bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping of Neuropeptide Y Expression inOctopusBrains
Authors: Winters Gabrielle C. , Polese Gianluca , Di Cosmo Anna , Moroz Leonid L.
Published: April 2020

Neuropeptide Y (NPY) is an evolutionarily conserved neurosecretory molecule implicated in a diverse complement of functions across taxa and in regulating feeding behavior and reproductive maturation inOctopus. However, little is known about the precise molecular circuitry of NPY-mediated behaviors and physiological processes, which likely involve a complex interaction of multiple signal molecules in specific brain regions. Here we examined the expression of NPY throughout theOctopuscentral nervous system. The sequence analysis ofOctopusNPY precursor confirmed the presence of both signal peptide and putative active peptides, which are highly conserved across bilaterians.In situhybridization revealed distinct expression of NPY in specialized compartments, including potential “integration centers,” where visual, tactile, and other behavioral circuitries converge. These centers integrating separate circuits may maintain and modulate learning and memory or other behaviors not yet attributed to NPY-dependent modulation inOctopus. Extrasomatic localization of NPY mRNA in the neurites of specific neuron populations in the brain suggests a potential demand for immediate translation at synapses and a crucial temporal role for NPY in these cell populations. We also verified the presence of NPY mRNA in a small cell population in the olfactory lobe, which is a component of theOctopusfeeding and reproductive control centers. However, the molecular mapping of NPY expression only partially overlapped with that produced by immunohistochemistry in previous studies. Our study provides a precise molecular map of NPY mRNA expression that can be used to design and test future hypotheses about molecular signaling in variousOctopusbehaviors.

Research Highlights/Graphical Abstract text

Neuropeptide Y (NPY), an evolutionarily conserved neurosecretory molecule, is expressed in specialized regions of theOctopusbrain controlling feeding, reproduction, and visual and tactile memory circuits. Extrasomatic mRNAs were found in neurites, suggesting synaptic synthesis of NPY.
Modified Bacterial Lipids Which Alter Membrane Surface Charge Reduce Binding of Antimicrobial Peptides
Authors: Simcock Patrick W. , Bublitz Maike , Cipcigan Flaviu , Ryadnov Maxim G. , Crain Jason , Stansfeld Phillip J. , Sansom Mark S.P.
Published: April 2020

Antimicrobial peptides (AMPs) initiate killing of bacteria by binding to and destabilizing their membranes. The multiple peptide resistance factor (MprF) provides a defence mechanism for bacteria against a broad range of AMPs. MprF reduces the negative charge of both Gram-positive and Gram--negative bacterial membranes through enzymatic conversion of the anionic lipid phosphatidyl glycerol (PG) to either zwitterionic alanyl-phosphatidyl glycerol (Ala-PG) or cationic lysylphosphatidyl glycerol (Lys-PG). The resulting change in membrane charge is suggested to reduce AMP-membrane binding and hinder downstream AMP activity. Using molecular dynamics to investigate the effects of these modified lipids on AMP-binding to model membranes, we show that AMPs have substantially reduced affinity for model membranes containing Ala-PG or Lys-PG. A total of ~7000 simulations are used to define the relationship between bilayer composition and binding for 5 different membrane active peptides. The reduction of degree of interaction of a peptide with the membrane is shown to correlate with the change in membrane surface charge density. Free energy profile (potential of mean force) calculations reveal that these lipid modifications alter the energy barrier to peptide helix penetration of the bilayer. These results will enable us to guide design of novel peptides which address the issue of resistance via MprF-mediated membrane modification.
Labile carbon limits late winter microbial activity near Arctic treeline
Authors: Sullivan Patrick F. , Stokes Madeline C. , McMillan Cameron K. , Weintraub Michael N.
Published: April 2020

It is well established that soil microbial communities remain active during much of the Arctic winter, despite soil temperatures that are often well below −10°C1. Overwinter microbial activity has important effects on global carbon (C) budgets2, nutrient cycling and vegetation community composition3. Microbial respiration is highly temperature sensitive in frozen soils, as liquid water and solute availability decrease rapidly with declining temperature4. Thus, temperature is considered the ultimate control on overwinter soil microbial activity in the Arctic. Warmer winter soils are thought to yield greater microbial respiration of available C, greater overwinter CO2efflux and a flush of nutrients that could be available for plant uptake at thaw3. Rising air temperature, combined with changes in timing and/or depth of snowpack development, is leading to warmer Arctic winter soils5. Using observational and experimental approaches in the field and in the laboratory, we demonstrate that persistently warm winter soils can lead to labile C starvation of the microbial community and reduced respiration rates, despite the high C content of most arctic soils. If Arctic winter soil temperatures continue to rise, microbial C limitation will reduce cold season CO2emissions and alter soil nutrient cycling, if not countered by greater labile C inputs.
Effect of salinity on modulation by ATP, protein kinases and FXYD2 peptide of gill (Na+, K+)-ATPase activity in the swamp ghost crabUcides cordatus(Brachyura, Ocypodidae)
Authors: Leone Francisco A. , Lucena Malson N. , Fabri Leonardo M. , Garçon Daniela P. , Fontes Carlos F.L. , Faleiros Rogério O. , Moraes Cintya M. , McNamara John C.
Published: April 2020

