bluuebunny/crossref_metadata_2025_split huggingface dataset:
INFLAMMATORY BOWEL DISEASE INDUCES α-SYNUCLEIN AGGREGATION IN GUT AND BRAIN
Authors: Espinosa-Oliva Ana M. , Ruiz Rocío , Soto Manuel Sarmiento , Boza-Serrano Antonio , Rodriguez-Perez Ana I. , Roca-Ceballos María A. , García-Revilla Juan , Santiago Marti , Serres Sébastien , Economopoulus Vasiliki , Carvajal Ana E. , Vázquez-Carretero María D. , García-Miranda Pablo , Klementieva Oxana , Oliva-Martín María J. , Deierborg Tomas , Rivas Eloy , Sibson Nicola R. , Labandeira-García José L. , Machado Alberto , Peral María J. , Herrera Antonio J. , Venero José L. , de Pablos Rocío M. 
Published: January 2022

ABSTRACTAccording to Braak’s hypothesis, it is plausible that Parkinsońs disease (PD) starts in the enteric nervous system (ENS) to spread the brain via the vagus nerve. Thus, we were wondering whether human inflammatory bowel diseases (IBD) can progress with appearance of pathogenic α-synuclein (α-syn) in the gastrointestinal tract and midbrain dopaminergic neurons. Analysis of human gastrointestinal tract sections from IBD patients demonstrated the presence of pathogenic phosphorylated α-syn in both myenteric (Auerbach’s) and submucosal (Meissner’s) plexuses. Remarkably, PD subjects exhibit α-syn pathology in identical gastrointestinal locations. Analysis of human midbrain sections from IBD subjects revealed a clear displacement of neuromelanin in some nigral neurons from the ventral mesencephalon, which were inherently associated with presence of α-syn aggregates reminiscent of pale bodies. We also used different dextran sodium sulfate (DSS)-based rat models of gut inflammation (subchronic and chronic) to study the appearance of phosphorylated α-syn inclusions in both Auerbach’s and Meissner’s plexuses (gut), and in dopaminergic neuritic processes (brain) along with degeneration of nigral dopaminergic neurons, which are considered classical hallmarks of PD. Vagotomized DSS-treated animals exhibited pathological α-syn in the gut but failed to show dopaminergic cells degeneration and α-syn aggregation in the ventral mesencephalon. Taken together, these results strongly suggest that Braak’s hypothesis is plausible.
Single mutation makes Escherichia coli an insect mutualist
Authors: Koga Ryuichi , Moriyama Minoru , Onodera-Tanifuji Naoko , Ishii Yoshiko , Takai Hiroki , Mizutani Masaki , Oguchi Kohei , Okura Reiko , Suzuki Shingo , Goto Yasuhiro , Hayashi Tetsuya , Seki Masahide , Suzuki Yutaka , Nishide Yudai , Hosokawa Takahiro , Wakamoto Yuichi , Furusawa Chikara , Fukatsu Takema 
Published: January 2022

AbstractWe report an experimental system in which Escherichia coli evolves into an insect mutualist. When the essential gut symbiont of the stinkbug Plautia stali was replaced by E. coli, a few survivor insects exhibited specific localization and vertical transmission of E. coli. Through trans-generational maintenance with P. stali, several hyper-mutating E. coli lines independently evolved host’s high adult emergence and improved body color. Such “mutualistic” E. coli lines exhibited independent mutations disrupting the carbon catabolite repression (CCR) global transcriptional regulator. Each of the mutations reproduced the mutualistic phenotypes when introduced into wild-type E. coli, confirming that the single CCR mutations instantly make E. coli an insect mutualist. Our discovery uncovers that evolution of elaborate mutualism can proceed more easily and rapidly than conventionally envisaged.
LCK-14-3-3ζ-TRPM8 axis for regulating TRPM8 function/assembly promotes pancreatic cancer malignancy
Authors: Huang Yuan , Li Shi , Wang Zhijie , Liu Qinfeng , Li Shunyao , Liu Lei , Zhao Weiwei , Wang Kai , Zhang Rui , Ali Declan , Michalak Marek , Chen Xing-Zhen , Zhou Cefan , Tang Jingfeng 
Published: January 2022

