Upon biofilm formation, production of extracellular matrix components and alteration in physiology and metabolism allows bacteria to build up multicellular communities which can facilitate nutrient acquisition during unfavorable conditions and provide protection towards various forms of environmental stresses to individual cells. Thus, bacterial cells become tolerant against antimicrobials and the immune system within biofilms. In the current study, we evaluated the antibiofilm activity of the macrolides clarithromycin and azithromycin. Clarithromycin showed antibiofilm activity against rdar (red, dry and rough) biofilm formation of the gastrointestinal pathogenSalmonella typhimuriumATCC14028 Nalrat 1.56 μM subinhibitory concentration in standing culture and dissolved cell aggregates at 15 μM in a microaerophilic environment suggesting that the oxygen level affects the activity of the drug. Treatment with clarithromycin significantly decreased transcription and production of the rdar biofilm activator CsgD, with biofilm genes such ascsgBandadrAto be consistently downregulated. WhilefliAand other flagellar regulon genes were upregulated, apparent motility was downregulated. RNA sequencing showed a holistic cell response upon clarithromycin exposure, whereby not only genes involved in the biofilm-related regulatory pathways, but also genes that likely contribute to intrinsic antimicrobial resistance, and the heat shock stress response were differentially regulated. Most significantly, clarithromycin exposure shifts the cells towards an apparent oxygen- and energy-depleted status, whereby the metabolism that channels into oxidative phosphorylation is downregulated, and energy gain by degradation of propane 1,2-diol, ethanolamine and L-arginine catabolism is upregulated. This initial analysis will allow the subsequent identification of novel intrinsic antimicrobial resistance determinants.
Precise optical control of gene expression inC. elegansusing genetic code expansion and Cre recombinase
Authors: Davis Lloyd , Radman Inja , Goutou Angeliki , Tynan Ailish , Baxter Kieran , Xi Zhiyan , O’Shea Jack M. , Chin Jason W. , Greiss Sebastian
Published: May 2020

Synthetic strategies for optically controlling gene expression may enable the precise spatiotemporal control of genes in any combination of cells that cannot be targeted with specific promoters. We develop an efficient genetic code expansion system inC. elegansand use it to create a photo-activatable Cre recombinase. We laser-activate Cre in single neurons within a bilaterally symmetric pair to selectively switch on expression of a loxP controlled optogenetic channel in the targeted neuron. We use the system to dissect, in freely moving animals, the individual contributions of the mechanosensory neurons PLML/PLMR to theC. eleganstouch response circuit, revealing distinct and synergistic roles for these neurons. We thus demonstrate how genetic code expansion and optical targeting can be combined to break the symmetry of neuron pairs and dissect behavioural outputs of individual neurons that cannot be genetically targeted.
Release of potential pro-inflammatory peptides from SARS-CoV-2 spike glycoproteins in neutrophil-extracellular traps
Authors: Blanco-Míguez Aitor , Sánchez Borja
Published: May 2020

COVID-2019 has progressed in around 10-15% of patients to an acute respiratory distress syndrome characterized by extensive pulmonary inflammation and elevated production of pro-inflammatory cytokines. Neutrophil activation seems to be crucial in the initiation and perpetuation of this exacerbated lung inflammation. However, the precise mechanisms by which this activation occurs remain yet elusive. To this end, this in silico study tried to identify potential proinflammatory inducing peptides (PIPs) produced by the action of the elastase released in neutrophil-extracellular traps over SARS-CoV-2 particles. We found nine potential PIPs exclusive from the SARS-CoV-2, showing homology against T cell recognition epitopes. Moreover, 78 percent of these exclusive PIPs were found produced by the enzymatic cleavage on the spike glycoproteins, suggesting that high PIP concentrations might be released following SARS-CoV-2 huge replication rate. Therefore, these PIPs might play a role in the exacerbated inflammatory response observed in some patients.

Highlights

Nine potential PIPs were predicted exclusive from the SARS-CoV-2.

SARS-CoV-2 PIPs showed homology against T cell recognition epitopes.

Most of PIPs were produced by enzymatic cleavage of the spike glycoproteins.

The release of these PIPs might be related to the increased inflammatory response observed in the patients.

