bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human-lineage-specific genomic elements: relevance to neurodegenerative disease andAPOEtranscript usage
Authors: Chen Zhongbo , Zhang David , Reynolds Regina H. , Gustavsson Emil K. , Ruiz Sonia García , D’Sa Karishma , Fairbrother-Browne Aine , Vandrovcova Jana ,   International Parkinson’s Disease Genomics Consortium (IPDGC), Hardy John , Houlden Henry , Taliun Sarah A. Gagliano , Botía Juan , Ryten Mina 
Published: April 2020

ABSTRACTKnowledge of genomic features specific to the human lineage may provide insights into brain-related diseases. We leverage high-depth whole genome sequencing data to generate a combined annotation identifying regions simultaneously depleted for genetic variation (constrained regions) and poorly conserved across primates. We propose that these constrained, non-conserved regions (CNCRs) have been subject to human-specific purifying selection and are enriched for brain-specific elements. We find that CNCRs are depleted from protein-coding genes but enriched within lncRNAs. We demonstrate that per-SNP heritability of a range of brain-relevant phenotypes are enriched within CNCRs. We find that genes implicated in neurological diseases have high CNCR density, includingAPOE, highlighting an unannotated intron-3 retention event. Using human brain RNA-sequencing data, we show the intron-3-retaining transcript/s to be more abundant in Alzheimer’s disease with more severe tau and amyloid pathological burden. Thus, we demonstrate the importance of human-lineage-specific sequences in brain development and neurological disease. We release our annotation through vizER (https://snca.atica.um.es/browser/app/vizER).
Controls on and consequences of specific leaf area variation with permafrost depth in a boreal forest
Authors: Anderson Carolyn G. , Bond-Lamberty Ben , Stegen James C. 
Published: April 2020

AbstractSpecific leaf area (SLA, leaf area per unit dry mass) is a key canopy structural characteristic, a measure of photosynthetic capacity, and an important input into many terrestrial process models. Although many studies have examined SLA variation, relatively few data exist from high latitude, climate-sensitive permafrost regions. We measured SLA and soil and topographic properties across a boreal forest permafrost transition, in which forest composition changed as permafrost deepened from 54 to >150 cm over 75 m hillslope transects in Caribou-Poker Creeks Research Watershed, Alaska. We characterized both linear and threshold relationships between topographic and edaphic variables and SLA and developed a conceptual model of these relationships. We found that the depth of the soil active layer above permafrost was significantly and positively correlated with SLA for both coniferous and deciduous boreal tree species. Intraspecific SLA variation was associated with a fivefold increase in net primary production, suggesting that changes in active layer depth due to permafrost thaw could strongly influence ecosystem productivity. While this is an exploratory study to begin understanding SLA variation in a non-contiguous permafrost system, our results indicate the need for more extensive evaluation across larger spatial domains. These empirical relationships and associated uncertainty can be incorporated into ecosystem models that use dynamic traits, improving our ability to predict ecosystem-level carbon cycling responses to ongoing climate change.
Stress reactivity elicits a tissue-specific reduction in telomere length in ageing zebrafish (Danio rerio)
Authors: Evans James R. , Torres-Pérez Jose V. , Miletto Petrazzini Maria Elena , Riley Riva , Brennan Caroline H. 
Published: April 2020

ABSTRACTTelomere length reflects cellular ageing. Increased telomere shortening in leukocytes is associated with a range of neurodegenerative and cardiovascular diseases, the onset and progression of which may be mediated by behavioural traits such as anxiety and stress reactivity. However, the effects of the hypothalamus-pituitary-adrenal axis stress response are shown to be tissue specific. As such, leukocyte telomere length may not give an accurate measure of the relationship between stress-reactivity and telomere length in disease relevant tissues. To test the hypothesis that stress-reactivity contributes to age-related telomere shortening in a tissue specific manner, we examined the correlation between telomere length in heart and brain tissue and stress-reactivity in a population of young (6-9 month) and ageing (18 month) zebrafish. Stress-reactivity was assessed by tank diving, a zebrafish version of the rodent open-field test, and through gene expression. Telomere length was assessed using quantitative polymerase chain reaction. We show that ageing zebrafish have shorter telomeres in both heart and brain. Telomere length is inversely related to stress-reactivity in heart but not brain of ageing individuals. These data support the hypotheses that an anxious predisposition contributes to telomere shortening in heart tissue, and by extension age-related heart disease, and that stress-reactivity contributes to age-related telomere shortening in a tissue-specific manner.
New genetic insights about hybridization and population structure of hawksbill and loggerhead turtles from Brazil
Authors: Arantes Larissa S. , Vilaça Sibelle T. , Mazzoni Camila J. , Santos Fabrício R. 
Published: April 2020