AbstractThe transient receptor potential melastatin 8 (TRPM8), function as a Ca2+-permeable channel in the plasma membrane (PM). Dysfunction of TRPM8 is associated with human pancreatic cancer and several other diseases in clinical patients, but with unclear underlying mechanisms. Here, we found lymphocyte-specific protein tyrosine kinase (LCK) directly interacts with TRPM8 and potentiates TRPM8 phosphorylation at Y1022. LCK positively regulated channel function characterized by increased TRPM8 currents densities through enhancing TRPM8 multimerization. Furthermore, 14-3-3ζ interacted with TRPM8 and positively modulated channel multimerization. LCK significantly enhanced the binding of 14-3-3ζ and TRPM8, whereas mutant TRPM8-Y1022F impaired TRPM8 multimerization and the binding of TRPM8 and 14-3-3ζ. Knockdown of 14-3-3ζ impaired the regulation of LCK on TRPM8 multimerization. Additionally, TRPM8 phosphotyrosine at Y1022 feedback regulated LCK activity by inhibition of Tyr505 phosphorylation and modulation of LCK ubiquitination. Finally, we revealed the importance of TRPM8 phosphorylation at Y1022 in the proliferation, migration and tumorigenesis of pancreatic cancer cells. Our findings demonstrate that LCK-14-3-3ζ-TRPM8 axis for regulating TRPM8 assembly, channel function, LCK activity and providing potential therapeutic targets for pancreatic cancer.
Steroidogenic factor-1 lineage origin of skin lesions in Carney complex syndrome
Authors: Sahut-Barnola Isabelle , Lefrancois-Martinez A-Marie , Dufour Damien , Botto Jean-Marie , Kamilaris Crystal , Faucz Fabio R. , Stratakis Constantine A. , Val Pierre , Martinez Antoine 
Published: January 2022

ABSTRACTCarney complex (CNC) is a rare familial multi-neoplastic syndrome predisposing to endocrine and non-endocrine tumors due to inactivating mutations of PRKAR1A leading to perturbations of the cAMP protein kinase A (PKA) signaling pathway. Skin lesions are the most common manifestation of CNC, including lentigines, blue nevi and cutaneous myxomas, in unusual locations such as oral and genital mucosa. Unlike endocrine disorders, the pathogenesis of skin lesions remains unexplained. Here, we show that embryonic invalidation of the Prkar1a gene in Steroidogenic Factor-1-expressing cells, leads to the development of familial skin pigmentation alterations reminiscent of those in patients. Immunohistological and molecular analyses coupled with genetic monitoring of recombinant cell lineages in mouse skin, suggest that familial lentiginosis and myxomas occurs in skin areas specifically enriched in dermal melanocytes. In lentigines and blue nevi-prone areas from mutant mice and patients, Prkar1a/PRKAR1A invalidation occurs in a subset of dermal fibroblasts capable of inducing, under the influence of PKA signaling, the production of pro-melanogenic EDN3 and HGF signals. Our model strongly suggests that the origin of the typical CNC cutaneous lesions is the result of non-cell-autonomous pro-melanogenic activity of a dermal fibroblast population sharing a community of origin with SF-1 lineage.
Microliter spotting and micro-colony observation: a rapid and simple approach for counting bacterial colony forming units
Authors: Bhuyan Shuvam , Yadav Mohit , Giri Shubhra Jyoti , Begum Shuhada , Das Saurav , Phukan Akash , Priyadarshani Pratiksha , Sarkar Sharmilee , Jayswal Anurag , Kabyashree Kristi , Kumar Aditya , Mandal Manabendra , Ray Suvendra Kumar 
Published: January 2022

ABSTRACTFor enumerating viable bacteria, traditional dilution plating to count colony forming units (CFU) has always been the preferred method in microbiology owing to its simplicity, albeit laborious and time-consuming. Similar CFU counts can be obtained by quantifying growing micro-colonies in conjunction with the perks of a microscope. Here, we employed a simple method of five microliter spotting of differently diluted bacterial culture multiple times on a single Petri dish followed by finding out CFU by counting micro-colonies using a phase-contrast microscope. In this method, the CFU of an Escherichia coli culture can be estimated within a four-hour period. Further, within a ten-hour period, CFU in a culture of Ralstonia solanacearum, a bacterium with a generation time of around 2 h, can be estimated. The CFU number determined by micro-colonies observed is comparable with that obtained by the dilution plating method. Micro-colonies number observed in the early hours of growth (2 h in case of E. coli and 8 h in case of R. solanacearum) were found to remain consistent at later hours, though there was a noticeable increase in the size of the colonies. It suggested that micro-colonies observed in the early hours indeed represent the bacterial number in the culture. Practical applications to this counting method were employed in studying the rifampicin-resistant mutation rate as well as performing the fluctuation test in E. coli. The method described here results in a 90% reduction of labour, time and resources. Thus, the method is likely to be adopted by many microbiologists in their routine laboratory research.
Epidermal clock integration and gating of brain signals guarantees skin homeostasis
Authors: Mortimer Thomas , Zinna Valentina M. , Atalay Muge , Laudanna Carmelo , Deryagin Oleg , Smith Jacob G. , García-Lara Elisa , Vaca-Dempere Mireia , Koronowski Kevin B. , Petrus Paul , Greco Carolina M. , Forrow Stephen , Sassone-Corsi Paolo , Welz Patrick-Simon , Muñoz-Cánoves Pura , Aznar Benitah Salvador 
Published: January 2022