Graphical abstract
Formation of biomolecular condensates in bacteria by tuning protein electrostatics
Authors: Yeong Vivian , Werth Emily G. , Brown Lewis M. , Obermeyer Allie C.
Published: May 2020

Biomolecular condensates provide a strategy for cellular organization without a physical membrane barrier while allowing for dynamic, responsive organization of the cell. To date, very few biomolecular condensates have been identified in prokaryotes, presenting an obstacle to engineering these compartments in bacteria. As a novel strategy for bacterial compartmentalization, protein supercharging and complex coacervation were employed to engineer liquid-like condensates inE. coli. A simple model for the phase separation of supercharged proteins was developed and used to predict intracellular condensate formation. Herein, we demonstrate that GFP-dense condensates formed by expressing GFP variants of sufficient charge in cells are dynamic and enrich specific nucleic acid and protein components. This study provides a fundamental characterization of intracellular phase separation inE. colidriven by protein supercharging and highlights future utility in designing functional synthetic membraneless organelles.
Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids
Authors: Duan Xiaohua , Han Yuling , Yang Liuliu , Nilsson-Payant Benjamin E. , Wang Pengfei , Zhang Tuo , Xiang Jenny , Xu Dong , Wang Xing , Uhl Skyler , Huang Yaoxing , Chen Huanhuan Joyce , Wang Hui , tenOever Benjamin , Schwartz Robert E. , Ho David. D. , Evans Todd , Pan Fong Cheng , Chen Shuibing
Published: May 2020

Summary Paragraph

The current COVID-19 pandemic is caused by SARS-coronavirus 2 (SARS-CoV-2). There are currently no therapeutic options for mitigating this disease due to lack of a vaccine and limited knowledge of SARS-CoV-2 biology. As a result, there is an urgent need to create new disease models to study SARS-CoV-2 biology and to screen for therapeutics using human disease-relevant tissues. COVID-19 patients typically present with respiratory symptoms including cough, dyspnea, and respiratory distress, but nearly 25% of patients have gastrointestinal indications including anorexia, diarrhea, vomiting, and abdominal pain. Moreover, these symptoms are associated with worse COVID-19 outcomes1. Here, we report using human pluripotent stem cell-derived colonic organoids (hPSC-COs) to explore the permissiveness of colonic cell types to SARS-CoV-2 infection. Single cell RNA-seq and immunostaining showed that the putative viral entry receptor ACE2 is expressed in multiple hESC-derived colonic cell types, but highly enriched in enterocytes. Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validatedin vivousing a humanized mouse model. We used hPSC-derived COs in a high throughput platform to screen 1280 FDA-approved drugs against viral infection. Mycophenolic acid and quinacrine dihydrochloride were found to block the infection of SARS-CoV-2 pseudo-entry virus in COs bothin vitroandin vivo, and confirmed to block infection of SARS-CoV-2 virus. This study established bothin vitroandin vivoorganoid models to investigate infection of SARS-CoV-2 disease-relevant human colonic cell types and identified drugs that blocks SARS-CoV-2 infection, suitable for rapid clinical testing.
Rapid adaptation of SARS-CoV-2 in BALB/c mice: Novel mouse model for vaccine efficacy
Authors: Gu Hongjing , Chen Qi , Yang Guan , He Lei , Fan Hang , Deng Yong-Qiang , Wang Yanxiao , Teng Yue , Zhao Zhongpeng , Cui Yujun , Li Yuchang , Li Xiao-Feng , Li Jiangfan , Zhang Nana , Yang Xiaolan , Chen Shaolong , Zhao Guangyu , Wang Xiliang , Luo Deyan , Wang Hui , Yang Xiao , Li Yan , Han Gencheng , He Yuxian , Zhou Xiaojun , Geng Shusheng , Sheng Xiaoli , Jiang Shibo , Sun Shihui , Qin Cheng-Feng , Zhou Yusen
Published: May 2020

Coronavirus disease 2019 (COVID-19) threatens global public health and economy. In order to develop safe and effective vaccines, suitable animal models must be established. Here we report the rapid adaption of SARS-CoV-2 in BALB/c mice, based on which a convenient, economical and effective animal model was developed. Specifically, we found that mouse-adapted SARS-CoV-2 at passage 6 (MACSp6) efficiently infected both aged and young wild-type BALB/c mice, resulting in moderate pneumonia as well as inflammatory responses. The elevated infectivity of MACSp6 in mice could be attributed to the substitution of a key residue (N501Y) in the receptorbinding domain (RBD). Using this novel animal model, we further evaluated the in vivo protective efficacy of an RBD-based SARS-CoV-2 subunit vaccine, which elicited highly potent neutralizing antibodies and conferred full protection against SARS-CoV-2 MACSp6 challenge. This novel mouse model is convenient and effective in evaluating thein vivoprotective efficacy of SARS-CoV-2 vaccine.

This study describes a unique mouse model for SARS-CoV-2 infection and confirms protective efficacy of a SARS-CoV-2 RBD subunit vaccine.
Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars
Authors: Raza Qasim , Riaz Awais , Bashir Khurram , Sabar Muhammad
Published: May 2020

Rice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied in detail before. Remarkably, all these genes corresponded to various stress associated functions, ranging from abiotic stress sensing to regulating plant stress responses, and included heat-shock genes (OsBiP2, OsMed37_1), transcription factors (OsNAS3, OsTEF1, OsWRKY10, OsWRKY21), transmembrane transporters (OsAAP7A, OsAMT2;1), sugar metabolizing (OsSUS4, α-Gal III) and abiotic stress (OsRCI2-7, SRWD1) genes. Functional data evidences fromArabidopsisheat-shock genes also suggest thatOsBIP2may be associated with thermotolerance of pollen tubes under heat stress conditions. Furthermore, promoters of identified genes were enriched with heat, dehydration, pollen and sugar responsive cis-acting regulatory elements, proposing a common regulatory mechanism might exist in rice for mitigsating reproductive stage heat stress. These findings strongly support our results and provide new candidate genes for fast-track development of heat-tolerant rice cultivars.

