bluuebunny/crossref_metadata_2025 huggingface dataset:
Extracellular Microenvironment in Patient-derived Hydrogel Organoids of Prostate Cancer Regulates Therapeutic Response
Authors: Mosquera Matthew J , Bareja Rohan , Bernheim Jacob M , Asad Muhammad , Cheung Cynthia , Sigouros Michael , Prabhu Varun , Allen Joshua , Martin M Laura , Puca Loredana , Rubin Mark , Beltran Himisha , Mosquera Juan Miguel , Elemento Olivier , Singh Ankur
Published: May 2020

Following treatment with androgen receptor (AR) pathway inhibitors, ~20% of prostate cancer patients progress by shedding their dependence on AR. These tumors undergo epigenetic reprogramming turning castration-resistant prostate cancer adenocarcinoma (CRPC-Adeno) into neuroendocrine prostate cancer (CRPC-NEPC). Currently, no targeted therapies are available for CRPC-NEPCs. A major hurdle in the development of new therapies and treatment of CRPC-NEPC is the lack of accurate models to test candidate treatments. Such models would ideally capture components of the tumor microenvironment (TME) factors, which likely regulate the phenotypic, genetic, and epigenetic underpinnings of this aggressive subset. The TME is a complex system comprised not only of malignant prostate cells but also stromal and inflammatory cells and a scaffold of extracellular matrix (ECM). ECM proteins are implicated in the survival and progression of cancer and development of chemoresistance, while are equally integral to the development of prostate cancer organoids. Here, using a combination of patient tumor proteomics and RNA sequencing, we define putative ECM cues that may guide the growth of prostate tumors in patients. Using this molecular information, we developed synthetic hydrogels that recapitulate the tumor ECM. Organoids cultured in the synthetic hydrogel niches demonstrate that ECM subtypes regulate the morphology, transcriptome, and epigenetics hallmarks of CRPC-Adeno and CRPC-NEPC. CRPC-NEPC organoid showed a differential response to small molecule inhibitors of epigenetic repressor EZH2 and Dopamine Receptor D2 (DRD2), the latter being a novel target in CRPC-NEPC when grown in tumor-specific ECM. Finally, in those synthetic ECM niches where drug resistance was observed in CRPC-NEPCs, cellular reprogramming by a synergistic combination of EZH2 inhibitors with DRD2 antagonists inhibited tumor growth. The synthetic platform can provide a more realistic prostate-specific microenvironment and subsequently enable the development of effective targeted therapeutics for prostate cancers.
COVID-19 Propagation and Mortality in a Two-Part Population
Authors: McGeoch Malcolm W , McGeoch Julie
Published: May 2020

There has recently emerged a striking consistency to the mortality from SARS-CoV-2, as a fraction of population, across many nations. We have constructed a model for the spread of the virus that reproduces this phenomenon via inclusion of two (or more) categories of susceptibility to the virus. In the simplest case, the population is given a smaller fraction of 10-20% with higher susceptibility and the balance of 80-90% with lower susceptibility. Susceptibility is taken to include the level of immunity to the virus combined with the societal circumstances of certain smaller groups within a population. This is programmed numerically by considering a realistic random rate of contacts, together with an assumed constant viral genome. The remaining major variable is the societal response of nations to the outbreak, with earlier or later application of various degrees of lockdown, tracing and sanitation. China, South Korea and other nations, including Germany, have stopped or greatly slowed the spread of the disease before it could run its course through a whole population. Using this model the extent of progress toward herd immunity is discussed, with an in-principle estimate of the remaining toll to be experienced.
Association of Angiotensin-Converting Enzyme Inhibitors and Angiotensin Receptor Blockers with the Risk of Hospitalization and Death in Hypertensive Patients with Coronavirus Disease-19
Authors: Khera Rohan , Clark Callahan , Lu Yuan , Guo Yinglong , Ren Sheng , Truax Brandon , Spatz Erica S , Murugiah Karthik , Lin Zhenqiu , Omer Saad B , Vojta Deneen , Krumholz Harlan M
Published: May 2020

Background: Whether angiotensin-converting enzyme (ACE) Inhibitors and angiotensin receptor blockers (ARBs) mitigate or exacerbate SARS-CoV-2 infection remains uncertain. In a national study, we evaluated the association of ACE inhibitors and ARB with coronavirus disease-19 (COVID-19) hospitalization and mortality among individuals with hypertension.

Methods: Among Medicare Advantage and commercially insured individuals, we identified 2,263 people with hypertension, receiving ≥1 antihypertensive agents, and who had a positive outpatient SARS-CoV-2 test (outpatient cohort). In a propensity score-matched analysis, we determined the association of ACE inhibitors and ARBs with the risk of hospitalization for COVID-19. In a second study of 7,933 individuals with hypertension who were hospitalized with COVID-19 (inpatient cohort), we tested the association of these medications with in-hospital mortality. We stratified all our assessments by insurance groups.