AbstractIn mammals, an integrated network of molecular oscillators drives daily rhythms of tissue-specific homeostatic processes. This circadian clock network is required for maintaining health and is compromised by disease and lifestyle choices, such as diet and exercise. However, critical properties of this systemic network, such as which tissues communicate to coordinate their respective programs of daily physiology, and the exact homeostatic processes requiring each communication pathway, remain undefined. To dissect daily inter-tissue communication, we have constructed in mice a minimal clock network comprising only two nodes: the peripheral epidermal clock and the central brain clock. By circadian transcriptomic and functional characterization of this isolated connection, we have identified a previously unknown gatekeeping function of the peripheral tissue clock with respect to systemic inputs. That is, the epidermal clock concurrently integrates and corrects brain signals to ensure timely execution of epidermal daily physiology. Specifying the integrative arm of the clock, we identify that timely cell cycle termination in the epidermal stem cell compartment is dependent upon incorporation of clock-driven signals originating from the brain. Unexpectedly, and in contrast, the epidermal clock corrects potentially disruptive feeding-related signals to ensure that DNA replication occurs at the optimum time of day. Together, we present a novel approach for cataloguing the systemic dependencies of a given tissue, and in turn identify an essential gate-keeping function of peripheral circadian clocks that guarantees tissue homeostasis.
Extinction risk, reconstructed catches, and management of chondrichthyan fishes in the Western Central Atlantic Ocean
Authors: Talwar Brendan S. , Anderson Brooke , Avalos-Castillo Cristopher G. , del Pilar Blanco-Parra María , Briones Alejandra , Cardeñosa Diego , Carlson John K. , Charvet Patricia , Cotton Charles F. , Crysler Zoe , Derrick Danielle H. , Heithaus Michael R. , Herman Katelyn B. , Koubrak Olga , Kulka David W. , Kyne Peter M. , Lasso-Alcalá Oscar M. , Mejía-Falla Paola A. , Morales-Saldaña Jorge Manuel , Naranjo-Elizondo Beatriz , Navia Andrés F. , Pacoureau Nathan , Peréz-Jiménez Juan C. , Pollom Riley A. , Rigby Cassandra L. , Schneider Eric V.C. , Simpson Nikola , Dulvy Nicholas K. 
Published: January 2022

ABSTRACTChondrichthyan fishes are among the most threatened vertebrates on the planet because many species have slow life histories that are outpaced by intense fishing. The Western Central Atlantic Ocean, which includes the greater Caribbean, is a hotspot of chondrichthyan biodiversity and abundance, but is historically characterized by extensive shark and ray fisheries and a lack of sufficient data for effective management and conservation. To inform future research and management decisions, we analyzed patterns in chondrichthyan extinction risk, reconstructed catches, and regulations in this region. We summarized the extinction risk of 180 sharks, rays, and chimaeras using contemporary IUCN Red List assessments and found that over one-third (35.6%) were assessed as Vulnerable, Endangered, or Critically Endangered largely due to fishing. Reconstructed catches from 1950 to 2016 reached their peak in 1992, then declined by 40.2% through the end of the series. The United States, Venezuela, and Mexico were responsible for most catches and hosted large proportions of the regional distributions of threatened species; these countries therefore held the greatest responsibility for chondrichthyan management. The abundance and resolution of fisheries landings data were poor in much of the region, and national-level regulations varied widely across jurisdictions. Deepwater fisheries represent an emerging threat, although many deepwater chondrichthyans currently find refuge beyond the depths of most fisheries. Regional collaboration as well as effective and enforceable management informed by more complete fisheries data, particularly from small-scale fisheries, are required to protect and recover threatened species and ensure sustainable fisheries.
Soil fungal communities vary more with soil characteristics than tree diversity at a local scale
Authors: Kutos Steve , Barnes Elle M. , Lewis J.D. 
Published: January 2022