Key Message

By integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be exploited through marker-assisted breeding for fast-track development of heat-tolerant rice cultivars.
LINE-1 DNA methylation in response to aging and vitamin D
Authors: Ong Lawrence T. C. , Schibeci Stephen D , Fewings Nicole L , Booth David R , Parnell Grant P
Published: May 2020

Retrotransposons are genetic elements capable of their own propagation and insertion into the human genome. Because of their mutagenic potential, retrotransposons are heavily suppressed by mechanisms including DNA methylation. Increased age is associated with decreasing DNA methylation of the LINE-1 retrotransposon and may partially explain the predisposition towards malignancy with advancing age. Vitamin D has been investigated for its effects on DNA methylation at LINE-1 elements with mixed results. This study hypothesised that LINE-1 DNA methylation is altered by vitamin D exposure and age. Using whole genome bisulfite sequencing of adult and newborn haematopoietic progenitors, DNA methylation at LINE-1 elements was not found to vary between cells cultured with or without calcitriol, both in adults and newborns. In contrast, several LINE-1 regions were found to be differentially methylated between adults and children, but these were not uniformly hypermethylated in paediatric cells. The results of this study suggest that at least in haematopoietic cells, vitamin D does not appear to affect LINE-1 methylation.
In vivoinducible reverse genetics in patients’ tumors to identify individual therapeutic targets
Authors: Carlet Michela , Völse Kerstin , Vergalli Jenny , Becker Martin , Herold Tobias , Arner Anja , Liu Wen-Hsin , Dill Veronika , Fehse Boris , Baldus Claudia D. , Bastian Lorenz , Lenk Lennart , Schewe Denis M. , Bagnoli Johannes W. , Jost Philipp J. , Miehting Cornelius , Riecken Kristoffer , Schmidt-Supprian Marc , Binder Vera , Jeremias Irmela
Published: May 2020

High-throughput sequencing describes multiple alterations in each tumor (1), but their functional relevance is often unclear. Clinic-close, individualized molecular model systems are required for functional validation and to identify therapeutic targets of high significance for each patient (2). Here, we established a Cre-ERT2-loxP based inducible RNAi-mediated gene silencing system in patient-derived xenograft (PDX) models of acute leukemiasin vivo. Mimicking anti-cancer therapy in patients, gene inhibition was initiated in mice harboring orthotopic tumors. Fluorochrome guided, competitivein vivotrials identified a major tumor-maintaining potency of the MLL-AF4 fusion protein and validated MCL1 as vulnerability in some, but not all patients’ tumors. We could prove DUX4 to play an essential role in patients’ leukemias carrying the recently described DUX4-IGH translocation. By individualizing functional genomics in established tumorsin vivo, our technique decisively complements the value chain of precision oncology. Being broadly applicable to tumors of all kinds, it will considerably reinforce personalizing anti-cancer treatment in the future.
Drosophilainsulin-like peptide 8 (DILP8) in ovarian follicle cells regulates ovulation and metabolism
Authors: Liao Sifang , Nässel Dick R.
Published: May 2020

InDrosophilaeight insulin-like peptides (DILP1-8) are encoded on separate genes. These DILPs are characterized by unique spatial and temporal expression patterns during the lifecycle. Whereas functions of several of the DILPs have been extensively investigated at different developmental stages, the role of DILP8 signaling is primarily known from larvae and pupae where it couples organ growth and developmental transitions. In adult female flies, a study showed that a specific set of neurons that express the DILP8 receptor, Lgr3, is involved in regulation of reproductive behavior. Here, we further investigated the expression ofdilp8/DILP8 andLgr3in adult female flies and the functional role of DILP8 signaling. The only site where we found bothdilp8expression and DILP8 immunolabeling was in follicle cells of mature ovaries.Lgr3expression was detected in numerous neurons in the brain and ventral nerve cord, a small set of peripheral neurons innervating the abdominal heart, as well as in a set of follicle cells close to the oviduct. Ovulation was affected indilp8mutants as well as afterdilp8-RNAi usingdilp8and follicle cell Gal4 drivers. More eggs were retained in the ovaries and fewer were laid, indicating that DILP8 is important for ovulation. Our data suggest that DILP8 signals locally toLgr3expressing follicle cells as well as systemically toLgr3expressing efferent neurons in abdominal ganglia that innervate oviduct muscle. Thus, DILP8 may act at two targets to regulate ovulation: follicle cell rupture and oviduct contractions. Furthermore, we could show that manipulations ofdilp8expression affect food intake and starvation resistance. Possibly this reflects a feedback signaling between ovaries and the CNS that ensures nutrients for ovary development. In summary, it seems that DILP8 signaling in regulation of reproduction is an ancient function, conserved in relaxin signaling in mammals.
Expression analysis of defense-related genes in cucumber (Cucumis sativusL.) againstPhytophthora melonis
Authors: Hashemi Lida , Golparvar Ahmad Reza , Esfahani Mehdi Nasr , Golabadi Maryam
Published: May 2020