Results: Among individuals in the outpatient and inpatient cohorts, 31.9% and 29.8%, respectively, used ACE inhibitors and 32.3% and 28.1% used ARBs. In the outpatient study, over a median 30.0 (19.0 - 40.0) days after testing positive, 12.7% were hospitalized for COVID-19. In propensity score-matched analyses, neither ACE inhibitors (HR, 0.77 [0.53, 1.13], P = 0.18), nor ARBs (HR, 0.88 [0.61, 1.26], P = 0.48), were significantly associated with risk of hospitalization. In analyses stratified by insurance group, ACE inhibitors, but not ARBs, were associated with a significant lower risk of hospitalization in the Medicare group (HR, 0.61 [0.41, 0.93], P = 0.02), but not the commercially insured group (HR: 2.14 [0.82, 5.60], P = 0.12; P-interaction 0.09). In the inpatient study, 14.2% died, 59.5% survived to discharge, and 26.3% had an ongoing hospitalization. In propensity score-matched analyses, neither use of ACE inhibitor (0.97 [0.81, 1.16]; P = 0.74) nor ARB (1.15 [0.95, 1.38]; P = 0.15) was associated with risk of in-hospital mortality, in total or in the stratified analyses.

Conclusions: The use of ACE inhibitors and ARBs was not associated with the risk of hospitalization or mortality among those infected with SARS-CoV-2. However, there was a nearly 40% lower risk of hospitalization with the use of ACE inhibitors in the Medicare population. This finding merits a clinical trial to evaluate the potential role of ACE inhibitors in reducing the risk of hospitalization among older individuals, who are at an elevated risk of adverse outcomes with the infection.
Cadherin-11 is required for neural crest determination and survival
Authors: Manohar Subrajaa , Camacho Alberto , Rogers Crystal D.
Published: May 2020

Neural crest (NC) cells are multipotent embryonic cells that form melanocytes, craniofacial bone and cartilage, and the peripheral nervous system in vertebrates. NC cells express many cadherin proteins, which control their specification, epithelial to mesenchymal transition (EMT), migration, and mesenchymal to epithelial transition. Abnormal NC development leads to congenital defects including craniofacial clefts as well as NC-derived cancers. Here, we identify the role of the type II cadherin protein, Cadherin-11 (CDH11), in early chicken NC development. CDH11 is crucial for NC cell migration in amphibian embryos and is linked to cell survival, proliferation, and migration in cancer cells. It has been linked to the complex neurocristopathy disorder, Elsahy‐Waters Syndrome, in humans. Using immunohistochemistry (IHC), we determined that CDH11 protein has dynamic expression that is first co-localized with neural progenitors in early embryos and subsequently upregulated specifically in NC cells as they are specified in the dorsal neural tube prior to migration. We identified that loss of CDH11 led to a reduction of bonafide NC cells in the dorsal neural tube combined with defects in cell migration and survival. Loss of CDH11 increased p53-mediated programmed-cell death, and blocking the p53 pathway rescued the NC phenotype. Our findings demonstrate an early requirement for CDH11 in NC development, and may increase our understanding of early cadherin-related NC developmental defects.

Chicken Cadherin-11 (CDH11), which is expressed in neural crest (NC) cells prior to NC cell migration, is necessary for the determination and survival of the premigratory NC population.
Multi-Antigenic Virus-like Particle of SARS CoV-2 produced inSaccharomyces cerevisiaeas a vaccine candidate
Authors: Arora Kajal , Rastogi Ruchir , Arora Nupur Mehrotra , Parashar Deepak , Paliwal Jeny , Naqvi Aelia , Srivastava Apoorva , Singh Sudhir Kumar , Kalyanaraman Sriganesh , Potdar Swaroop , Kumar Devanand , Arya Vidya Bhushan , Bansal Sarthi , Rautray Satabdi , Singh Indrajeet , Fengade Pankaj Surendra , Kumar Bibekanand , Kundu Prabuddha Kumar
Published: May 2020

Spike, Envelope and Membrane proteins from the SARS CoV-2 virus surface coat are important vaccine targets. We hereby report recombinant co-expression of the three proteins (Spike, Envelope and Membrane) in a engineeredSaccharomyces cerevisiaeplatform (D-Crypt™) and their self-assembly as Virus-like particle (VLP). This design as a multi-antigenic VLP for SARS CoV-2 has the potential to be a scalable vaccine candidate. The VLP is confirmed by transmission electron microscopy (TEM) images of the SARS CoV-2, along with supportive HPLC, Dynamic Light Scattering (DLS) and allied analytical data. The images clearly outline the presence of a “Corona” like morphology, and uniform size distribution.
Expanding Biomaterial Surface Topographical Design Space through Natural Surface Reproduction
Authors: Vermeulen Steven , Honig Floris , Vasilevich Aliaksei , Roumans Nadia , Carlier Aurélie , Romero Manuel , Williams Paul , Uquillas Jorge Alfredo , de Boer Jan
Published: May 2020