ABSTRACTSoil fungal communities vary spatially due to factors including variations in plant diversity and soil characteristics; however, the relative influences of these factors on composition and therefore function remain unclear. Small-scale variation in fungal communities may drive local variation in nutrient cycling and decomposition and may respond more to local factors compared with large climatic variations. Clarifying the roles of these factors can improve our predictions of soil fungal community and biogeochemical cycling responses to anthropogenic changes. Therefore, we examined relationships among abiotic and biotic factors and soil fungal communities associated with Quercus rubra and Pinus resinosa saplings and mature trees in a mixed-hardwood woodland. We also compared community composition and fungal enzymatic activity. Fungal community composition was associated with spatial heterogeneity of soil characteristics, while host sapling and tree species identity were poor predictors of community composition. Further, most of the compositional variation was unexplained by measured variables, suggesting stochasticity and other environmental characteristics may drive spatial variation in these communities. Additionally, enzymatic activity did not clearly correlate with fungal community composition. Overall, soil fungal communities and enzymatic activity adjacent to saplings in this woodland are influenced primarily by soil characteristics and stochasticity and not plant identity.
When host populations move north, but disease moves south: counter-intuitive impacts of climate warming on disease spread
Authors: Moran E. Joe , Martignoni Maria M. , Lecomte Nicolas , Leighton Patrick , Hurford Amy 
Published: January 2022

AbstractEmpirical observations and mathematical models show that climate warming can lead to the northern (or, more generally, poleward) spread of host species ranges and their corresponding diseases. Here, we explore an unexpected possibility whereby climate warming induces disease spread in the opposite direction to the directional shift in the host species range. To test our hypothesis, we formulate a reaction-diffusion equation model with a Susceptible-Infected (SI) epidemiological structure for two host species, both susceptible to a disease, but spatially isolated due to distinct thermal niches, and where prior to climate warming the disease is endemic in the northern species only. Previous theoretical results show that species’ distributions can lag behind species’ thermal niches when climate warming occurs. As such, we find that climate warming, by shifting both species’ niches forward, may increase the overlap between northern and southern host species ranges, due to the northern species lagging behind its thermal tolerance limit, thus facilitating a southern disease spread. As our model is general, our findings may apply to viral, bacterial, and prion diseases that do not have thermal tolerance limits and are inextricably linked to their hosts’ distributions, such as the spread of rabies from arctic to red foxes.
WAT3R: Recovery of T-Cell Receptor Variable Regions From 3’ Single-Cell RNA-Sequencing
Authors: Ainciburu Marina , Morgan Duncan M. , DePasquale Erica A. K. , Love J. Christopher , Prósper Felipe , van Galen Peter 
Published: January 2022

AbstractSummaryDiversity of the T-cell receptor (TCR) repertoire is central to adaptive immunity. The TCR is composed of α and β chains, encoded by the TRA and TRB genes, of which the variable regions determine antigen specificity. To generate novel biological insights into the complex functioning of immune cells, combined capture of variable regions and single-cell transcriptomes provides a compelling approach. Recent developments enable the enrichment of TRA and TRB variable regions from widely used technologies for 3’-biased single-cell RNA-sequencing (scRNA-seq). However, a comprehensive computational pipeline to process TCR-enriched data from 3’ scRNA-seq is not available. Here we present an analysis pipeline to process TCR variable regions enriched from 3’ scRNA-seq cDNA. The tool reports TRA and TRB nucleotide and amino acid sequences linked to cell barcodes, enabling the reconstruction of T-cell clonotypes with associated transcriptomes. We demonstrate the software using peripheral blood mononuclear cells (PBMCs) from a healthy donor and detect TCR sequences in a high proportion of single T-cells. Detection of TCR sequences is negligible in non-T-cell populations, demonstrating specificity. Finally, we show that TCR clones are larger in CD8 Memory T-cells than other T-cell types, indicating an association between T-cell clonotypes and differentiation states.Availability and implementationThe Workflow for Association of T-cell receptors from 3’ single-cell RNA-seq (WAT3R), including test data, is available on GitHub (https://github.com/mainciburu/WAT3R), Docker Hub (https://hub.docker.com/r/mainciburu/wat3r), and a workflow on the Terra platform (https://app.terra.bio). The test dataset is available on GEO (accession number pending).
Preclinical stage abundance and nuclear antigen reactivity of fecal Immunoglobulin A (IgA) varies among males and females of lupus-prone mouse models
Authors: Gudi Radhika , Roy Soumyabrata , Sun Wei , Vasu Chenthamarakshan 
Published: January 2022