Phytophthora melonisis the causal agent of damping-off or crown rot, one of the most destructive cucumber diseases that causes severe economic losses in Iran and some other parts of the world. Despite intense research efforts made in the past years, no permanent cure currently exists for this disease. With the aim to understand the molecular mechanisms of defense againstP. melonis, root collars and leaves of four cucumber genotypes consisting of resistant Ramezz; moderately resistant Baby and very susceptible Mini 6-23 and Extrem, were monitored for quantitative gene expression analysis of five antifungal and/or anti-oomycete genes (CsWRKY20, CsLecRK6.1, PR3, PR1-1aandLOX1) at three points after inoculation withP. melonis. The gene expression analysis indicated thatP. melonisstrongly enhanced the expression of these genes after inoculation in both leaves and root collars. Further, not only the transcript levels of these genes were significantly higher in the resistant and moderately resistance genotypes, but also the time point of the highest relative expression ratio for the five genes was different in the four cucumber genotypes.CsWRKY20andPR3showed the maximum expression in Ramezz at 48 hours post inoculation (hpi) whileCsLecRK6.1, andLOX1showed the highest expression at 72 hpi. In addition,PR1-1ashowed the maximum expression in the Baby at 72 hpi. Root collars responded faster than leaves and some responses were more strongly up-regulated in root collars than in leaves. The genes found to be involved in disease resistance in two different organs of cucumber after pathogen infection. The results suggest that increased expression of these genes led to activation of defense pathways and could be responsible for a reducedP. meloniscolonization capacity in Ramezz and Baby. Overall, this work represents a valuable resource for future functional genomics studies to unravel the molecular mechanisms ofC. sativus-P. melonisinteraction.
Wood structure explained by complex spatial source-sink interactions
Authors: Friend Andrew D.
Published: May 2020

Wood is a remarkable material. It is responsible for the sequestration of significant anthropogenic CO21, aids understanding of past climates2, has unique acoustic, thermal, and strength properties, and is an endlessly renewable source of energy3. However, we lack a general integrated understanding of how its structure is created. A theoretical framework of wood formation is presented here that explains a diverse range of poorly understood observations, including: (i) the anatomy of growth rings, with a transition from low-density earlywood to high-density latewood; (ii) the high sensitivity of latewood density to temperature; (iii) cell-size regulation; and (iv) relationships between growth and temperature. These features arise from interactions in time and space between the production of cells, the dynamics of developmental zones, and the supply of carbohydrates. Carbohydrate distribution is critical for the final density profile, challenging current theory which emphasises compensation between the rates and durations of cell enlargement and wall thickening. These findings have implications for our understanding of how growth responds to environmental variability and the interpretation of tree rings as proxies of past climates. In addition, they provide a framework for the incorporation of explicit growth processes into models, such as those used to predict the role of vegetation in the future global carbon cycle. Finally, divergent responses in volume and mass with increasing temperature suggest caution in interpreting observations based on volume alone.
Probabilistic Approach to Understand Errors in Sequencing and its based Applications
Authors: Singh Anuj
Published: May 2020

Next Generation Sequencing has been applied in many areas of biology, including quantification of gene expression, Genome-Wide Association Study (GWAS), gene finding, Motif discovery and much more. Due to the vast area of application and importance in key findings in the field, massive genomic data is being generated using high throughput sequencing. Therefore, sequencing quality also needs to be evaluated in light of different applications. In order to develop effective diagnostic and therapeutic approaches, we need to accurately characterize and identify sequencing errors and distinguish these errors from their true genetic variant in sequencing, i.e. misreads follow a binomial distribution and it further can be approximated to the Poisson process for longer sequences. However, the insertion and deletion rates are 1000 times lower than substitution error rates and, therefore, less significant. The model assumes that error arrival at a position is not dependent on an error at other positions. Furthermore, errors in sequences can cause an error in studies based on multiple sequences and they also follow Binomial – Poisson Distribution (for example – Alignment is a merging of two Binomial processes for short sequences and it further can be approximated to Poisson for long sequences (for example – genomic sequence). It provides a systematic way to evaluate the accuracy in sequencing-based applications. Many error suppressing algorithms or techniques are there, and our Binomial Poisson model can provide a further systematic understanding of error behavior in short sequences so that more techniques for error removal can be developed with much efficient suppression rates.
NuMA interaction with chromatin is vital for proper nuclear architecture in human cells
Authors: Rajeevan Ashwathi , Keshri Riya , Kotak Sachin
Published: May 2020