Surface topography guides cell behavior and is a tool to endow biomaterials with bioactive properties. The large number of possible designs makes it challenging to find the optimal surface structure to induce a specific cell response. The TopoChip platform is currently the largest collection of topographies with 2176 in silico designed micro-topographies. Still, it is exploring only a small part of the design space due to the boundary conditions of the design algorithm and the surface engineering strategy. Inspired by the diversity of natural surfaces, we assessed to what extend we could expand the topographical design space and consequently the resulting cellular responses using natural surfaces. To this end, we replicated twenty-six plant and insect surfaces in polystyrene and quantified their surface properties using white light interferometry, image analysis and principle component analysis. Next, we quantified mesenchymal stem cell morphology and the pattern ofPseudomonas aeruginosacolonization and compared it to previous data from TopoChip screens. Our data show that natural surfaces extended the TopoChip design space. Moreover, the natural surfaces induced MSC morphologies and bacterial attachment patterns not previously observed on the TopoChip. In the future, we will train our design algorithms with the results obtained by natural surface imprint experiments to further explore the design space and bio-active properties of surface topography.
Novel insights into the structure and transport mechanisms of TAPT1
Authors: Parvez Md Sorwer Alam , Rahman Mohammad Mahfujur , Morshed Md Niaz , Rahman Dolilur , Anwar Saeed , Coucke Paul J. , Hosen Mohammad Jakir
Published: May 2020

Transmembrane anterior-posterior transformation protein 1 (TAPT1), encoded by theTAPT1gene expressed in the basal ciliary body, plays a crucial role in cilia formation as well as axial skeletal patterning. Mutations in this gene have been reported to cause several ciliopathies and osteo-related diseases. Unfortunately, the cellular and molecular pathogenic mechanisms are still unclear also due to the lack of X-ray crystallographic structure and further characterization of TAPT1 protein. In this study, we attempted to characterize this protein byin silicotechniques. A 3D structure of TAPT1 was generated by theab initiomethod, which was further used for the analysis of the substrate-binding site, to determine pore size and for the prediction of the possible substrate(s). Validation by using different software packages revealed a reliable 3D model of TAPT1. Topology modeling revealed that TAPT1 has eight transmembrane helices with a total number of 27 helices in secondary structure. The amino acid residues H235, R323, K443, N446, S447, L450, K453, S454, Y457, K511, N513, D533, K535, D536, and T538 were found to form the pore surface as well as involved in the binding interaction with the substrate(s). This study predicted flavonoids as the possible substrate for TAPT1, which could further be confirmed by ingenuity pathway analysis. Moreover, our analysis indicated that TAPT1 might localize in the mitochondrial membrane in addition to the ciliary basal body. Our study gives novel insights for TAPT1 structure and its function.
Single molecule structure sequencing reveals RNA structural dependencies, breathing and ensembles
Authors: Bizuayehu Teshome Tilahun , Labun Kornel , Jakubec Martin , Jefimov Kirill , Niazi Adnan , Valen Eivind
Published: May 2020

RNA molecules can form secondary and tertiary structures that can regulate their localization and function. Using enzymatic or chemical probing together with high-throughput sequencing, secondary structure can be mapped across the entire transcriptome. However, a limiting factor is that only population averages can be obtained since each read is an independent measurement. Although long-read sequencing has recently been used to determine RNA structure, these methods still used aggregate signals across the strands to detect structure. Averaging across the population also means that only limited information about structural heterogeneity across molecules or dependencies within each molecule can be obtained. Here, we present Single-Molecule Structure sequencing (SMS-seq) that combines structural probing with native RNA sequencing to provide non-amplified, structural profiles of individual molecules with novel analysis methods. Our new approach using mutual information enabled single molecule structural interrogation. Each RNA is probed at numerous bases enabling the discovery of dependencies and heterogeneity of structural features. We also show that SMS-seq can capture tertiary interactions, dynamics of riboswitch ligand binding, and mRNA structural features.
A meta-analytic approach to mapping co-occurrent grey matter volume increases and decreases in psychiatric disorders
Authors: Mancuso Lorenzo , Fornito Alex , Costa Tommaso , Ficco Linda , Liloia Donato , Manuello Jordi , Duca Sergio , Cauda Franco
Published: May 2020

Numerous studies have investigated gray matter (GM) volume changes in diverse patient groups. Reports of disorder-related GM reductions are common in such work, but many studies also report evidence for GM volume increases in patients. It is unclear whether these GM increases and decreases independent or related in some way. Here, we address this question using a novel meta-analytic network mapping approach. We used a coordinate-based meta-analysis of 64 voxel-based morphometry studies of psychiatric disorders to calculate the probability of finding a GM increase or decrease in one region given an observed change in the opposite direction in another region. Estimating this co-occurrence probability for every pair of brain regions allowed us to build a network of concurrent GM changes of opposing polarity. Our analysis revealed that disorder-related GM increases and decreases are not independent; instead, a GM change in one area is often statistically related to a change of opposite polarity in other areas, highlighting distributed yet coordinated changes in GM volume as a function of brain pathology. Most regions showing GM changes linked to an opposite change in a distal area were located in salience, executive-control and default mode networks, as well as the thalamus and basal ganglia. Moreover, pairs of regions showing coupled changes of opposite polarity were more likely to belong to different canonical networks than to the same one. Our results suggest that regional GM alterations in psychiatric disorders are often accompanied by opposing changes in distal regions that belong to distinct functional networks.
Glycan processing in the Golgi – optimal information coding and constraints on cisternal number and enzyme specificity
Authors: Yadav Alkesh , Vagne Quentin , Sens Pierre , Iyengar Garud , Rao Madan
Published: May 2020