AbstractAn extremely high incidence of hybridization among sea turtles is found along the Brazilian coast. To understand this atypical phenomenon and its impact on sea turtle conservation, research focused in the evolutionary history of sea turtles is fundamental. We assessed high quality multilocus haplotypes of 143 samples of the five species of sea turtles that occur along the Brazilian coast to investigate the hybridization process and the population structure of hawksbill (Eretmochelys imbricata) and loggerhead turtles (Caretta caretta). The multilocus data were initially used to characterize interspecific hybrids. Introgression (F2 hybrids) was only confirmed in hatchlings of F1 hybrid females (hawksbill × loggerhead), indicating that introgression was either previously overestimated and F2 hybrids may not survive to adulthood, or the first-generation hybrid females nesting in Brazil were born as recent as few decades ago. Phylogenetic analyses using nuclear markers recovered the mtDNA-based Indo-Pacific and Atlantic lineages for hawksbill turtles, demonstrating a deep genetic divergence dating from the early Pliocene. In addition, loggerhead turtles that share a common feeding area and belong to distinct Indo-Pacific and Atlantic mtDNA clades present no clear genetic differentiation at the nuclear level. Finally, our results indicate that hawksbill and loggerhead rookeries along the Brazilian coast are likely connected by male-mediated gene flow.
Classes for the masses: Systematic classification of unknowns using fragmentation spectra
Authors: Dührkop Kai , Nothias Louis Felix , Fleischauer Markus , Ludwig Marcus , Hoffmann Martin A. , Rousu Juho , Dorrestein Pieter C. , Böcker Sebastian 
Published: April 2020

ABSTRACTMetabolomics experiments can employ non-targeted tandem mass spectrometry to detect hundreds to thousands of molecules in a biological sample. Structural annotation of molecules is typically carried out by searching their fragmentation spectra in spectral libraries or, recently, in structure databases. Annotations are limited to structures present in the library or database employed, prohibiting a thorough utilization of the experimental data. We present a computational tool for systematic compound class annotation: CANOPUS uses a deep neural network to predict 1,270 compound classes from fragmentation spectra, and explicitly targets compounds where neither spectral nor structural reference data are available. CANOPUS even predicts classes for which no MS/MS training data are available. We demonstrate the broad utility of CANOPUS by investigating the effect of the microbial colonization in the digestive system in mice, and through analysis of the chemodiversity of different Euphorbia plants; both uniquely revealing biological insights at the compound class level.
Osmotic and ionic regulation by hololimnetic freshwater crustaceans: a molecular role for gill ion transporters
Authors: Mantovani Milene , McNamara John Campbell 
Published: April 2020