NuMA is an abundant long-coiled-coil protein that plays a prominent role in spindle organization during mitosis. In interphase, NuMA is localized to the nucleus and hypothesized to control gene expression and chromatin organization. However, because of the prominent mitotic phenotype upon NuMA loss, its precise function in the interphase nucleus remains elusive. Here, we report that NuMA is associated with chromatin in interphase and prophase but released upon nuclear envelope breakdown(NEBD) by the action of Cdk1. We uncovered that NuMA directly interacts with DNA via evolutionarily conserved sequences in its C-terminus. Notably, the expression of the DNA-binding mutant of NuMA affects chromatin decondensation at the mitotic exit, and nuclear shape in interphase. The impact on nuclear shape by mutant NuMA expression is due to its potential to polymerize into high-order fibrillar structures. This study links the chromatin binding ability of NuMA with the maintenance of nuclear shape and architecture, which has a well-studied role in regulating gene expression during development and diseases.
Structure of the full kinetoplastids mitoribosome and insight on its large subunit maturation
Authors: Soufari Heddy , Waltz Florent , Parrot Camila , Durrieu Stéphanie , Bochler Anthony , Kuhn Lauriane , Sissler Marie , Hashem Yaser
Published: May 2020

Kinetoplastids are unicellular eukaryotic parasites responsible for human pathologies such as Chagas disease, sleeping sickness or Leishmaniasis1. They possess a single large mitochondrion, essential for the parasite survival2. In kinetoplastids mitochondrion, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes3. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes4,5. Structural studies performed inTrypanosoma bruceialready highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit3,6. However, several important aspects mainly related to the large subunit remain elusive, such as the structure and maturation of its ribosomal RNA3. Here, we present a cryo-electron microscopy study of the protozoansLeishmania tarentolaeandTrypanosoma cruzimitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the large subunit as well as previously unidentified ribosomal proteins. Most importantly, we introduce the structure of an LSU assembly intermediate in presence of 16 identified maturation factors. These maturation factors act both on the intersubunit and solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.
Enhanced FGFR3 activity in post-mitotic principal neurons during brain development results in cortical dysplasia and axon miswiring
Authors: Huang Jui-Yen , Krebs Bruna Baumgarten , Miskus Marisha Lynn , Russell May Lin , Duffy Eamonn Patrick , Graf Jason Michael , Lu Hui-Chen
Published: May 2020

Abnormal levels of fibroblast growth factors (FGFs) and FGF receptors (FGFRs) have been detected in various neurological disorders. The potent impact of FGF-FGFR in multiple embryonic developmental processes makes it challenging to elucidate their roles in post-mitotic neurons. Taking an alternative approach, we directly examined the impact of aberrant FGFR function after neurogenesis by generating a FGFR gain-of-function (GOF) transgenic mouse which expresses constitutively activated FGFR3 (FGFR3K650E) in post-mitotic glutamatergic neurons. We found that enhanced FGFR activity in glutamatergic neurons results in abnormal radial migration and axonal miswiring. Regarding the lamination phenotype in GOF brains, we found later-born Cux1-positive neurons are dispersed throughout the GOF cortex. Such a cortical migration deficit is likely caused, at least in part, by a significant reduction of the radial processes normally projecting from the radial glia cells (RGCs). In addition, FGFR3 GOF also results in the misrouting of several long-range axonal projections, including the corpus callosum, anterior commissure, and postcommissural fornix. RNA-sequencing analysis of the GOF embryonic cortex reveals significant alterations in several pathways involved in cell cycle regulation and axonal pathfinding. Collectively, our results suggest that FGFR hyperfunction in post-mitotic neurons at the late embryonic stage result in cortical dysplasia and circuit miswiring.
Steric blockage of lysenin toxin by crowding
Authors: Munguira Ignacio L.B. , Barbas Alfonso
Published: May 2020

bioRxiv has withdrawn this manuscript in response to an institutional investigation by INSERM.
Structural basis for control of antibiotic production by bacterial hormones
Authors: Zhou Shanshan , Bhukya Hussain , Malet Nicolas , Harrison Peter J. , Rea Dean , Belousoff Matthew J. , Venugopal Hariprasad , Sydor Paulina K. , Styles Kathryn M. , Song Lijiang , Cryle Max J. , Alkhalaf Lona M. , Fülöp Vilmos , Challis Gregory L. , Corre Christophe
Published: May 2020