Many proteins that undergo sequential enzymatic modification in the Golgi cisternae are displayed at the plasma membrane as cell identity markers. The modified proteins, called glycans, represent a molecular code. The fidelity of thisglycan codeis measured by how accurately the glycan synthesis machinery realises the desired target glycan distribution for a particular cell type and niche. In this paper, we quantitatively analyse the tradeoffs between the number of cisternae and the number and specificity of enzymes, in order to synthesize a prescribed target glycan distribution of a certain complexity. We find that to synthesize complex distributions, such as those observed in real cells, one needs to have multiple cisternae and precise enzyme partitioning in the Golgi. Additionally, for fixed number of enzymes and cisternae, there is an optimal level of specificity of enzymes that achieves the target distribution with high fidelity. Our results show how the complexity of the target glycan distribution places functional constraints on the Golgi cisternal number and enzyme specificity.
Multidimensional Chromatin Regulation of Cell Lineage Differentiation in a Metazoan Embryo
Authors: Zhao Zhiguang , Fan Rong , Xu Weina , Wang Yangyang , Ma Xuehua , Du Zhuo
Published: May 2020

How chromatin dictates cell differentiation is an intriguing question in developmental biology. Here, a reporter gene integrated throughout the genome was used as a sensor to map the chromatin activity landscape in lineage-resolved cells duringC. elegansembryogenesis. Single-cell analysis of chromatin dynamics across critical dimensions of cell differentiation was performed, including lineage, tissue, and symmetry. During lineage progression, chromatin gradually diversifies in general and exhibits switch-like changes following specific cell division, which is predictive of anterior-posterior fate asymmetry. Upon tissue differentiation, chromatin of cells from distinct lineages converge to tissue-specific states but retain “memory” of each cell’s lineage history, which contributes to intra-tissue heterogeneity. However, cells with a morphologically left-right symmetric organization utilize a predetermination chromatin strategy to program analogous regulatory states in early progenitor cells. Additionally, chromatin co-regulation drives the functional coordination of the genome. Collectively, this work reveals the role of multidimensional chromatin regulation in cell differentiation.
Whole-Brain High-Resolution Metabolite Mapping with 3D Compressed-Sensing-SENSE-LowRank1H FID-MRSI
Authors: Klauser Antoine , Klauser Paul , Grouiller Frédéric , Courvoisier Sebastien , Lazeyras Francois
Published: May 2020

There is a growing interest in the neuroscience community to map the distribution of brain metabolites in vivo. Magnetic resonance spectroscopic imaging (MRSI) is often limited by either a poor spatial resolution and/or a long acquisition time which severely limits its applications for clinical or research purposes. Building on a recently developed technique of acquisition-reconstruction for 2D MRSI, we combined fast Cartesian1H-FID-MRSI acquisition sequence, compressed-sensing acceleration, and low-rank total-generalized-variation constrained reconstruction to produce 3D high-resolution whole-brain MRSI with a significant acquisition time reduction. We first evaluated the acceleration performance using retrospective undersampling of a fully-sampled dataset. Second, a 20 min accelerated MRSI acquisition was performed on the brain of three healthy volunteers resulting in metabolite maps with 5 mm isotropic resolution. The metabolite maps exhibited the detailed neurochemical composition of all brain regions and revealed parts of the underlying brain anatomy. The latter assessment used previous reported knowledge and a brain atlas-based analysis to show consistency of the concentration contrasts and ratio across all brain regions. These results acquired on a clinical 3 Tesla MRI successful combinae of the 3D1H-FID-MRSI with a constrained reconstruction to produce detailed mapping of metabolite concentrations at high-resolution over the whole brain, with an acquisition time suitable for clinical or research settings.
Resistance to pirimiphos-methyl in West AfricanAnophelesis spreading via duplication and introgression of theAce1locus
Authors: Grau-Bové Xavier , Lucas Eric , Pipini Dimitra , Rippon Emily , van’t Hof Arjèn , Constant Edi , Dadzie Samuel , Egyir-Yawson Alexander , Essandoh John , Chabi Joseph , Djogbénou Luc , Harding Nicholas J. , Miles Alistair , Kwiatkowski Dominic , Donnelly Martin J. , Weetman David ,   The Anopheles gambiae 1000 Genomes Consortium
Published: May 2020

Vector population control using insecticides is a key element of current strategies to prevent malaria transmission in Africa. The introduction of effective insecticides, such as the organophosphate pirimiphos-methyl, is essential to overcome the recurrent emergence of resistance driven by the highly diverseAnophelesgenomes. Here, we use a population genomic approach to investigate the basis of pirimiphos-methyl resistance in the major malaria vectorsAnopheles gambiaeandA. coluzzii. A combination of copy number variation and a single non-synonymous substitution in the acetylcholinesterase gene,Ace1, provides the key resistance diagnostic in anA. coluzziipopulation from Côte d’Ivoire that we used for sequence-based association mapping, with replication in other West African populations. TheAce1and substitution and duplications occur on a unique resistance haplotype that evolved inA. gambiaeand introgressed intoA. coluzzii, and is now common in West Africa probably due to cross-resistance with previously used insecticides. Our findings highlight the phenotypic value of this complex resistance haplotype and clarify its evolutionary history, providing tools to understand the current and future effectiveness of pirimiphos-methyl based interventions.
Reduced expression of TCF7L2 in adipocyte impairs glucose tolerance associated with decreased insulin secretion, incretins levels and lipid metabolism dysregulation in male mice
Authors: Nguyen-Tu Marie-Sophie , Martinez-Sanchez Aida , Leclerc Isabelle , Rutter Guy A. , da Silva Xavier Gabriela
Published: May 2020