The gill (Na+, K+)-ATPase is the main enzyme that underpins osmoregulatory ability in crustaceans that occupy biotopes like mangroves, characterized by salinity variation. We evaluated osmotic and ionic regulatory ability in the semi-terrestrial mangrove crabUcides cordatusafter 10-days acclimation to different salinities. We also analyzed modulation by exogenous FXYD2 peptide and by endogenous protein kinases A and C, and Ca2+- calmodulin-dependent kinase of (Na+, K+)-ATPase activity. Hemolymph osmolality was strongly hyper-/hypo-regulated in crabs acclimated at 2 to 35 ‰S. Cl-was well hyper-/hypo- regulated although Na+much less so, becoming iso-natremic at high salinity. (Na+, K+)- ATPase activity was greatest in isosmotic crabs (26 ‰S), diminishing progressively from 18 and 8 ‰S (≈0.5 fold) to 2 ‰S (0.04-fold), and decreasing notably at 35 ‰S (0.07-fold). At low salinity, the (Na+, K+)-ATPase exhibited a low affinity ATP-binding site that showed Michaelis-Menten behavior. Above 18 ‰S, an additional, high affinity ATP-binding site, corresponding to 10-20% of total (Na+, K+)-ATPase activity appeared. Activity is stimulated by exogenous pig kidney FXYD2 peptide, while endogenous protein kinases A and C and Ca2+/calmodulin-dependent kinase all inhibit activity. This is the first demonstration of inhibitory phosphorylation of a crustacean (Na+, K+)-ATPase by Ca2+/calmodulin-dependent kinase. Curiously, hyper-osmoregulation inU. cordatusshows little dependence on gill (Na+, K+)-ATPase activity, suggesting a role for other ion transporters. These findings reveal that the salinity acclimation response inU. cordatusconsists of a suite of osmoregulatory and enzymatic adjustments that maintain its osmotic homeostasis in a challenging, mangrove forest environment.

Graphical abstract

Highlights

Gill (Na+, K+)-ATPase activity is greatest in isosmotic crabs, diminishing in lower and higher salinities.

A high affinity ATP-binding site (10-20% of total activity) is exposed above 18 ‰S.

Exogenous FXYD2 peptide stimulates activity; endogenous PKA, PKC and CaMK inhibit activity.

First demonstration of inhibitory phosphorylation of crustacean (Na+, K+)-ATPase by CaMK.

Hyper-osmoregulation shows little dependence on (Na+, K+)-ATPase activity.
Tumor-infiltrating nerves create an electro-physiologically active microenvironment and contribute to treatment resistance
Authors: Kovacs Attila , Vermeer Daniel W. , Madeo Marianna , Reavis Hunter D. , Vermeer Samuel J. , Williamson Caitlin S. , Rickel Alex , Stamp Jillian , Lucido Christopher T. , Cain Jacob , Bell Maria , Morgan Mark , Yoon Ju-Yoon , Mitchell Marilyn A. , Tulina Natalia , Stuckelberger Sarah , Budina Anna , Omran Dalia K. , Jung Euihye , Schwartz Lauren E. , Eichwald Tuany , Hong Zhongkui , Weimer Jill , Hooper Jody E. , Godwin Andrew K. , Talbot Sebastien , Drapkin Ronny , Vermeer Paola D.
Published: April 2020

Patients with densely innervated tumors do poorly as compared to those with sparsely innervated disease. Why some tumors heavily recruit nerves while others do not, remains unknown as does the functional contribution of tumor-infiltrating nerves to cancer. Moreover, while patients receive chemotherapeutic treatment, whether these drugs affect nerve recruitment has not been tested. Using a murine model of ovarian cancer, we show that tumor-infiltrating sensory nerves potentiate tumor growth, decrease survival, and contribute to treatment resistance. Furthermore, matched patient samples show significantly increased tumor innervation following chemotherapy.In vitroanalysis of tumor-released extracellular vesicles (sEVs) shows they harbor neurite outgrowth activity. These data suggest that chemotherapy may alter sEV cargo, endowing it with robust nerve recruiting capacity.
Overcoming bias in gene-set enrichment analyses of brain-wide transcriptomic data
Authors: Fulcher Ben D. , Arnatkevičiūtė Aurina , Fornito Alex
Published: April 2020

The recent availability of whole-brain atlases of gene expression, which quantify the transcriptional activity of thousands of genes across many different brain regions, has opened new opportunities to understand how gene-expression patterns relate to spatially varying properties of brain structure and function. To aid interpretation of a given neural phenotype, gene-set enrichment analysis (GSEA) has become a standard statistical methodology to identify functionally related groups of genes, annotated using systems such as the Gene Ontology (GO), that are associated with a given phenotype. While GSEA has identified groups of genes related to diverse aspects of brain structure and function in mouse and human, here we show that these results are affected by substantial statistical biases. Quantifying the falsepositive rates of individual GO categories across an ensemble of random phenotypic maps, we found an average 875-fold inflation of significant findings relative to expectation in mouse, and a 582-fold inflation in human, with some categories being judged as significant for over 20% of random phenotypes. Concerningly, the probability of a GO category being reported as significant in the extant literature increases with its estimated false-positive rate, suggesting that published reports are strongly affected by the reporting of false-positive bias. We show that the bias is primarily driven by within-category gene–gene coexpression and spatial autocorrelation, which are not accounted for in conventional GSEA nulls, and we introduce flexible ensemble-based null models that can account for these effects. Testing a range of structural connectivity and cell density phenotypes in mouse and human, we demonstrate that many GO categories that would conventionally be judged as highly significant are in fact consistent with ensembles of random phenotypes. Our results highlight major pitfalls with applying standard GSEA to brain-wide transcriptomic data and outline solutions to this pervasive problem, which is made available as an open toolbox.
Genetic differences between extreme and composite constitution types from whole exome sequences reveal actionable variations
Authors: Abbas Tahseen , Kutum Rintu , Pandey Rajesh , Dakle Pushkar , Narang Ankita , Manchanda Vijeta , Patil Rutuja , Aggarwal Dheeraj , Bansal Gourja , Sharma Pooja , Chaturvedi Gaura , Girase Bhushan , Srivastava Ankita , Juvekar Sanjay , Dash Debasis , Prasher Bhavana , Mukerji Mitali
Published: April 2020