Actinobacteria produce numerous antibiotics and other specialised metabolites with important applications in medicine and agriculture. Diffusible hormones frequently control the production of such metabolites by binding TetR family transcriptional repressors (TFTRs), but the molecular basis for this remains unclear. The production of methylenomycin antibiotics inStreptomyces coelicolorA3(2) is initiated by binding of 2-alkyl-4-hydroxymethylfuran-3-carboxylic acid (AHFCA) hormones to the TFTR MmfR. Here, we report the X-ray crystal structure of an MmfR-AHFCA complex, establishing the structural basis for hormone recognition. We also elucidate the mechanism for DNA release upon hormone binding by single particle cryo-electron microscopy of an MmfR-operator complex. Electrophoretic mobility shift assays with MmfR mutants and synthetic AHFCA analogues illuminate the role played by individual amino acid residues and hormone functional groups in ligand recognition and DNA release. These findings will facilitate the exploitation of Actinobacterial hormones and their associated TFTRs in synthetic biology and novel antibiotic discovery.
Multiethnic catalog of structural variants and their translational impact for disease phenotypes across 19,652 genomes
Authors: Sedlazeck Fritz J. , Yu Bing , Mansfield Adam J. , Chen Han , Krasheninina Olga , Tin Adrienne , Qi Qibin , Zarate Samantha , Traynelis Joshua L. , Menon Vipin ,   BCM HGSC Sequencing Lab, Hu Jianhong , Doddapaneni Harsha , Metcalf Ginger A. , Coresh Josef , Kaplan Robert C. , Muzny Donna M. , Jun Goo , Gibbs Richard A. , Salerno William J. , Boerwinkle Eric
Published: May 2020

Genome sequencing at population scale provides unprecedented access to the genetic foundations of human phenotypic diversity, but genotype-phenotype association analyses limited to small variants have failed to comprehensively characterize the genetic architecture of human health and disease because they ignore structural variants (SVs) known to contribute to phenotypic variation and pathogenic conditions1–3. Here we demonstrate the significance of SVs when assessing genotype-phenotype associations and the importance of ethnic diversity in study design by analyzing SVs across 19,652 individuals and the translational impact on 4,156 aptamerbased proteomic measurements across 4,021 multi-ethnic samples. The majority of 304,533 SVs detected are rare, although we identified 2,336 protein-coding genes impacted by common SVs.\

We identified 64 significant SV-protein associations that comprise 36 cis- and 28 trans-acting relationships, and 21 distinct SV regions overlapped with genome-wide association study loci. These findings represent a more comprehensive mapping of regulatory and translational endophenotypes underlying health and disease.
Inferring entire spiking activity from local field potentials with deep learning
Authors: Ahmadi Nur , Constandinou Timothy G. , Bouganis Christos-Savvas
Published: May 2020

Extracellular recordings are typically analysed by separating them into two distinct signals: local field potentials (LFPs) and spikes. Understanding the relationship between these two signals is essential for gaining deeper insight into neuronal coding and information processing in the brain and is also relevant to brain-machine interface (BMI) research. Previous studies have shown that spikes, in the form of single-unit activity (SUA) or multiunit activity (MUA), can be inferred solely from LFPs with moderately good accuracy. These spiking activities that are typically extracted via threshold-based technique may not be reliable when the recordings exhibit a low signal-to-noise ratio (SNR). Another spiking activity in the form of a continuous signal, referred to as entire spiking activity (ESA), can be extracted by a threshold-less, fast, and automated technique and has led to better performance in several tasks. However, its relationship with the LFPs has not been investigated. In this study, we aim to address this issue by employing a deep learning method to infer ESA from LFPs intracortically recorded from the motor cortex area of two monkeys performing different tasks. Results from long-term recording sessions and across different tasks revealed that the inference accuracy of ESA yielded consistently and significantly higher accuracy than that of SUA and MUA. In addition, local motor potential (LMP) was found to be the most highly predictive feature compared to other LFP features. The overall results indicate that LFPs contain substantial information about the spikes, particularly ESA, which could be useful for the development of LFP-based BMIs. The results also suggest the potential use of ESA as an alternative neuronal population activity measure for analysing neural responses to stimuli or behavioural tasks.
Predicting the activation of the androgen receptor by mixtures of ligands using Generalized Concentration Addition
Authors: Schlezinger Jennifer J , Heiger-Bernays Wendy , Webster Thomas F
Published: May 2020