Transcription factor 7-like 2 (TCF7L2) is a downstream effector of the Wnt/beta-catenin signalling pathway and its expression is critical for adipocyte development. The precise role of TCF7L2 in glucose and lipid metabolism in adult adipocytes remains to be defined. Here, we aim to investigate how changes in TCF7L2 expression in mature adipocytes affect glucose homeostasis.Tcf7l2was selectively ablated from mature adipocytes in C57BL/6J mice using an adiponectin promoter-drivenCrerecombinase to recombine alleles floxed at exon 1 of theTcf7l2gene. Mice lackingTcf7l2in mature adipocytes displayed normal body weight. Male mice exhibited normal glucose homeostasis at eight weeks of age. Male heterozygote knockout mice (aTCF7L2het) exhibited impaired glucose tolerance (AUC increased 1.14 ± 0.04 -fold, p=0.03), as assessed by intraperitoneal glucose tolerance test, and changes in fat mass at 16 weeks (increased by 1.4 ± 0.09-fold, p=0.007). Homozygote knockout mice exhibited impaired oral glucose tolerance at 16 weeks of age (AUC increased 2.15 ± 0.15-fold, p=0.0001). Islets of Langerhans exhibited impaired glucose-stimulated insulin secretionin vitro(decreased 0.54 ± 0.13-fold aTCF7L2KO vs control, p=0.02), but no changes inin vivoglucose-stimulated insulin secretion. Female mice in which one or two alleles of theTcf7l2gene was knocked out in adipocytes displayed no changes in glucose tolerance, insulin sensitivity or insulin secretion. Plasma levels of glucagon-like peptide-1 and gastric inhibitory polypeptide were lowered in knockout mice (decreased 0.57 ± 0.03-fold and 0.41 ± 0.12-fold, p=0.04 and p=0.002, respectively), whilst plasma free fatty acids and Fatty Acid Binding Protein 4 circulating levels were increased by 1.27 ± 0.07 and 1.78 ± 0.32-fold, respectively (p=0.05 and p=0.03). Mice with biallelicTcf7l2deletion exposed to high fat diet for 9 weeks exhibited impaired glucose tolerance (p=0.003 at 15 min after glucose injection) which was associated with reducedin vivoglucose-stimulated insulin secretion (decreased 0.51 ± 0.03-fold, p=0.02). Thus, our data indicate that loss ofTcf7l2gene expression in adipocytes leads to impairments on metabolic responses which are dependent on gender, age and nutritional status. Our findings further illuminate the role of TCF7L2 in the maintenance of glucose homeostasis.
Skeletal muscle DNMT3A plays a necessary role in endurance exercise by regulating oxidative capacity of red muscles
Authors: Villivalam Sneha Damal , You Dongjoo , Ebert Scott M. , Kim Jinse , Xiao Han , Palacios Hector H. , Adams Christopher M. , Kang Sona
Published: May 2020

Exercise interventions alter the DNA methylation profile in skeletal muscle, yet little is known about the role of the DNA methylation machinery in exercise capacity. In this study, we found that in oxidative red muscle, DNMT3A expression increases greatly following a bout of endurance exercise. Mice lackingDnmt3ain skeletal muscle fibers had reduced tolerance to endurance exercise, accompanied by reduced oxidative capacity and reduced mitochondrial counts. Moreover, during exercise, the knockout muscles overproduced reactive oxygen species (ROS), which are major contributors to muscle dysfunction. In mechanistic terms, we demonstrated thatAldh1l1is a key target of repression by DNMT3A in red muscles. DNMT3A directly regulated the Aldh1l1 transcription by binding to theAldh1l1promoter region and altering DNA methylation and histone modification. Enforcing ALDH1L1 expression, leading to elevated NADPH, led to overproduction of ROS by the NADPH oxidase complex (NOX) in myotubes, ultimately resulting in mitochondrial defects. Moreover, both genetic inhibition of ALDH1L1 and pharmacological inhibition of NOX rescued oxidative stress and mitochondrial decline inDnmt3a-deficient myotubes, confirming the essential role of ALDH1L1-dependent ROS generation as a downstream effector of DNMT3A loss of function. Together, our results reveal that DNMT3A in skeletal muscle plays a pivotal role in endurance exercise by controlling intracellular oxidative stress.
Monitoring the microbiome for food safety and quality using deep shotgun sequencing
Authors: Beck Kristen L. , Haiminen Niina , Chambliss David , Edlund Stefan , Kunitomi Mark , Huang B. Carol , Kong Nguyet , Ganesan Balasubramanian , Baker Robert , Markwell Peter , Kawas Ban , Davis Matthew , Prill Robert J. , Krishnareddy Harsha , Seabolt Ed , Marlowe Carl H. , Pierre Sophie , Quintanar André , Parida Laxmi , Dubois Geraud , Kaufman James , Weimer Bart C.
Published: May 2020