AbstractOwing to their extraordinary niche diversity, the Crustacea are ideal for comprehending the evolution of osmoregulation. The processes that effect systemic hydro-electrolytic homeostasis maintain hemolymph ionic composition via membrane transporters located in highly specialized gill ionocytes. We evaluated physiological and molecular hyper- and hypo-osmoregulatory mechanisms in two phylogenetically distant, freshwater crustaceans, the crabDilocarcinus pageiand the shrimpMacrobrachium jelskii, when osmotically challenged for up to 10 days. When in distilled water, hemolymph osmolality and [Cl−] increased briefly inD. pagei, stabilizing at initial values, while [Na+] decreased continually. Gill V(H+)-ATPase, Na+/K+-ATPase and Na+/K+/2Cl−gene expressions were unchanged. InM. jelskii, hemolymph osmolality, [Cl−] and [Na+] decreased continually for 12 h, the shrimps no longer surviving. Gill transporter gene expressions increased 2- to 5-fold. After 10-days exposure to brackish water,D. pageiwas isosmotic, iso-chloremic and iso-natriuremic. Gill V(H+)-ATPase expression decreased while Na+/K+-ATPase and Na+/K+/2Cl−expressions were unchanged. InM. jelskii, the hemolymph was hypo-regulated, particularly [Cl−]. Transporter expressions initially increased 3- to 12-fold, declining to control values. Gill V(H+)-ATPase expression underlies the ability ofD. pageito survive in fresh water while Na+/K+-ATPase and Na+/K+/2Cl−expressions enableM. jelskiito deal with osmotic challenge. These findings reveal divergent responses in two unrelated crustaceans habiting a similar osmotic niche. WhileD. pageihas maintained the capacity to tolerate elevated cellular isosmoticity despite its inability to secrete salt,M. jelskiidisplays clear hypo-osmoregulatory ability. Each species has developed distinct strategies at the transcription and systemic levels during adaptation to fresh water.Summary statementDuring their evolutionary adaptation to fresh water, unrelated hololimnetic crustaceans have developed physiological strategies like tolerating elevated cellular isosmoticity or regulating hypo-osmoregulatory ability at the gene transcription level.
Towards resilient beef cattle production systems: Impact of truck contamination and information sharing on foot-and-mouth disease spreading
Authors: Yang Qihui , Gruenbacher Don M. , Heier Stamm Jessica L. , Amrine David E. , Brase Gary L. , DeLoach Scott A. , Scoglio Caterina M. 
Published: April 2020

AbstractAs cattle movement data in the United States are scarce due to the absence of mandatory traceability programs, previous epidemic models for U.S. cattle production systems heavily rely on contact rates estimated based on expert opinions and survey data. These models are often based on static networks and ignore the sequence of movement, possibly overestimating the epidemic sizes. In this research, we adapt and employ an agent-based model that simulates beef cattle production and transportation in southwest Kansas to analyze the between-premises transmission of a highly contagious disease, the foot-and-mouth disease. First, we assess the impact of truck contamination on the disease transmission with the truck agent following an independent clean-infected-clean cycle. Second, we add an information-sharing functionality such that producers/packers can trace back and forward their trade records to inform their trade partners during outbreaks. Scenario analysis results show that including indirect contact routes between premises via truck movements can significantly increase the amplitude of disease spread, compared with equivalent scenarios that only consider animal movement. Mitigation strategies informed by information sharing can dramatically improve the system resilience against epidemics, highlighting the benefit of promoting information sharing in the cattle industry. In addition, we identify salient characteristics that must be considered when designing an information-sharing strategy, including the number of days to trace back and forward in the trade records and the role of different cattle supply chain stakeholders. Sensitivity analysis results show that epidemic sizes are sensitive to variations in parameters of fomite survival time and indirect contact transmission probability and future studies can focus on a more accurate estimation of these parameters.
Genetic variations (eQTLs) in muscle transcriptome and mitochondrial genes, and trans-eQTL molecular pathways in feed efficiency from Danish breeding pigs
Authors: Carmelo Victor AO. , Kadarmideen Haja N. 
Published: April 2020

AbstractFeed efficiency (FE) is a key trait in pig production, as it has both high economic and environmental impact. FE is a challenging phenotype to study, as it is complex and affected by many factors, such as metabolism, growth and activity level. Furthermore, testing for FE is expensive, as it requires costly equipment to measure feed intake of individual animals, making FE biomarkers valuable. Therefore, there has been a desire to find single nucleotide polymorphisms (SNPs) as biomarkers, to assist with improved selection and improve our biological understanding of FE. We have done a cis- and trans-eQTL (expressed quantitative trait loci) analysis, in a population of Danbred Durocs (N=11) and Danbred Landrace (N=27) using both a linear and Anova model. We used bootstrapping and enrichment analysis to validate and analyze our detected eQTLs. We identified 15 eQTLs with FDR < 0.01, affecting several genes found in previous studies of commercial pig breeds. Examples include IFI6, PRPF39, TMEM222, CSRNP1,PARK7 and MFF. The bootstrapping results showed statistically significant enrichment of eQTLs with p-value < 0.01 (p-value < 2.2×0-16) in both cis and trans-eQTLs. Based on this, enrichment analysis of top trans-eQTLs revealed high enrichment for gene categories and gene ontologies associated with genomic context and expression regulation. This includes transcription factors (p-value=1.0×10-13), DNA-binding (GO:0003677, p-value=8.9×10-14), DNA-binding transcription factor activity (GO:0003700,) nucleus gene (GO:0005634, p-value<2.2×10-16), positive regulation of expression (GO:0010628), negative regulation of expression (GO:0010629, p-value<2.2×10-16). These results would be useful for future genome assisted breeding of pigs to improve FE, and in the improved understanding of the functional mechanism of trans-eQTLs.
Spatially Resolved Measurement of Dynamic Glucose Uptake in Live Ex Vivo Tissues
Authors: Dunn Austin F. , Catterton Megan A. , Dixon Drake D. , Pompano Rebecca R. 
Published: April 2020

