bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parabrachial complex processes dura inputs through a direct trigeminal ganglion-to-parabrachial connection
Authors: Uddin Olivia , Anderson Michael , Smith Jesse , Masri Radi , Keller Asaf 
Published: October 2020

AbstractMigraines cause significant disability and contribute heavily to healthcare costs. Irritation of the meninges’ outermost layer (the dura mater), and trigeminal ganglion activation contribute to migraine initiation. Maladaptive changes in central pain-processing regions are also important in maintaining pain. The parabrachial complex (PB) is a central region that mediates chronic pain. PB receives diverse sensory information, including a direct input from the trigeminal ganglion. We hypothesized that PB processes inputs from the dura. Usingin vivoelectrophysiology recordings from single units in anesthetized rats we identified 58 neurons in lateral PB that respond reliably and with short latency to electrical dura stimulation. After injecting tracer into PB, anatomical examination reveals retrogradely labeled cell bodies in the trigeminal ganglion. Neuroanatomical tract-tracing revealed a population of neurons in the trigeminal ganglion that innervate the dura and project directly to PB. These findings indicate that PB is strategically placed to process dura inputs, and suggest that it is directly involved in the pathogenesis of migraine headaches.
Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure
Authors: Zoni Valeria , Shinoda Wataru , Vanni Stefano 
Published: October 2020

AbstractLipid droplets (LD) are intracellular organelles responsible for lipid storage, and they emerge from the endoplasmic reticulum (ER) upon the accumulation of neutral lipids, mostly triglycerides (TG), between the two leaflets of the ER membrane. LD biogenesis takes place at ER sites that are marked by the protein seipin, which subsequently recruits additional proteins to catalyse LD formation. Deletion of seipin, however, does not abolish LD biogenesis, and its precise role in controlling LD assembly remains unclear. Here we use molecular dynamics simulations to investigate the molecular mechanism through which seipin promotes LD formation. We find that seipin clusters TG molecules inside its unconventional ring-like oligomeric structure, and that both its luminal and transmembrane regions contribute to this process. Diacylglycerol, the precursor of TG, also clusters inside the seipin oligomer, in turn promoting TG accumulation. Our results suggest that seipin remodels the membrane of specific ER sites to prime them for LD biogenesis.Significance statementMetabolic disorders related to aberrant fat accumulation, including lipodystrophy and obesity, are a particularly serious health concern. In cells, fat accumulates in intracellular organelles, named lipid droplets (LDs). LDs form in the endoplasmic reticulum, where triglycerides, the most abundant form of fat, is produced. The Bernardinelli-Seip congenital lipodystrophy type 2 protein, seipin, has been identified as a key regulator of LD formation, but its mechanism of action remains debated and its molecular details mostly obscure. Here, we use molecular dynamics simulations to investigate the mechanism of seipin. We find that seipin can cluster and trap both triglycerides and its precursor, diacylglycerol. Our results suggest that seipin organizes the lipid composition of specific ER sites to prime them for LD biogenesis.
Reef environments shape microbial partners in a highly connected coral population
Authors: Kriefall NG , Kanke MR , Aglyamova GV , Davies SW 
Published: October 2020

ABSTRACTCorals from more thermally variable environments often fare better under thermal stress compared to those from less thermally variable environments, an important finding given that ocean warming threatens corals worldwide. Evidence is mounting that thermal tolerance can be attributed to the coral itself, as well as microbial communities present within the holobiont (coral host and its associated microorganisms). However, few studies have characterized how thermally variable environments structure multiple holobiont membersin situ. Here, using 2b-RAD sequencing of the coral and metabarcoding of algal (ITS2) and bacterial (16S) communities, we show evidence that reef zones (locales differing in proximity to shore, physical characteristics, and environmental variability) structure algal and bacterial communities at different scales within a highly connected coral population (Acropora hyacinthus) in French Polynesia. Fore reef (more stable) algal communities were on average more diverse than the back reef (more variable), suggesting that variability constrains algal diversity. In contrast, microbial communities were structured on smaller scales with site-specific indicator species and enriched functions across reef zones. Our results illuminate how associations with unique microbial communities can depend on spatial scale across highly dispersive coral populations, which may have fitness consequences in thermally divergent regions and rapidly changing oceans.
Fast volumetric mapping of human brain slices
Authors: Pesce Luca , Laurino Annunziatina , Gavryusev Vladislav , Mazzamuto Giacomo , Sancataldo Giuseppe , Scardigli Marina , Roffilli Matteo , Silvestri Ludovico , Costantini Irene , Pavone Francesco Saverio 
Published: October 2020