In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix filtering step that improved microbe detection specificity to >99.96% duringin silicovalidation. The pipeline identified 119 microbial genera per HPP sample on average with 65 genera present in all samples. The most abundant of these wereBacteroides, Clostridium, Lactococcus, Aeromonas, andCitrobacter.We also observed shifts in the microbial community corresponding to ingredient composition differences. When comparing culture-based results forSalmonellawith total RNA sequencing, we found thatSalmonellagrowth did not correlate with multiple sequence analyses. We conclude that microbiome sequencing is useful to characterize complex food microbial communities, while additional work is required for predicting specific species’ viability from total RNA sequencing.
Lipid Droplet Is an Ancient and Inheritable Organelle in Bacteria
Authors: Chi Xiang , Ogunsade Ololade Omolara , Zhou Ziyun , Li Zemin , Li Xuehan , Zhang Mengwei , Song Fuhang , Wang Jun , Hammad Mirza Ahmed , Zhang Xuelin , Zhang Shuyan , Wan Xia , Zhang Lixin , Zhang Congyan , Liu Pingsheng
Published: May 2020

Lipid droplet (LD) is a monolayer phospholipid membrane-bound organelle found in all eukaryotes and several prokaryotes which plays key roles in cellular lipid homeostasis and human health. The origin and evolution of the organelle remains unknown. Here, we report that through screening over 660 bacteria using biophysical and biochemical methods, plus LD isolation and proteomic tool, LDs were identified in most of these microbes, affiliated with five main bacterial phyla. Moreover, LDs were also identified in E. coli overexpressing lipid synthesis enzymes, indicating that bacteria without detectable LDs possessed the ability of LD biogenesis. The similarity of isolated LDs from representative strains and evolutionary analysis of LD major protein PspA demonstrate that LDs were conserved in bacteria. Furthermore, time-lapse imaging revealed that LDs were inheritable accompanying with bacterial growth and division. Finally, a common ancestor of LD-containing bacteria was predicted to originate 3.19 billion years ago by a phylogenetic analysis. Our findings suggest that LD is a widespread and inheritable organelle from an ancient common ancestor.
Antiviral activity of Glucosylceramide synthase inhibitors against SARS-CoV-2 and other RNA virus infections
Authors: Vitner Einat. B. , Avraham Roy , Achdout Hagit , Tamir Hadas , Agami Avi , Cherry Lilach , Yahalom-Ronen Yfat , Politi Boaz , Erez Noam , Melamed Sharon , Paran Nir , Israely Tomer
Published: May 2020

The need for antiviral drugs is real and relevant. Broad spectrum antiviral drugs have a particular advantage when dealing with rapid disease outbreaks, such as the current COVID-19 pandemic. Since viruses are completely dependent on internal cell mechanisms, they must cross cell membranes during their lifecycle, creating a dependence on processes involving membrane dynamics. Thus, in this study we examined whether the synthesis of glycosphingolipids, biologically active components of cell membranes, can serve as an antiviral therapeutic target. We examined the antiviral effect of two specific inhibitors of GlucosylCeramide synthase (GCS); (i) Genz-123346, an analogue of the FDA-approved drug Cerdelga®, (ii) GENZ-667161, an analogue of venglustat which is currently under phase III clinical trials. We found that both GCS inhibitors inhibit the replication of four different enveloped RNA viruses of different genus, organ-target and transmission route: (i) Neuroinvasive Sindbis virus (SVNI), (ii) West Nile virus (WNV), (iii) Influenza A virus, and (iv) SARS-CoV-2. Moreover, GCS inhibitors significantly increase the survival rate of SVNI-infected mice. Our data suggest that GCS inhibitors can potentially serve as a broad-spectrum antiviral therapy and should be further examined in preclinical and clinical trial. Analogues of the specific compounds tested have already been studied clinically, implying they can be fast-tracked for public use. With the current COVID-19 pandemic, this may be particularly relevant to SARS-CoV-2 infection.

One Sentence Summary

An analogue of Cerdelga®, an FDA-approved drug, is effective against a broad range of RNA-viruses including the newly emerging SARS-CoV-2.
Cytotoxic effects of tRNA-derived fragments and tRNA halves from non-pathogenicEscherichia colistrain on colorectal cancer cells
Authors: Cao Kai-Yue , Pan Yu , Yan Tong-Meng , Tao Peng , Xiao Yi , Jiang Zhi-Hong
Published: May 2020

Transfer RNAs (tRNAs) purified from non-pathogenicE. colistrain (NPECS) possess cytotoxic properties on colorectal cancer cells. In the present study, the bioactivity of tRNA halves and tRNA fragments (tRFs) derived from NPECS are investigated for their anticancer potential. Both tRNA halves and tRF mimics studied exhibited significant cytotoxicity on colorectal cancer cells, with the latter being more effective suggesting that tRFs may be important contributors to the bioactivities of tRNAs derived from gut microbiota. Through high-throughput screening, EC83 mimic, a double-strand RNA with a 22 nt 5’-tRF derived from tRNA-Leu(CAA) as antisense chain, was identified as one with the highest potency (IC50=52 nM). Structure-activity investigations revealed that 2’-O-methylation of the ribose of guanosine may enhance the cytotoxic effects of EC83 mimicviaincreasing the stability of its tertiary structure. Consistently, 4-thiouridine substitution reversed this increased stability and the enhanced cytotoxic effects. This provides the first evidence that the bioactivity of tRF mimics would be impacted by chemical modifications. Furthermore, the present study provides the first evidence to suggest that novel tRNA fragments derived from the gut microbiota may possess anti-cancer properties and have the potential to be potent and selective therapeutic molecules.