Personalized medicine relies on successful identification of genome-wide variations that governs inter-individual differences in phenotypes and system level outcomes. In Ayurveda, assessment of composite constitution types “Prakriti”forms the basis for risk stratification, predicting health and disease trajectories and personalized recommendations. Here, we report a novel method for identifying pleiotropic genes and variants that associate with healthy individuals of three extreme and contrasting “Prakriti”constitutions through exome sequencing and state-of-the-art computational methods. Exome Seq of three extremePrakrititypes from 108 healthy individuals 54 each from genetically homogeneous populations of North India (NI, Discovery cohort) and Western India (VADU, Replication cohort) were evaluated. Fisher’s Exact Test was applied betweenPrakrititypes in both cohorts and further permutation based p-value was used for selection of exonic variants. To investigate the effect of sample size per genetic association test, we performed power analysis. Functional impact of differentiating genes and variations were inferred using diverse resources -Toppfun, GTEx, GWAS, PheWAS, UK Biobank and mouse knockdown/knockout phenotype (MGI). We also applied supervised machine learning approach to evaluate the association of exonic variants with multisystem phenotypes ofPrakriti. Our targeted investigation into exome sequencing from NI (discovery) and VADU (validation) cohorts datasets provide ~7,000 differentiating SNPs. Closer inspection further identified a subset of SNPs (2407 (NI) and 2393 (VADU)), that mapped to an overlapping set of 1181 genes. This set can robustly stratify the Prakriti groups into three distinct clusters with distinct gene ontological (GO) enrichments. Functional analysis further strengthens the potential pleiotropic effects of these differentiating genes/variants and multisystem phenotypic consequences. Replicated SNPs map to some very prominent genes likeFIG4, EDNRA, ANKLE1, BCKDHA, ATP5SL, EXOCS5,IFIT5, ZNF502, PNPLA3 and IL6R. Lastly, multivariate analysis using random forest uncovered rs7244213 within urea transporterSLC14A2, that associate with an ensemble of features linked to distinct constitutions. Our results reinforce the concept of integration of Prakriti based deep phenotypes for risk stratification of healthy individuals and provides markers for early actionable interventions.
Klf4 methylated by Prmt1 is required for lineage segregation of epiblast and primitive endoderm
Authors: Zuo Zhen-yu , Yang Guang-hui , Wang Hai-yu , Zhang Yan-jun , Cai Yun , Chen Fei , Xiao Yi , Cheng Mo-bin , Huang Yue , Zhang Ye
Published: April 2020

The second cell fate decision in the early stage of mammalian embryonic development is pivotal; however, the underlying molecular mechanism is largely unexplored. Here, we report that Prmt1 acts as an important regulator in primitive endoderm (PrE) formation. First, an embryonic chimeric assay showed that Prmt1 inhibition induces the integration of mouse embryonic stem cells (ESCs) into the PrE. Second, Prmt1 inhibition promotes Gata6 expression in both mouse blastocysts and ESCs. Single-cell RNA sequencing and flow cytometry assays demonstrated that Prmt1 depletion in ESCs contributes to an emerging cluster, where PrE genes are upregulated significantly. Furthermore, the efficiency of extraembryonic endoderm stem cell induction increased in Prmt1-depleted ESCs. Finally, we showed that the pluripotency factor Klf4 methylated at Arg396 by Prmt1 is required for recruitment of the repressive mSin3a/HDAC complex to silence PrE genes. Therefore, we reveal a regulatory mechanism for cell fate decisions centered on Prmt1-mediated Klf4 methylation.
Characterising a stable five-species microbial community for use in experimental evolution and ecology
Authors: Castledine Meaghan , Pennycook Joseph , Newbury Arthur , Lear Luke , Erdos Zoltan , Lewis Rai , Kay Suzanne , Sanders Dirk , Sünderhauf David , Buckling Angus , Hesse Elze , Padfield Daniel
Published: April 2020

Model microbial communities are regularly used to test ecological and evolutionary theory as they are easy to manipulate and have fast generation times, allowing for large-scale, high throughput experiments. A key assumption for most model microbial communities is that they stably coexist, but this is rarely tested experimentally. Here we report the (dis)assembly of a five-species microbial community from a metacommunity of soil microbes that can be used for future experiments. Using reciprocal invasion from rare experiments we show that all species can coexist and we demonstrate that the community is stable for a long time (∼600 generations). Crucially for future work, we show that each species can be identified by their plate morphologies, even after >1 year in co-culture. We characterise pairwise species interactions and produce high-quality reference genomes for each species. This stable five-species community can be used to test key questions in microbial ecology and evolution.
CREB1 contributes colorectal cancer cell plasticity by regulating lncRNA CCAT1 and NF-κB pathways
Authors: Li Bin , Zheng Li-Si , Zhang Chen-Min , Huang Qiao-Juan , Guo Yan-Hua , Wang Lu-Qin , Yu Peng , Liu Shu-Rong , Lin Qiao , Luo Yu-Xia , Zhou Hui , Yang Jian-Hua , Qu Liang-Hu
Published: April 2020