Concentration/dose addition (CA) is widely used for compounds that act by similar mechanisms. But, CA cannot make predictions for mixtures of full and partial agonists for effect levels above that of the least efficacious component. As partial agonists are common, we developed Generalized Concentration Addition (GCA), which has been successfully applied to systems in which ligands compete for a single binding site. Here, we applied a pharmacodynamic model for a system with two binding sites, the androgen receptor (AR). AR acts according to the classic homodimer activation model: each cytoplasmic AR protein binds ligand, undergoes a conformational change that relieves inhibition of dimerization, and binds to DNA response elements as a dimer. We generated individual dose-response data for full (dihydroxytestosterone, BMS564929) and partial (TFM-4AS-1) agonists and a competitive antagonist (MDV3100) using reporter data generated in the MDA-kb2 cell line. We used the Schild method to estimate the binding affinity of AR for MDV3100. Data for individual compounds fit the AR pharmacodynamic model well. The partial agonist had agonistic effects at low effect levels and antagonistic effects at high levels, as predicted by pharmacological theory. The GCA model fit the empirical mixtures data—full/full agonist, full/partial agonist and full agonist/antagonist—as well or better than relative potency factors (a special case of CA) or effect summation. The ability of generalized concentration addition to predict the activity of mixtures of different types of androgen receptor ligands is important as a number of environmental compounds act as partial AR agonists or antagonists.
Inside-out regulation of E-cadherin conformation and adhesion
Authors: Koirala Ramesh , Priest Andrew Vae , Yen Chi-Fu , Cheah Joleen S. , Pannekoek Willem-Jan , Gloerich Martijn , Yamada Soichiro , Sivasankar Sanjeevi
Published: May 2020

Cadherin cell-cell adhesion proteins play key roles in tissue morphogenesis and wound healing. Cadherin ectodomains bind in two conformations, X-dimers and strand-swap dimers, with different adhesive properties. However, the mechanisms by which cells regulate ectodomain conformation are unknown. Cadherin intracellular regions associate with several actin-binding proteins including vinculin, which are believed to tune cell-cell adhesion by remodeling the actin cytoskeleton. Here, we show at the single molecule level, that vinculin association with the cadherin cytoplasmic region allosterically converts weak X-dimers into strong strand-swap dimers, and that this process is mediated by myosin II dependent changes in cytoskeletal tension. We also show that in epithelial cells, ∼70% of apical cadherins exist as strand-swap dimers while the remaining form X-dimers, providing two cadherin pools with different adhesive properties. Our results demonstrate, for the first time, the inside-out regulation of cadherin conformation and establish a mechanistic role for vinculin in this process.

SIGNIFICANCE STATEMENT

Cadherin cell-cell adhesion proteins play key roles in the formation and maintenance of tissues. Their adhesion is carefully regulated to orchestrate complex movement of cells. While cadherin ectodomains bind in two conformations with different adhesive properties, the mechanisms by which cells regulate the conformation (and consequently adhesion) of individual cadherins are unknown. Here, we demonstrate that the association of intracellular vinculin to the cadherin cytoplasmic region, regulates cadherin adhesion by switching ectodomains from a weak binding to the strongly adhesive conformation. In contrast with the prevailing view which suggests that vinculin regulates adhesion solely by remodeling the cytoskeleton, we show that vinculin can directly modulate single cadherin ectodomain conformation and that this process is mediated by changes in cytoskeletal tension.
A novel method for classification of tabular data using convolutional neural networks
Authors: Buturović Ljubomir , Miljković Dejan
Published: May 2020

Convolutional neural networks (CNNs) represent a major breakthrough in image classification. However, there has not been similar progress in applying CNNs, or neural networks of any kind, to classification of tabular data. We developed and evaluated a novel method, TAbular Convolution (TAC), for classification of such data using CNNs by transforming tabular data to images and then classifying the images using CNNs. The transformation is performed by treating each row of tabular data (i.e., vector of features) as an image filter (kernel), and applying the filter to a fixed base image. A CNN is then trained to classify the filtered images. We applied TAC to classification of gene expression data derived from blood samples of patients with bacterial or viral infections. Our results demonstrate that off-the-shelf ResNet can classify the gene expression data as accurately as the current non-CNN state-of-the-art classifiers.
Infanticide by females is a leading source of juvenile mortality in a large social carnivore
Authors: Brown Ally K , Pioon Malit O , Holekamp Kay E , Strauss Eli D
Published: May 2020

Social animals benefit from their groupmates, so why do they sometimes kill each other’s offspring? Using 30 years of data from multiple groups of wild spotted hyenas, we address three critical aims for understanding infanticide in any species: (1) quantify the contribution of infanticide to overall mortality (2) describe the circumstances under which infanticide occurs and (3) evaluate hypotheses about the evolution of infanticide. We find that, although observed only rarely, infanticide is in fact a leading source of juvenile mortality. Infanticide accounted for 24% of juvenile mortality, and 1 in 10 hyenas born in our population perished due to infanticide. In all observed cases of infanticide, killers were adult females, but victims could be of both sexes. Of four hypotheses regarding the evolution of infanticide, we found the most support for the hypothesis that infanticide in spotted hyenas reflects competition over social status among matrilines.
Understanding potential drivers of aquatic metabolism in a subtropical treatment wetland
Authors: Julian Paul , Osborne Todd Z.
Published: May 2020