IMPORTANCE

While the gut microbiota has been increasingly recognized to be of vital importance to human health and disease, the current literature shows that there is a lack of attention given on the non-pathogenicEscherichia colistrain. Moreover, the biological activities of tRNA fragments (tRFs) derived from bacteria have rarely been investigated. The findings from this study revealed tRFs as a new class of bioactive constituents derived from gut microorganisms, suggesting that studies on biological functional molecules in intestinal microbiota should not neglect tRFs. The research of tRFs would play an important role in biological research of gut microorganisms, including bacteria-bacteria interaction, gut-brain axis, gut-liver axis, etc. Furthermore, the guidance on the rational design of tRF therapeutics provided in this study indicates that further investigations should pay more attention to these therapeutics from probiotics. The innovative drug research of tRFs as potent druggable RNA molecules derived from intestinal microorganisms would open a new area in biomedical sciences.
Depression and loneliness during COVID-19 restrictions in the United States, and their associations with frequency of social and sexual connections
Authors: Rosenberg Molly , Luetke Maya , Hensel Devon , Kianersi Sina , Fu Tsung-chieh , Herbenick Debby
Published: May 2020

Purpose

To estimate the prevalence of depression and loneliness during the US COVID-19 response, and examine their associations with frequency of social and sexual connections.

Methods

We conducted an online cross-sectional survey of a nationally representative sample of American adults (n=1010), aged 18-94, running from April 10-20, 2020. We assessed depressive symptoms (CES-D-10 scale), loneliness (UCLA 3-Item Loneliness scale), and frequency of in-person and remote social connections (4 items, e.g. hugging family member, video chats) and sexual connections (4 items, e.g. partnered sexual activity, dating app use).

Results

One-third of participants (32%) reported depressive symptoms, and loneliness was high [mean (SD): 4.4 (1.7)]. Those with depressive symptoms were more likely to be women, age 20-29, unmarried, and low-income. Frequent in-person connections were associated with lower depression and loneliness; frequent remote connections were not.

Conclusions

Depression and loneliness were elevated during the early US COVID-19 response. Those who maintained frequent in-person, but not remote, social and sexual connections had better mental health outcomes. While COVID-19 social restrictions remain necessary, it will be critical to expand mental health services to serve those most at-risk and identify effective ways of maintaining social and sexual connections from a distance.
Prediction of protein subcellular localization using deep learning and data augmentation
Authors: Eftekhar Majid Ghorbani
Published: May 2020

Identifying subcellular localization of protein is significant for understanding its molecular function. It provides valuable insights that can be of tremendous help to protein’s function research and the detection of potential cell surface/secreted drug targets. The prediction of protein subcellular localization using bioinformatics methods is an inexpensive option to experimentally approaches. Many computational tools have been built during the past two decades, however, producing reliable prediction has always been the challenge. In this study, a Deep learning (DL) technique is proposed to enhance the precision of the analytical engine of one of these tools called PSORTb v3.0. Its conventional SVM machine learning model was replaced by the state-of-the-art DL method (BiLSTM) and a Data augmentation measure (SeqGAN). As a result, the combination of BiLSTM and SeqGAN outperformed SVM by improving its precision from 57.4% to 75%. This method was applied on a dataset containing 8230 protein sequences, which was experimentally derived by Brinkman Lab. The presented model provides promising outcomes for the future research. The source code of the model is available athttps://github.com/mgetech/SubLoc.
The impact of super-spreaders in COVID-19: mapping genome variation worldwide
Authors: Gómez-Carballa Alberto , Bello Xabier , Pardo-Seco Jacobo , Martinón-Torres Federico , Salas Antonio
Published: May 2020

The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the 21stcentury. We analyzed >4,700 SARS-CoV-2 genomes and associated meta-data retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and >160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a uniform mutation occurrence along branches that could complicate the design of future vaccines. The root of SARS-CoV-2 genomes locates at the Chinese haplogroup B1, with a TMRCA dating to 12 November 2019 - thus matching epidemiological records. Sub-haplogroup A2a originates in China and represents the major non-Asian outbreak. Multiple founder effect episodes, most likely associated with super-spreader hosts, explain COVID-19 pandemic to a large extent.
Metagenomic association analysis of gut symbiontLactobacillus reuteriwithout host-specific genome isolation
Authors: Park Sein , Steinegger Martin , Cho Ho-Seong , Chun Jongsik
Published: May 2020

Lactobacillus reuteriis a model symbiont colonizing the guts of vertebrates used for studies on host adaptation of the gut symbiont. Previous studies investigated host-specific phylogenetic and functional properties by isolating its genomic sequence. This dependency on genome isolation is a significant bottleneck. Here we propose a method to study the association betweenL. reuteriand its hosts directly from metagenomic reads without strain isolation by using pan-genomes.