AbstractWe still lack a detailed map of the anatomical disposition of neurons in the human brain. A complete map would be an important step for deeply understanding the brain function, providing anatomical information useful to decipher the neuronal pattern in healthy and diseased conditions. Here, we present several important advances towards this goal, obtained by combining a new clearing method, advanced Light Sheet Microscopy and automated machinelearning based image analysis. We perform volumetric imaging of large sequentially stained human brain slices, labelled for two different neuronal markers NeuN and GAD67, discriminating the inhibitory population and reconstructing the brain connectivity.
A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics
Authors: Kessler Camille , Brambilla Alice , Waldvogel Dominique , Camenisch Glauco , Biebach Iris , Leigh Deborah M , Grossen Christine , Croll Daniel 
Published: October 2020

AbstractGenetic variation is a major factor determining susceptibility to diseases. Polymorphism at the major histocompatibility complex (MHC) and other immune function loci can underlie health and reproductive success of individuals. Endangered species of low population size could be severely compromised to evolve disease resistance due to reduced adaptive variation. A major impediment to screen adaptive genetic variation in wild species is the difficulty to comprehensively genotype immune-related loci based on low input material. Here, we design and validate a targeted amplicon sequencing assay to parallelize the analysis of a thousand loci of the MHC, other immunity-related genes, and genome-wide markers for the assessment of population structure. We apply the approach to Alpine ibex, one of the most successful examples of restoration of a large mammal in Europe. We used 51 whole genome sequenced individuals to select representative target SNPs. We integrated SNP call data from four related species for amplification robustness and genotyped 158 Alpine ibex individuals for validation. We show that the genome-wide markers perform equally well at resolving population structure as RAD-seq or low-coverage genome sequencing datasets with orders of magnitude more markers. The targeted amplicon sequencing assay is robust to >100-fold variation in input DNA quantity and generates useful genotype information from fecal samples. The amplicon marker set also identified recent species hybridization events with domestic goats. The immune loci show unexpectedly high degrees of differentiation within the species. Our assay strategy can realistically be implemented into population genetic surveys of a large range of species.
Developmental and MAPK-responsive transcription factors drive distinct malignant subtypes and genetic dependencies in pancreatic cancer
Authors: Laise Pasquale , Turunen Mikko , Garcia Alvaro Curiel , Tomassoni Lorenzo , Maurer H. Carlo , Elyada Ela , Schmierer Bernhard , Worley Jeremy , Kesner Jordan , Tan Xiangtian , Fernandez Ester Calvo , Wong Kelly , Wasko Urszula N , Tagore Somnath , Wang Alexander L. E. , Ge Sabrina , Iuga Alina C. , Griffin Aaron , Wong Winston , Manji Gulam A. , Alvarez Mariano J. , Notta Faiyaz , Tuveson David A. , Olive Kenneth P. , Califano Andrea 
Published: October 2020

ABSTRACTDespite extensive efforts, reproducible assessment of pancreatic ductal adenocarcinoma (PDA) heterogeneity and plasticity at the single cell level remains elusive. Systematic, network-based analysis of regulatory protein activity in single cells identified three PDA Developmental Lineages (PDLs), coexisting in virtually all tumors, whose transcriptional states are mechanistically driven by aberrant activation of Master Regulator (MR) proteins associated with gastrointestinal lineages (GLS state), morphogen and EMT pathways (MOS state), and acinar-to-ductal metaplasia (ALS state), respectively. Each PDL is further subdivided into sub-states characterized by low vs. high MAPK pathway activity. This taxonomy was remarkably conserved across multiple cohorts, cell lines, and PDX models, and harmonized with bulk profile analyses. Cross-state plasticity and MR essentiality was confirmed by barcode-based lineage tracing and CRISPR/Cas9 assays, respectively, while MR ectopic expression induced PDL transdifferentiation. Together these data provide a mechanistic foundation for PDA heterogeneity and a roadmap for targeting PDA cellular subtypes.
Exploring the role of life history traits and introduction effort in understanding invasion success in mammals: A case study of Barbary ground squirrels
Authors: van der Marel Annemarie , Waterman Jane M. , López-Darias Marta 
Published: October 2020