The CREB1 gene encodes a pleiotropic transcription factor that frequently dysregulated in cancers. CREB1 can regulates tumour cell status of proliferation or migration, however, the molecular basis for this switch involvement in cell plasticity has not been fully understood. Here, we show that knocking out CREB1 triggered a remarkable effect of epithelial-mesenchymal transition (EMT) and led to the occurrence of inhibited proliferation and enhanced motility in cancer cells. Mechanistically, CREB1-knockout cells showed arrest in the G0/G1 phase as a result of impaired CREB1-dependent transcription of CCAT1 and E2F1. Interestingly, the competition between the coactivator CBP/p300 for CREB1 and p65 leads to the activation of the NF-κB pathway in cells with CREB1 disrupted, which induces an EMT phenotype and enhances motility. These studies identified previously unknown mechanisms of CREB1 in cell plasticity via its lncRNA and protein effector pathways, revealing an important feature that should be considered in CREB1-targeted tumour therapies.
DrosophilaSex Peptide Controls the Assembly of Lipid Microcarriers in Seminal Fluid
Authors: Wainwright S. Mark , Mendes Cláudia C. , Sekar Aashika , Kroeger Benjamin , Hellberg Josephine E.E.U. , Fan Shih-Jung , Pavey Abigail , Marie Pauline , Leiblich Aaron , Gandy Carina , Corrigan Laura , Patel Rachel , Wigby Stuart , Morris John F. , Goberdhan Deborah C.I. , Wilson Clive
Published: April 2020

Seminal fluid plays an essential role in promoting male reproductive success and modulating female physiology and behaviour. In the fruit fly,Drosophila melanogaster, Sex Peptide (SP) is the best-characterised protein mediator of these effects. It is secreted from the paired male accessory glands (AGs), which, like the mammalian prostate and seminal vesicles, generate most of the seminal fluid contents. After mating, SP binds to spermatozoa and is retained in the female sperm storage organs. It is gradually released by proteolytic cleavage and induces several long-term post-mating responses including ovulation, elevated feeding and reduced receptivity to remating, primarily signalling through the SP receptor (SPR). Here, we demonstrate a previously unsuspected SPR-independent function for SP. We show that, in the AG lumen, SP and secreted proteins with membrane-binding anchors are carried on abundant, large neutral lipid-containing microcarriers, also found in other SP-expressingDrosophilaspecies. These microcarriers are transferred to females during mating, where they rapidly disassemble. Remarkably, SP is a key assembly factor for microcarriers and is also required for the female disassembly process to occur normally. Males expressing non-functional SP mutant proteins that affect SP’s binding to and release from sperm in females also do not produce normal microcarriers, suggesting that this male-specific defect contributes to the resulting widespread defects in ejaculate function. Our data therefore reveal a novel role for SP in formation of seminal macromolecular assemblies, which may explain the presence of SP inDrosophilaspecies, which lack the signalling functions seen inD. melanogaster.

Significance Statement

Seminal fluid plays a critical role in reprogramming female physiology and behaviour to promote male reproductive success. We show in the fruit fly that specific seminal proteins, including the archetypal ‘female-reprogramming’ molecule Sex Peptide, are stored in male seminal secretions in association with large neutral lipid-containing microcarriers, which rapidly disperse in females. Related structures are also observed in other Sex Peptide-expressingDrosophilaspecies. Males lacking Sex Peptide have structurally defective microcarriers, leading to abnormal cargo loading and transfer to females. Our data reveal that this key signalling molecule inDrosophilaseminal fluid is also a microcarrier assembly factor that controls transfer of other seminal factors, and that this may be a more evolutionarily ancient role of this protein.
Increased prostaglandin-D2in male but not female STAT3-deficient hearts shifts cardiac progenitor cells from endothelial to white adipocyte differentiation
Authors: Stelling Elisabeth , Ricke-Hoch Melanie , Erschow Sergej , Hoffmann Steve , Bergmann Anke Katharina , Heimerl Maren , Pietzsch Stefan , Battmer Karin , Haase Alexandra , Stapel Britta , Scherr Michaela , Balligand Jean-Luc , Binah Ofer , Hilfiker-Kleiner Denise
Published: April 2020