AbstractSystemic lupus erythematosus (SLE) is characterized by the production of pathogenic autoantibodies with nuclear antigen (nAg) specificity. Using (SWRxNZB)F1 (SNF1) mice, we showed higher levels of IgA production in the intestine and the nAg reactivity of fecal IgA under lupus susceptibility. Here, we determined if the fecal IgA abundance and nAg reactivity are higher in, different among, various lupus-prone preclinical models (MRL/lpr, NZBxNZW-F1, SNF1, NZM2410 and NZM2328). We also determined if the fecal IgA nAg reactivity at pre-seropositive ages correlates with the eventual serum autoantibody levels in males and females of these mouse models. We show that age dependent increase in the abundance and nAg reactivity of fecal IgA can vary among different lupus-prone mouse models. Importantly, fecal IgA in these mice show significant levels of nAg reactivity, starting as early as at juvenile age. Furthermore, the pre-seropositive stage nAg reactivity of fecal IgA in most lupus-prone strains correlates well with that of eventual, seropositive stage systemic autoantibody levels. Gender differences in serum autoantibody levels were preceded by similar differences in the fecal IgA abundance and nAg reactivity. These observations suggest that fecal IgA features, nAg reactivity particularly, could serve as a biomarker for early prediction of the eventual systemic autoimmunity in lupus-prone subjects.
Sex-Specific Genes Identified in Sea Urchin Gonads are Expressed Prior to Metamorphosis
Authors: Pieplow Cosmo , Wessel Gary M. 
Published: January 2022

AbstractA great collaboration between the germline and somatic cells of an organism is the creation of a functional gonad. Here we begin to test this mechanism in a sea urchin by use of RNA-seq, and quantitative mRNA measurements throughout the life cycle of the sea urchin, Lytechinus variegatus (Lv). We found through de novo analyses that the ovary and testis of this echinoderm contains the many transcripts predicted for gamete morphology and function, but we also discovered many uncharacterized gene products unique to each gonad. We found that transcripts involved in glycolysis are highly enriched in the ovary compared to the testis, and that Lv has an expansion of nanos genes not observed in other sequenced echinoderms. We developed a pipeline integrating timepoint RNA-seq data throughout development to identify hallmark gene expression in gonads. We found activation of meiotic genes surprisingly early in development, and observed that candidate genes involved in sex determination are first expressed during larval growth, well before metamorphosis. We further discovered that individual larvae express varying levels of male- or female-hallmark genes before metamorphosis, including factors for the germ line, oocyte, sperm, and meiosis related genes. Together these data support the hypothesis that sex determination in the sea urchin is initiated prior to metamorphosis, from a shared profile of male and female factors, and that the many uncharacterized genes unique to the gonads may reveal unique pathways and mechanisms in echinoderm reproduction.HighlightTestis and Ovary of the sea urchin, Lytechinus variegatus, have distinct transcriptome profilesL. variegatus gonad RNA-seq reveals the expression of 9 nanos genesThe ovary in the sea urchin uniquely expresses genes of the glycolytic pathway, including an ovary-specific transcript of GAPDHGenes involved in meiosis and in sex determination are expressed early in larval developmentFrom gene expression profiles we conclude here that sex determination is initiated prior to metamorphosis in this echinoderm
Modeling Pulse Dynamics of Juvenile Fish Enables the Short-term Forecasting of Population Dynamics in Japanese Pufferfish: A Latent Variable Approach
Authors: Nishijima Shota , Suzuki Shigenori , Fukuta Ryo , Okada Makoto 
Published: January 2022

ABSTRACTThe time lag between data collection and management implementation is a source of uncertainty and bias in the calculation of acceptable biological catch. Here, we developed a method to use small-scale survey data for juvenile Japanese pufferfish (Takifugu rubripes) to shorten this time lag and achieve accurate short-term forecasting. A survey of juvenile fish at a local sandy beach in Ise-Mikawa Bay, Japan provides data for the strength of year classes before fisheries recruitment; however, it is difficult to use the raw data owing to the small sample size and large observation errors. We found that a random-effect model overcame these problems and more accurately predicted pulse patterns of catch rates to derive a standardized recruitment index compared with a fixed-effect model. We then showed that a stock assessment model using the standardized recruitment index from the random-effect model outperformed models without the standardized recruitment index with respect to retrospective forecasting ability. This study highlights the applicability of a latent-variable approach for standardizing small-scale survey data and thereby for unbiased forecasting of short-term fish dynamics.