AbstractInvasive species –species that have successfully overcome the barriers of transport, introduction, establishment, and spread– are a risk to biodiversity and ecosystem function. Introduction effort is one of the main factors underlying invasion success, but life history traits are also important as they influence population growth. In this contribution, we first investigated life history traits of the Barbary ground squirrel, Atlantoxerus getulus, a species with a very low introduction effort. We then studied if their invasion success was due to a very fast life history profile by comparing their life history traits to those of other successful invasive mammals. Next, we examined whether the number of founders and/or a fast life history influences the invasion success of squirrels. Barbary ground squirrels were on the fast end of the “fast-slow continuum”, but their life history was not the only contributing factor to their invasion success, as the life history profile is comparable to other invasive species that do not have such a low introduction effort. We also found that neither life history traits nor the number of founders explained the invasion success of introduced squirrels in general. These results contradict the concept that introduction effort is the main factor explaining invasion success, especially in squirrels. Instead, we argue that invasion success can be influenced by multiple aspects of the new habitat or the biology of the introduced species.
M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity
Authors: Bag Indira , Chen Shue , Rosin Leah F. , Chen Yang , Liu Chen-Yu , Yu Guo-Yun , Lei Elissa P. 
Published: October 2020

ABSTRACTGenome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified theDrosophilatranscription factor Motif 1 Binding Protein (M1BP) in physical association with thegypsychromatin insulator core complex, including the universal insulator protein CP190. M1BP is required for enhancer-blocking and barrier activities of thegypsyinsulator as well as its proper nuclear localization. Genome-wide, M1BP specifically colocalizes with CP190 at Motif 1-containing promoters, which are enriched at topologically associating domain (TAD) borders. M1BP facilitates CP190 chromatin binding at many shared sites and vice versa. Both factors promote Motif 1-dependent gene expression and transcription near TAD borders genome-wide. Finally, loss of M1BP reduces chromatin accessibility and increases both inter- and intra-TAD local genome compaction. Our results reveal physical and functional interaction between CP190 and M1BP to activate transcription at TAD borders and mediate chromatin insulator-dependent genome organization.
Transcriptome and Chromatin Landscape of iNKT cells are Shaped by Subset Differentiation and Antigen Exposure
Authors: Murray Mallory Paynich , Engel Isaac , Seumois Gregory , Herrera de la Mata Sara , Rosales Sandy Lucette , Sethi Ashu , Logandha Ramamoorthy Premlal Ashmitaa , Seo Goo-Young , Greenbaum Jason , Vijayanand Pandurangan , Scott-Browne James P. , Kronenberg Mitchell 
Published: October 2020

AbstractInvariant natural killer T cells (iNKT cells) differentiate into thymic and peripheral NKT1, NKT2 and NKT17 subsets. We determined if the gene programs associated with these thymic subsets were maintained in peripheral sites, the influence of tissue location, and if there were large-scale changes after antigen exposure. RNA-seq and ATAC-seq analyses showed that iNKT cells in any subset were similar, regardless of tissue location. Lung iNKT cell subsets possessed the most distinct location-specific features, shared with other innate lymphocytes in the lung, possibly consistent with increased activation. After antigenic stimulation, iNKT cells underwent chromatin and transcription changes leading to two populations: one similar to follicular helper T cells and the other like NK or effector cells. Phenotypic analysis indicated these changes were observed long-term, suggesting that iNKT cells gene programs are not fixed, but they are capable of chromatin remodeling after antigen to give rise to several new subsets.
Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase inMycobacterium tuberculosis
Authors: Wang Heng , Xu Min , Engelhart Curtis A , Zhang Xi , Yan Baohua , Pan Miaomiao , Xu Yuanyuan , Fan Shilong , Liu Renhe , Xu Lan , Hua Lan , Schnappinger Dirk , Chen Shawn 
Published: October 2020