Changes of dissolved oxygen (DO) in aquatic ecosystems integrates dynamic biological, physical and chemical processes that control the rate of ecosystem metabolism. Aquatic ecosystem metabolism can be characterized by the diel change in DO changes over time and is expressed as the net aquatic productivity (NAP). This study investigated aquatic metabolism of dominant emergent and submerged aquatic vegetation (EAV and SAV, respectively) within two treatment flow-ways (FW) of Stormwater Treatment Area 2 (STA-2) in the Everglades ecosystem. The hypothesis of this study is that aquatic metabolism will differ between aquatic vegetation communities with SAV communities will have a greater GPP and ER rate than EAV communities driven by biophysical, hydrodynamic and biogeochemical differences between systems. Aquatic metabolism observed in this study vary spatially (along FWs) and temporally (diel to days) controlled by different effects related biological, physical and chemical processes. This study suggests that ecosystem metabolism is controlled differently across FWs with varying levels of response to loading/transport and water column attributes resulting in differences in organic matter accumulation, C turnover and phosphorus cycling.
Network Analysis Reveals Different Cellulose Degradation Strategies acrossTrichoderma harzianumStrains Associated with XYR1 and CRE1
Authors: Rosolen Rafaela Rossi , Aono Alexandre Hild , Almeida Déborah Aires , Filho Jaire Alves Ferreira , Horta Maria Augusta Crivelente , de Souza Anete Pereira
Published: May 2020

Trichoderma harzianum, whose gene expression is tightly controlled by the transcription factors (TFs) XYR1 and CRE1, is a potential candidate for hydrolytic enzyme production. Here, we performed a network analysis ofT. harzianumIOC-3844 andT. harzianumCBMAI-0179 to explore how the regulation of these TFs varies between these strains. In addition, we explored the evolutionary relationships of XYR1 and CRE1 protein sequences amongTrichodermaspp. The results of theT. harzianumstrains were compared with those ofTrichoderma atrovirideCBMAI-0020, a mycoparasitic species. Although transcripts encoding carbohydrate-active enzymes (CAZymes), TFs, transporters, and proteins with unknown functions were coexpressed withcre1orxyr1, other proteins indirectly related to cellulose degradation were identified. The enriched GO terms describing the transcripts of these groups differed across all strains, and several metabolic pathways with high similarity between both regulators but strain-specific differences were identified. In addition, the CRE1 and XYR1 subnetworks presented different topology profiles in each strain, likely indicating differences in the influences of these regulators according to the fungi. The hubs of thecre1andxyr1groups included transcripts not yet characterized or described as being related to cellulose degradation. The first-neighbor analyses confirmed the results of the profile of the coexpressed transcripts incre1andxyr1. The analyses of the shortest paths revealed that CAZymes upregulated under cellulose degradation conditions are most closely related to both regulators, and new targets between such signaling pathways were discovered. Although the evaluatedT. harzianumstrains are phylogenetically close and their amino acid sequences related to XYR1 and CRE1 are very similar, the set of transcripts related toxyr1andcre1differed, suggesting that eachT. harzianumstrain used a specific regulation strategy for cellulose degradation. More interestingly, our findings may suggest that XYR1 and CRE1 indirectly regulate genes encoding proteins related to cellulose degradation in the evaluatedT. harzianumstrains. An improved understanding of the basic biology of fungi during the cellulose degradation process can contribute to the use of their enzymes in several biotechnological applications and pave the way for further studies on the differences across strains of the same species.
Modeling the photosynthetic system I as complex interacting network
Authors: Montepietra D. , Bellingeri M. , Scotognella F. , Cassi D.
Published: May 2020

In this paper we model the excitation energy transfer (EET) of the photosynthetic system I (PSI) of the common pea plantPisum Sativumas complex interacting network. The magnitude of the link energy transfer between nodes-chromophores is computed by Forster Resonant Energy Transfer (FRET) using the pairwise physical distances between chromophores from the PDB (Protein Data Bank). We measure the global PSI network EET efficiency adopting well-known network theory indicators: the network efficiency (Eff) and the largest connected component (LCC). We find that when progressively removing the weak links of lower EET, the network efficiency (Eff) decreases while the EET paths integrity (LCC) is still preserved. This finding would show that the PSI is a resilient system owning a large window of functioning feasibility and it is completely impaired only when removing most of the network links. Furthermore, we perform nodes removal simulations to understand how the nodes-chromophores malfunctioning may affect the PSI functioning. We discover that the removal of the core chlorophylls triggers the fastest decrease in the network efficiency (Eff), unveiling them as the key component boosting the high EET efficiency. Our outcomes open new perspectives of research, such comparing the PSI energy transfer efficiency of different natural and agricultural plant species and investigating the light-harvesting mechanisms of artificial photosynthesis both in plant agriculture and in the field of solar energy applications.