ABSTRACTHighly proliferative cells depend heavily on glycolysis as a source of energy and biological precursor molecules, and glucose uptake is a useful readout of this aspect of metabolic activity. Glucose uptake is commonly quantified by using flow cytometry for cell cultures and positron emission tomography for organs in vivo. However, methods to detect spatiotemporally resolved glucose uptake in intact tissues are far more limited, particularly those that can quantify changes in uptake over time in specific tissue regions and cell types. Using lymph node metabolism as a case study, we developed a novel assay of dynamic and spatially resolved glucose uptake in living tissue by combining ex vivo tissue slice culture with a fluorescent glucose analogue. Live slices of murine lymph node were treated with the glucose analogue 2-[N-(7-nitrobenz-2-oxa-1,3-dia-xol-4-yl)amino]-2-deoxyglucose (2-NBDG). Incubation parameters were optimized to differentiate glucose uptake in activated versus naïve lymphocytes. Regional glucose uptake could be imaged at both the tissue level, by widefield microscopy, and at the cellular level, by confocal microscopy. Furthermore, the assay was readily multiplexed with live immunofluorescence labelling to generate maps of 2-NBDG uptake across tissue regions, revealing highest uptake in T cell-dense regions. The signal was predominantly intracellular and localized to lymphocytes rather than stromal cells. Finally, we demonstrated that the assay was repeatable in the same slices, and imaged the dynamic distribution of glucose uptake in response to ex vivo T cell stimulation for the first time. We anticipate that this assay will serve as a broadly applicable, user-friendly platform to quantify dynamic metabolic activities in complex tissue microenvironments.
BRET sensors unravel thatPlasmodium falciparumserpentine receptor 12 (PfSR12) increases surface expression of mammalian GPCRs in HEK293 cells
Authors: Pereira Pedro H. S. , Brito Gabriela , Moraes Miriam S. , Kiyan Camila L. , Avet Charlotte , Bouvier Michel , Garcia Celia R. S. 
Published: April 2020

ABSTRACTMalaria causes millions of deaths worldwide and is considered a huge public health problem for underdeveloped countries. The most severe cases of malaria present complications of the host circulatory system, which may cause clogging and rupture of blood vessels, leading to death or important sequelae. Because of the previously suggested role of thrombin and platelet aggregation inPlasmodium falciparumbiology, we hypothesized that one of the GPCR-like proteins identified in the genome of the parasite,P. falciparumserpentine receptor 12 (PfSR12), could be a thrombin-activated GPCR. To test this hypothesis we used a series of Bioluminescence and Bioluminescence Resonance Energy Transfer (BRET)-based biosensors to investigate the signaling activity of PfSR12. Using an Obelin based biosensor, thrombin promoted a PfSR12-dependent cytosolic Ca2+rise in HEK293 cells. This Ca2+mobilization was accompanied by DAG formation and PKC activation as detected using DAG and PKC BRET-based biosensors indicating a Gq/PLC/IP3 signaling pathway. The role of Gq was confirm using Gq/11knockout HEK293 cells as well as the Gq-selective inhibitor, YM254890. Further investigation revealed that PfSR12 is not itself a thrombin receptor but rather promotes the increase of cell surface expression of an endogenous thrombin receptor. This chaperone-like effect was not selective for thrombin receptors as PfSR12 expression also promoted an increased muscarinic type 3 receptor (M3R)-promoted DAG and PKC responses. This increase response was accompanied by an increase in surface expression of M3R. Our data indicate that PfSR12 acts as a chaperone and increases the expression of several GPCRs resulting in increased responsiveness to various hormones of mammalian cells that could contribute to the deleterious effects ofPlasmodium falciparuminfection.
Selective amplification of ipRGC signals accounts for interictal photophobia in migraine
Authors: McAdams Harrison , Kaiser Eric A , Igdalova Aleksandra , Haggerty Edda B , Cucchiara Brett , Brainard David H , Aguirre Geoffrey K 
Published: April 2020