AbstractMycobacteria tuberculosis(Mtb) remains the deadliest pathogenic bacteria worldwide. The search for new antibiotics to treat drug-sensitive as well as drug-resistant tuberculosis has become a priority. The essential enzyme phenylalanyl-tRNA synthetase (PheRS) is an antibacterial drug target because of the large differences between bacterial and human PheRS counterparts. In a high-throughput screening of 2148 bioactive compounds, PF-3845, which is a known inhibitor of human fatty acid amide hydrolase (FAAH), was identified inhibiting Mtb PheRS atKi∼0.73 ± 0.055 µM. The inhibition mechanism was studied with enzyme kinetics, protein structural modelling and crystallography, in comparison to a PheRS inhibitor of the noted phenyl-thiazolylurea-sulfonamide class. The 2.3-Å crystal structure of Mtb PheRS in complex with PF-3845 revealed its novel binding mode, in which a trifluoromethyl-pyridinylphenyl group occupies the Phe pocket while a piperidine-piperazine urea group binds into the ATP pocket through an interaction network enforced by a sulfate ion. It represents the first non-nucleoside bi-substrate competitive inhibitor of bacterial PheRS. PF-3845 inhibits thein vitrogrowth of Mtb H37Rv at ∼24 µM, and the potency of PF-3845 increased against Mtb pheS-FDAS, suggesting on target activity in mycobacterial whole cells. PF-3845 does not inhibit human cytoplasmic or mitochondrial PheRSs in biochemical assay, which can be explained from the crystal structures. Further elaboration of the piperidine-piperazine urea moiety by medicinal chemistry effort will produce potential antibacterial lead with improved selectivity on the cellular level.
Voltage-gated Ca2+influx in murine white fat adipocytes: stimulation by growth hormone but not membrane depolarization
Authors: Akaniro-Ejim Nneoma E , Smith Paul A. 
Published: October 2020

AbstractIn white fat adipocytes voltage-gated Ca2+channels are constitutively active. Since the adipocyte membrane potential (Vm) is controlled by Cl−we investigated if changes in [Cl−]ocan affect the activity of voltage-gated Ca2+channels and intracellular calcium, [Ca2+]i.Adipocytes were isolated from epididymal fat of CD-1 mice. [Ca2+]iwas imaged with epifluorescent microscopy at 28°C. Constitutive voltage-gated channel activity was confirmed by the ability of verapamil to decrease [Ca2+]i.Substitution of [Cl−]oto 113, 53 and 18 mM with the membrane impermeant gluconate anion decreased [Ca2+]ifrom 114±8.7 to 106±7.5, 101±7.1 and 97±6 nM respectively. Substitution of [Cl−]owith glutamate mimicked the ability of gluconate to decrease [Ca2+]i.To explore if anions affected [Ca2+]ivia chelation of external Ca2+, [Ca2+]owas analyzed by potentiometry. Gluconate, glutamate, aspartate and methylsulphonate had Ca2+association constants of 17±1.8, 12±1, 8.2±4.1 and 3.3±0.5 L−1M respectively.Substitution of 134 mM [Cl−]owith gluconate decreased [Ca2+]ofrom 2.6 mM to 200 μM; the effect of this anion on [Ca2+]iwas mimicked by a decrease of [Ca2+]oto 200 μM in standard [Cl−]osolution. Conversely, titration of [Ca2+]ofrom 200 μM back to 2.6 mM in 134 mM gluconate solutions abolished the effect of this anion on [Ca2+]i. Substitution of [Cl−]owith methylsulphonate to affect Vm did not affect [Ca2+]i. Whereas, growth hormone at 10-20 nM increased [Ca2+]i, an effect blocked by verapamil or absence of [Ca2+]o. In conclusion, growth hormone, but not changes in Vm, can increase voltage-gated Ca2+channel activity and [Ca2+]iin white fat adipocytes.Key points[Ca2+]iplays a key role in the metabolic and endocrine functions of white fat adipocytes.In adipocytes basal [Ca2+]iis maintained by voltage-gated Ca2+channels constitutively active at their resting membrane potential, Vm, which is predominantly controlled by Cl−permeability.Substitution of [Cl−]oto depolarize Vm with gluconate or glutamate, did not increase but decreased [Ca2+]i. an action due to chelation of extracellular Ca2+. This effect was not seen with methylsulphonate, which did no chelate Ca2+but did not affect [Ca2+]i.Growth hormone elevated, [Ca2+]ian effect blocked by inhibitors of voltage-gated Ca2+channelsIn adipocytes, voltage-gated Ca2+channel activity appear recalcitrant to changes in Vm, but are however gated by growth hormone.
Salvage NAD+Biosynthetic Pathway Enzymes Moonlight as Molecular Chaperones to Protect Against Proteotoxicity
Authors: Pinkerton Meredith , Ruetenik Andrea , Bazylianska Viktoriia , Nyvltova Eva , Barrientos Antoni 
Published: October 2020