Cardiac levels of the signal transducer and activator of transcription factor-3 (STAT3) decline with age, and male but not female mice with a cardiomyocyte-specific STAT3 deficiency (CKO) display premature age-related heart failure associated with reduced cardiac capillary density. In the present study isolated male and female CKO-cardiomyocytes exhibit increased prostaglandin (PG)-generating cyclooxygenase-2 (COX-2) expression. The PG-degrading hydroxyprostaglandin-dehydrogenase-15 (HPGD) expression is only reduced in male cardiomyocytes, which is associated with increased PGD2secretion from isolated male but not female CKO-cardiomyocytes. Reduced HPGD expression in male cardiomyocytes derive from impaired androgen-receptor-(AR)-signaling due to loss of its co-factor STAT3. Elevated PGD2secretion in males is associated with increased white adipocyte accumulation in aged male but not female hearts. Adipocyte differentiation is enhanced in isolated SCA-1+-cardiac-progenitor-cells (CPC) from young male CKO-mice compared to the adipocyte differentiation of male wildtype (WT)-CPC and CPC isolated from female mice. Epigenetic analysis in freshly isolated male CKO-CPC display hypermethylation in pro-angiogenic genes (Fgfr2,Epas1) and hypomethylation in the white adipocyte differentiation geneZfp423associated with upregulated ZFP423 expression and a shift from endothelial to white adipocyte differentiation compared to WT-CPC. The expression of the histone-methyltransferase EZH2 is reduced in male CKO-CPC compared to male WT-CPC whereas no differences in the EZH2 expression in female CPC were observed. Clonally expanded CPC can differentiate into endothelial cells or into adipocytes depending on the differentiation conditions. ZFP423 overexpression is sufficient to induce white adipocyte differentiation of clonal CPC. In isolated WT-CPC, PGD2stimulation reduces the expression of EZH2 thereby upregulating ZFP423 expression and promoting white adipocyte differentiation.

Thus, cardiomyocyte STAT3-deficiency leads to age-related and sex-specific cardiac remodeling and failure in part due to sex-specific alterations in PGD2secretion and subsequent epigenetic impairment of the differentiation potential of CPC. Causally involved is the impaired AR signaling in absence of STAT3, which reduces the expression of the PG degrading enzyme HPGD.
It takes two to tango: M-current swings with the persistent sodium current to set the speed of locomotion
Authors: Verneuil Jeremy , Brocard Cécile , Villard Laurent , Peyronnet-Roux Julie , Brocard Frédéric
Published: April 2020

The central pattern generator (CPG) for locomotion is set of pacemaker neurons endowed with inherent bursting driven by the persistent sodium current (INaP). How they proceed to regulate the locomotor rhythm remained unknown. Here, in neonatal rodents, we identified a persistent potassium current, critical in regulating pacemakers and locomotion speed. This current recapitulates features of the M-current (IM); a subthreshold non-inactivating outward current blocked by XE991 and enhanced by ICA73. Immunostaining and mutant mice highlight an important role of axonal Kv7.2 channels in mediatingIM. Pharmacological modulation ofIMregulates the emergence and the frequency regime of both pacemaker and CPG activities, and controls the speed of locomotion. Computational models captured these results and show howed an interplay betweenIMandINaPthat endows the locomotor CPG with rhythmogenic properties. Overall, this study provides fundamental insights into howIMandINaPwork in tandem to set the speed of locomotion.
Repetitive Transcranial Magnetic Stimulation Activates Glial Cells and Inhibits Neurogenesis after Pneumococcal Meningitis
Authors: Muri Lukas , Oberhänsli Simone , Buri Michelle , Le Ngoc Dung , Grandgirard Denis , Bruggmann Rémy , Müri René M. , Leib Stephen L.
Published: April 2020

Pneumococcal meningitis (PM) causes damage to the hippocampus, a brain structure critically involved in learning and memory. Hippocampal injury – which compromises neurofunctional outcome – occurs as apoptosis of progenitor cells and immature neurons of the hippocampal dentate granule cell layer thereby impairing the regenerative capacity of the hippocampal stem cell niche. Repetitive transcranial magnetic stimulation (rTMS) harbours the potential to modulate the proliferative activity of this neuronal stem cell niche. In this study, specific rTMS protocols – namely continuous and intermittent theta burst stimulation (cTBS and iTBS) – were applied on infant rats microbiologically cured from PM by five days of antibiotic treatment. Following two days of exposure to TBS, differential gene expression was analysed by whole transcriptome analysis using RNAseq. cTBS provoked a prominent effect in inducing differential gene expression in the cortex and the hippocampus, whereas iTBS only affect gene expression in the cortex. TBS induced polarisation of microglia and astrocytes towards an inflammatory phenotype, while reducing neurogenesis, neuroplasticity and regeneration. cTBS was further found to induce the release of pro-inflammatory cytokinesin vitro. We conclude that cTBS intensified neuroinflammation after PM, which translated into increased release of pro-inflammatory mediators thereby inhibiting neuroregeneration.
Differential effects of novel kappa opioid receptor antagonists on dopamine neurons using acute brain slice electrophysiology
Authors: Margolis Elyssa B. , Wallace Tanya L. , Van Orden Lori Jean , Martin William J.
Published: April 2020