AbstractSecond only to headache, photophobia is the most debilitating symptom reported by people with migraine. While the melanopsin-containing, intrinsically photosensitive retinal ganglion cells (ipRGCs) are thought to play a role, how cone and melanopsin signals are integrated in this pathway to produce visual discomfort is poorly understood.We studied 60 people: 20 without headache and 20 each with interictal photophobia from migraine with or without aura. Participants viewed pulses of spectral change that selectively targeted melanopsin, the cones, or both, and rated the degree of visual discomfort produced by these stimuli while we also recorded pupil responses.We examined the data within a model that describes how cone and melanopsin signals are weighted and combined at the level of the retina, and how this combined signal is transformed into a rating of discomfort or pupil response. Our results indicate that people with migraine do not differ from headache-free controls in the manner in which melanopsin and cone signals are combined. Instead, people with migraine demonstrate an amplification of integrated ipRGC signals for discomfort. This effect of migraine is selective for ratings of visual discomfort, in that an amplification of pupil responses was not seen in the migraine group, nor were group differences found in surveys of other behaviors putatively linked to ipRGC function (chronotype, seasonal sensitivity, presence of a photic sneeze reflex).By revealing a dissociation in the amplification of discomfort versus pupil response, our findings suggest a post-retinal alteration in processing of ipRGC signals for photophobia in migraine.SignificanceThe melanopsin-containing, intrinsically photosensitive retinal ganglion cells (ipRGCs) may contribute to photophobia in migraine. We measured visual discomfort and pupil responses to cone and melanopsin stimulation—the photoreceptor inputs to the ipRGCs—in people with and without migraine. We find that people with migraine do not differ from those without headaches in how cone and melanopsin signals are weighted and combined to produce visual discomfort. Instead, migraine is associated with an amplification of ipRGC signals for discomfort. This effect of migraine upon ipRGC signals is limited to photophobia, as we did not find an enhancement of pupil responses or a change in other behaviors linked to ipRGC function. Our findings suggest a post-retinal amplification of ipRGC signals for photophobia in migraine.
Cryo-EM structures of human TRPC5 reveal interaction of a xanthine-based TRPC1/4/5 inhibitor with a conserved lipid binding site
Authors: Wright David J. , Simmons Katie J. , Johnson Rachel M. , Beech David J. , Muench Stephen P. , Bon Robin S. 
Published: April 2020

AbstractTRPC1/4/5 channels are non-specific cation channels implicated in a wide variety of diseases, and TRPC1/4/5 inhibitors have recently entered the first clinical trials. However, fundamental and translational studies require a better understanding of TRPC1/4/5 channel regulation by endogenous and exogenous factors. Although several potent and selective TRPC1/4/5 modulators have been reported, the paucity of mechanistic insights into their modes-of-action remains a barrier to the development of new chemical probes and drug candidates. The xanthine class of modulators includes the most potent and selective TRPC1/4/5 inhibitors described to date, as well as TRPC5 activators. Our previous studies suggest that xanthines interact with a, so far, elusive pocket of TRPC1/4/5 channels that is essential to channel gating. Targeting this pocket may be a promising strategy for TRPC1/4/5 drug discovery. Here we report the first structure of a small molecule-bound TRPC1/4/5 channel – human TRPC5 in complex with the xanthine Pico145 – to 3.0 Å. We found that Pico145 binds to a conserved lipid binding site of TRPC5, where it displaces a bound phospholipid. Our findings explain the mode-of-action of xanthine-based TRPC1/4/5 modulators, and suggest a structural basis for TRPC1/4/5 modulation by endogenous factors such as (phospho)lipids and Zn2+ions. These studies lay the foundations for the structure-based design of new generations of TRPC1/4/5 modulators.