AbstractHuman neurodegenerative proteinopathies are disorders associated with abnormal protein depositions in brain neurons. They include polyglutamine (polyQ) conditions such as Huntington’s disease (HD) and α-synucleinopathies such as Parkinson’s disease (PD). Overexpression of NMNAT/Nma1, an enzyme in the NAD+biosynthetic salvage pathway, acts as an efficient suppressor of proteotoxicities in yeast, fly, and mouse models. Screens in yeast models of HD and PD allowed us to identify three additional enzymes of the same pathway that achieve similar protection against proteotoxic stress: Npt1, Pnc1, and Qns1. Here, we report that their ability to maintain proteostasis is independent of their catalytic activity and does not require cellular protein quality control systems such as the proteasome or autophagy. Furthermore, we show that, under proteotoxic stress, the four proteins are recruited as molecular chaperones with holdase and foldase activities. The NAD+salvage proteins act by preventing misfolding and, together with the Hsp90 chaperone, promoting the refolding of extended polyQ domains or α-synuclein. We conclude that the entire salvage NAD+biosynthetic pathway links NAD+metabolism and proteostasis and emerges as a target for therapeutics to combat age-associated neurodegenerative proteotoxicities. Our observations also illustrate the existence of an evolutionarily conserved strategy of repurposing or moonlighting housekeeping enzymes under stress conditions to maintain proteostasis.
The Endothelin Receptor Antagonist Macitentan Ameliorates Endothelin-Mediated Vasoconstriction and Promotes Neuroprotection of Retinal Ganglion Cells in Rats
Authors: Stankowska Dorota L. , Zhang Wei , He Shaoqing , Krishnamoorthy Vignesh R. , Harris Payton , Hall Trent , Chaphalkar Renuka M. , Kodati Bindu , Chavala Sai H. , Krishnamoorthy Raghu R. 
Published: October 2020

AbstractPurposeTo determine if dietary administration of the dual ETA/ ETBreceptor antagonist, macitentan, could protect retinal ganglion cells (RGCs) following endothelin-1 (ET-1) mediated vasoconstriction in Brown Norway rats.MethodsAdult male and female Brown Norway rats were either untreated or treated with macitentan (5 mg/kg body weight) once a day for 3 days followed by intravitreal injection of either 4 μl of 500 μM ET-1 (2 nmole/eye) or vehicle in one eye. Imaging of the retinal vasculature using fluorescein angiography was carried out at various time points, including, 5, 10, 15, 25 and 30 minutes. Following the imaging of the vasculature, rats were either treated with macitentan (5 mg/kg/body weight in dietary gels) or untreated (control gels without medication). Following treatments, rats were euthanized, retinal flat mounts were prepared, immunostained for RGC marker Brn3a, imaged and surviving RGCs were counted in a masked manner.ResultsVasoconstrictive effects following intravitreal ET-1 injection were greatly reduced in rats administered with macitentan in the diet prior to the ET-1 administration. ET-1 intravitreal injection produced a 31% loss of RGCs which was significantly reduced in macitentan-treated rats. Following ET-1 administration, GFAP immunostaining was increased in the ganglion cell layer as well as in the retrolaminar region, suggestive of astrocytic activation by ET-1 administration. RGC numbers in macitentan treated and ET-1 injected rats were similar to that observed in control retinas.ConclusionsET-1-mediated neurodegeneration could occur through both vascular and cellular mechanisms. The endothelin receptor antagonist, macitentan, has neuroprotective effects in retinas of Brown Norway rats that occurs through different mechanisms, including, enhancement of RGC survival and reduction ET-1 mediated vasoconstriction.