Activation of the kappa opioid receptor (KOR) contributes to the aversive properties of stress, and modulates key neuronal circuits underlying many neurobehavioral disorders. KOR agonists directly inhibit ventral tegmental area (VTA) dopaminergic neurons, contributing to aversive responses [1,2]; therefore, selective KOR antagonists represent a novel therapeutic approach to restore circuit function. We used whole cell electrophysiology in acute rat midbrain slices to evaluate pharmacological properties of four novel KOR antagonists: BTRX-335140, BTRX-395750, PF-04455242, and JNJ-67953964. Each compound concentration-dependently reduced the outward current induced by the KOR selective agonist U-69,593. BTRX-335140 and BTRX-395750 fully blocked U-69,593 currents (IC50= 1.3 ± 0.9 and 4.6 ± 0.9 nM, respectively). JNJ-67953964 showed an IC50of 0.3 ± 1.3 nM. PF-04455242 (IC50= 19.6 ± 16 nM) exhibited partial antagonist activity (∼60% maximal blockade). In 50% of neurons, 1 μM PF-04455242 generated an outward current independent of KOR activation. BTRX-335140 (10 nM) did not affect responses to saturating concentrations of the mu opioid receptor (MOR) agonist DAMGO or the delta opioid receptor (DOR) agonist DPDPE, while JNJ-67953964 (10 nM) partially blocked DAMGO responses and had no effect on DPDPE responses. Importantly, BTRX-335140 (10 nM) rapidly washed out with complete recovery of U-69,593 responses within 10 min. Collectively, we show electrophysiological evidence of key differences amongst KOR antagonists that could impact their therapeutic potential and have not been observed using recombinant systems. The results of this study demonstrate the value of characterizing compounds in native neuronal tissue and within disorder-relevant circuits implicated in neurobehavioral disorders.
Regulatory interactions between Vax1, Pax6, and miR-7 regionalize the lateral Ventricular-Subventricular Zone during post-natal Olfactory Bulb neurogenesis in mice
Authors: Coré Nathalie , Erni Andrea , Mellon Pamela L. , Hoffmann Hanne M. , Béclin Christophe , Cremer Harold
Published: April 2020

Several subtypes of interneurons destined for the olfactory bulb are continuously generated after birth by neural stem cells located in the ventricular-subventricular zones of the lateral ventricles. Future neuronal identity depends on the positioning of pre-determined neural stem cells along the ventricle walls, which, in turn, depends on delimited expression domains of transcription factors and their cross regulatory interactions. However, mechanisms underlying positional identity of neural stem cells are still poorly understood. Here we show that the transcription factor Vax1 controls the production of two specific neuronal sub-types. First, it is directly necessary to generate Calbindin expressing interneurons from ventro-lateral progenitors. Second, it represses the generation of dopaminergic neurons by dorso-lateral progenitors through inhibiting Pax6 expression in the dorso-lateral wall. We provide evidence that this repression occurs via activation of microRNA miR-7, targeting Pax6 mRNA.
Rescoring ensembles of protein-protein docking poses using consensus approaches
Authors: Launay Guillaume , Ohue Masahito , Santero Julia Prieto , Matsuzaki Yuri , Hilpert Cécile , Uchikoga Nobuyuki , Hayashi Takanori , Martin Juliette
Published: April 2020

Scoring is a challenging step in protein-protein docking, where typically thousands of solutions are generated. Successful scoring is more often based on physicochemical evaluation of the generated interfaces and/or statistical potentials that reproduce known interface properties. Another route is offered by consensus-based rescoring, where the set of solutions is used to build statistics in order to identify recurrent solutions. We explore several ways to perform consensus-based rescoring on the ZDOCK decoy set for Benchmark 4. We show that the information of the interface size is critical for successful rescoring. We combine consensus-based rescoring with the ZDOCK native scoring function and show that this improves the initial results.
Wei2GO: weighted sequence similarity-based protein function prediction
Authors: Reijnders Maarten J.M.F
Published: April 2020

Background

Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases.

Methods

This paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations.

Results

Wei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, Fmax scores, and Smin scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes.

Availability

Wei2GO is written in Python 3, and can be found athttps://gitlab.com/mreijnders/Wei2GO
Local externalization of phosphatidylserine mediates developmental synaptic pruning by microglia
Authors: Scott-Hewitt Nicole , Perrucci Fabio , Morini Raffaella , Erreni Marco , Mahoney Matthew , Witkowska Agata , Carey Alanna , Faggiani Elisa , Schuetz Lisa Theresia , Mason Sydney , Tamborini Matteo , Bizzotto Matteo , Passoni Lorena , Filipello Fabia , Jahn Reinhard , Stevens Beth , Matteoli Michela
Published: April 2020

Neuronal circuits assembly requires the fine equilibrium between synapse formation and elimination. Microglia, through the elimination of supernumerary synapses, have an established role in this process. While the microglial receptor TREM2 and the soluble complement proteins C1q and C3 are recognized key players in this process, the neuronal molecular components that tag synapses to be eliminated are still undefined. Here we show that exposed phosphatidylserine (PS) represents a neuronal ‘eat-me’ signal enabling microglial-mediated synapse pruning. In hippocampal neuron and microglia co-cultures, synapse elimination can be prevented by blocking accessibility of exposed PS using Annexin V or through microglial loss of TREM2.In vivo, exposed PS is detectable at both hippocampal and retinogeniculate synapses, where exposure coincides with the onset of synapse elimination and increased PS engulfment by microglia. Mice deficient in C1q, which fail to properly refine retinogeniculate connections, display elevated exposed PS and reduced PS engulfment by microglia. These data provide mechanistic insight into microglial-mediated synapse pruning and identify a novel role of developmentally regulated PS exposure that is common among developing brain structures.
Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells
Authors: Stanifer Megan L. , Kee Carmon , Cortese Mirko , Triana Sergio , Mukenhirn Markus , Kraeusslich Hans-Georg , Alexandrov Theodore , Bartenschlager Ralf , Boulant Steeve
Published: April 2020