We characterized the host-specificity ofL. reuteriin metagenomic samples not only in the previously studied organisms (mice and pigs) but additionally in dogs. For each sample, two types of profiles were generated: (1) genome-based strain type abundance profiles and (2) gene composition profiles. Our profiles showed host-association ofL. reuteriin both phylogenetic and functional aspects without depending on the host-specific genome isolation. We could observe not only the presence of host-specific lineages but also the dominant lineages associated with the different hosts.

Furthermore, we show that metagenome-assembled genomes provide detailed insights into the host-specificity ofL. reuteri. We could infer evolutionary trajectories of host-associativeL. reuteristrains in the metagenomic samples by placing the metagenome-assembled genomes into a phylogenetic tree and identify novel host-specific genes which were unannotated in existing pan-genome databases.

Our pan-genomic approach drops the need for time-consuming and expensive host-specific genome isolation while producing consistent results with previous host-association findings in mice and pigs. Additionally, we could predict associations that have not yet been studied in dogs.
Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in a Dutch drinking water treatment plant
Authors: Poghosyan Lianna , Koch Hanna , Frank Jeroen , van Kessel Maartje A.H.J. , Cremers Geert , van Alen Theo , Jetten Mike S.M. , Op den Camp Huub J.M. , Lücker Sebastian
Published: May 2020

Elevated concentrations of ammonium and methane in groundwater can cause severe problems during drinking water production. To avoid their accumulation, raw water in the Netherlands, and many other countries, is purified by sand filtration. These drinking water filtration systems select for microbial communities that mediate the biodegradation of organic and inorganic compounds. In this study, the active layers and wall biofilm of a Dutch drinking water treatment plant (DWTP) were sampled at different locations along the filtration units of the plant over three years. We used high-throughput sequencing in combination with differential coverage and sequence composition-based binning to recover 56 near-complete metagenome-assembled genomes (MAGs) with an estimated completion of ≥70% and with ≤10% redundancy. These MAGs were used to characterize the microbial communities involved in the conversion of ammonia and methane. The methanotrophic microbial communities colonizing the wall biofilm (WB) and the granular material of the primary rapid sand filter (P-RSF) were dominated by members of theMethylococcaceaeandMethylophilaceae.The abundance of these bacteria drastically decreased in the secondary rapid sand filter (S-RSF) samples. In all samples, complete ammonia-oxidizing (comammox)Nitrospirawere the most abundant nitrifying guild. Clade A comammoxNitrospiradominated the P-RSF, while clade B was most abundant in WB and S-RSF, where ammonium concentrations were much lower. In conclusion, the knowledge obtained in this study contributes to understanding the role of microorganisms in the removal of carbon and nitrogen compounds during drinking water production. We furthermore found that drinking water treatment plants represent valuable model systems to study microbial community function and interaction.

Highlights

Microbial distribution was mainly influenced by sampling location within the DWTP

Clade A comammoxNitrospirawere the dominant nitrifiers in the primary sand filter

Clade B was most abundant in samples from wall biofilm and the secondary filter

A novelMethylophilaceae-affiliated methanotroph dominated the primary sand filter
Protective role of neuronal and lymphoid cannabinoid CB2 receptors in neuropathic pain
Authors: Cabañero David , Ramírez-López Angela , Drews Eva , Schmöle Anne , Otte David M. , Wawrzczak-Bargiela Agnieszka , Encabo Hector Huerga , Kummer Sami , Przewlocki Ryszard , Zimmer Andreas , Maldonado Rafael
Published: May 2020

Cannabinoid CB2 receptor (CB2r) agonists are potential painkillers void of psychotropic effects. Peripheral immune cells, neurons and glia express CB2r, however the involvement of CB2r from these cells in neuropathic pain remains unresolved. We explored spontaneous neuropathic pain through on-demand self-administration of the selective CB2r agonist JWH133 in wild-type and knockout mice lacking CB2r in neurons, monocytes or constitutively. Operant self-administration reflected drug-taking to alleviate spontaneous pain, nociceptive and affective manifestations. While constitutive deletion of CB2r disrupted JWH133-taking behavior, this behavior was not modified in monocyte-specific CB2r knockouts and was increased in mice defective in neuronal CB2r knockouts suggestive of increased spontaneous pain. Interestingly, CB2r-positive lymphocytes infiltrated the injured nerve and possible CB2r transfer from immune cells to neurons was found. Lymphocyte CB2r depletion also exacerbated JWH133 self-administration and inhibited antinociception. This work identifies a simultaneous activity of neuronal and lymphoid CB2r that protects against spontaneous and evoked neuropathic pain.
Deciphering the genetic diversity of landraces with high-throughput SNP genotyping of DNA bulks: methodology and application to the maize 50k array
Authors: Arca Mariangela , Mary-Huard Tristan , Gouesnard Brigitte , Bérard Aurélie , Bauland Cyril , Combes Valérie , Madur Delphine , Charcosset Alain , Nicolas Stéphane D.
Published: May 2020

Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains however poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on SNP Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger’s genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 SSRs using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.