SARS-CoV-2 is an unprecedented worldwide health problem that requires concerted and global approaches to better understand the virus in order to develop novel therapeutic approaches to stop the COVID-19 pandemic and to better prepare against potential future emergence of novel pandemic viruses. Although SARS-CoV-2 primarily targets cells of the lung epithelium causing respiratory infection and pathologies, there is growing evidence that the intestinal epithelium is also infected. However, the importance of the enteric phase of SARS-CoV-2 for virus-induced pathologies, spreading and prognosis remains unknown. Here, using both colon-derived cell lines and primary non-transformed colon organoids, we engage in the first comprehensive analysis of SARS-CoV-2 lifecycle in human intestinal epithelial cells. Our results demonstrate that human intestinal epithelial cells fully support SARS-CoV-2 infection, replication and production of infectiousde-novovirus particles. Importantly, we identified intestinal epithelial cells as the best culture model to propagate SARS-CoV-2. We found that viral infection elicited an extremely robust intrinsic immune response where, interestingly, type III interferon mediated response was significantly more efficient at controlling SARS-CoV-2 replication and spread compared to type I interferon. Taken together, our data demonstrate that human intestinal epithelial cells are a productive site of SARS-CoV-2 replication and suggest that the enteric phase of SARS-CoV-2 may participate in the pathologies observed in COVID-19 patients by contributing in increasing patient viremia and by fueling an exacerbated cytokine response.
Human CD8+T cells exhibit a shared antigen threshold for different effector responses
Authors: Abu-Shah Enas , Trendel Nicola , Kruger Philipp , Nguyen John , Pettmann Johannes , Kutuzov Mikhail , Dushek Omer
Published: April 2020

T cells recognising cognate pMHC antigens become activated to elicit a myriad of cellular responses, such as target cell killing and the secretion of different cytokines, that collectively contribute to adaptive immunity. These effector responses have been hypothesised to exhibit different antigen dose and affinity thresholds, suggesting that pathogen-specific information may be encoded within the nature of the antigen. Here, using systematic experiments in a reductionist system, where primary human CD8+T cell blasts are stimulated by recombinant pMHC antigen alone, we show that different inflammatory cytokines have comparable antigen dose thresholds across a 25,000-fold variation in affinity. Although co-stimulation by CD28, CD2, and CD27 increased cytokine production in this system, the antigen threshold remained comparable across different cytokines. When using primary human memory CD8+T cells responding to autologous antigen presenting cells equivalent thresholds were also observed for cytokine production and killing. These findings imply a simple phenotypic model of TCR signalling where multiple T cell responses share a common rate-limiting threshold and a conceptually simple model of antigen recognition, where the chance factor of antigen dose and affinity do not provide any additional response-specific information.
Heme Attenuates Endogenous Opioid Levels in Leukocytes of HIV positive individuals with Chronic Widespread Pain
Authors: Aggarwal Saurabh , DeBerry Jennifer J , Ahmad Israr , Lynn Prichard , Dewitte Cary , Malik Simran , Merlin Jessica S , Goodin Burel R , Heath Sonya L , Matalon Sadis
Published: April 2020

The prevalence of chronic widespread pain (CWP) in people with HIV (PWH) is high, yet the underlying mechanisms are elusive. Leukocytes synthesize the endogenous opioid, β-endorphin (β-END), within their endoplasmic reticulum (ER). When released into plasma, β-END dampens nociceptive transmission by binding to opioid receptors on sensory neurons. In the present study, we hypothesized that heme-induced ER stress attenuates leukocyte levels/release of β-END, thereby increasing pain sensitivity in PWH. Results demonstrate that PWH with CWP have fragile erythrocytes, high plasma levels of cell-free heme, and impaired heme metabolism. Leukocytes from PWH with CWP also had high ER stress and low β-END compared to PWH without CWP and HIV-negative individuals with or without pain.In vitroheme exposure decreased β-END levels/secretion in murine monocytes/macrophages, which was prevented by treatment with sodium 4-phenylbutyrate, an ER stress inhibitor. To mimic hemolytic effects in a preclinical modelin vivo, C57BL/6 mice were injected with phenylhydrazine hydrochloride (PHZ). PHZ increased cell-free heme and ER stress, decreased leukocyte β-END levels and hindpaw mechanical sensitivity thresholds. Treatment of PHZ-injected mice with the heme scavenger, hemopexin, blocked these effects, suggesting that heme-induced ER stress and a subsequent decrease in leukocyte β-END may contribute to CWP in PWH.
Targeted stimulation of an orbitofrontal network disrupts decisions based on inferred, not experienced outcomes
Authors: Wang Fang , Howard James D. , Voss Joel L. , Schoenbaum Geoffrey , Kahnt Thorsten
Published: April 2020

When direct experience is unavailable, animals and humans can imagine or infer the future to guide decisions. Behavior based on direct experience versus inference may recruit distinct but overlapping brain circuits. In rodents, the orbitofrontal cortex (OFC) contains neural signatures of inferred outcomes, and OFC is necessary for behavior that requires inference but not for responding driven by direct experience. In humans, OFC activity is also correlated with inferred outcomes, but it is unclear whether OFC activity is required for inference-based behavior. To test this, we used non-invasive network-based continuous theta burst stimulation (cTBS) to target lateral OFC networks in the context of a sensory preconditioning task that was designed to isolate inference-based behavior from responding that can be based on direct experience alone. We show that relative to sham, cTBS targeting this network impairs reward-related behavior in conditions in which outcome expectations have to be mentally inferred. In contrast, OFC-targeted stimulation does not impair behavior that can be based on previously experienced stimulus-outcome associations. These findings suggest that activity in the targeted OFC network supports decision making when outcomes have to be mentally simulated, providing converging cross-species evidence for a critical role of OFC in model-based but not model-free control of behavior.
Effect of prolonged captivity on the hemolymph profile ofTachypleus gigas
Authors: Akbar John B. , Sheikh Hassan I , Solachuddin J.A. Ichwan , Kamaruzzaaman B.Y.
Published: April 2020

Horseshoe crabs amebocyte cells degranulate to form a gel clot when in contact with endotoxins. This phenomenon is the basis of both Horseshoe crab immune system and detection of endotoxin in biologicals. The present study investigates the amebocyte cells quality inTachypleus gigaspre and post bleeding under captivity. Wild and captive horseshoe crabs (5 months captivity) were bled in 6 anticoagulant formulations (A, B, C, D, E and F). No profound difference in cell density between captive and wild groups with the mean value of 0.883×107a cells/mL and 0.917×107cells/mL, respectively. while, the cell viability of the captive group was significantly lower than the wild crabs (F=808.075, p<0.001). Anticoagulant formulation significantly affected cell viability and cell morphology in both captive and wild groups (p<0.001). Amebocyte cells collected from the wildT. gigasusing optimum anticoagulant (formula C) showed 0.6 ×107cells/mL cell density and 86.9% cell viability, while morphology analysis revealed the percentage of contracted, granular flattened and degranulated flattened cells were 14.62%, 71.39% and 14%, respectively. The anticoagulant formulations showed varying capabilities in maintaining cell viability due to its buffering and chelating capacity. We conclude that captivity has a negative effect on the amebocyte cell quality.

HIGHLIGHTS

Captivity has a negative impact on amebocyte quality in horseshoe crab (Tachypleus gigas).

No significant difference in cell density between captive and wild crabs.

Anticoagulant formulations have significant impact on the cell density, viability and morphology

Captive crabs were immunocompromised due to single specific feed intake.
Complementary α-arrestin - Rsp5 ubiquitin ligase complexes control selective nutrient transporter endocytosis in response to amino acid availability
Authors: Ivashov Vasyl , Zimmer Johannes , Schwabl Sinead , Kahlhofer Jennifer , Weys Sabine , Gstir Ronald , Jakschitz Thomas , Kremser Leopold , Bonn Günther K. , Lindner Herbert , Huber Lukas A. , Léon Sébastien , Schmidt Oliver , Teis David
Published: April 2020

How cells adjust transport across their membranes is incompletely understood. Previously, we have shown thatS.cerevisiaebroadly re-configures the nutrient transporters at the plasma membrane in response to amino acid availability, through selective endocytosis of sugar- and amino acid transporters (AATs) (Müller et al., 2015). A genome-wide screen now revealed that Art2/Ecm21, a member of the α-arrestin family of Rsp5 ubiquitin ligase adaptors, is required for the simultaneous endocytosis of four AATs and induced during starvation by the general amino acid control pathway. Art2 uses a basic patch to recognize C-terminal acidic sorting motifs in these AATs and instructs Rsp5 to ubiquitinate proximal lysine residues. In response to amino acid excess, Rsp5 instead uses TORC1-activated Art1 to detect N-terminal acidic sorting motifs within the same AATs, which initiates exclusive substrate-induced endocytosis of individual AATs. Thus, amino acid availability activates complementary α-arrestin-Rsp5-complexes to control selective endocytosis for nutrient acquisition.
Gene expression in the cardiovascular system of the domestic sheep (Ovis aries); a new tool to advance our understanding of cardiovascular disease
Authors: Tsang Hiu-Gwen , Clark Emily L. , Markby Greg R. , Bush Stephen J. , Hume David A. , Corcoran Brendan M. , MacRae Vicky E. , Summers Kim M.
Published: April 2020

Large animal models are of increasing importance in cardiovascular disease research as they demonstrate more similar cardiovascular features (in terms of anatomy, physiology and size) to humans than do rodent species. The maintenance of a healthy cardiovascular system requires expression of genes that contribute to essential biological activities and repression of those that are associated with functions likely to be detrimental to cardiovascular homeostasis. In this study we have used the transcriptome of the sheep, which has been utilised extensively to model human physiology and disease, to explore genes implicated in the process of vascular calcification. Vascular calcification is a major disruption to cardiovascular homeostasis where tissues of the cardiovascular system undergo ectopic calcification and consequent dysfunction. We investigate the gene expression profiles of genes involved in vascular calcification in a wide array of cardiovascular tissues and across multiple developmental stages, using RT-qPCR. The majority of transcriptomic studies on the mammalian cardiovascular system to date have focused on regional expression of specific genes. Here we also use RNA sequencing results from the sheep heart and cardiac valves to further explore the transcriptome of the cardiovascular system in this large animal. Our results demonstrate that there is a balance between genes that promote and those that suppress mineralisation during development and across cardiovascular tissues. We show extensive expression of genes encoding proteins involved in formation and maintenance of the extracellular matrix in cardiovascular tissues, and high expression of haematopoietic genes in the cardiac valves. Our analysis will support future research into the functions of implicated genes in the development of vascular calcification, and increase the utility of the sheep as a large animal model for understanding cardiovascular disease. This study provides a foundation to explore the transcriptome of the developing cardiovascular system and is a valuable resource for the fields of mammalian genomics and cardiovascular research.