bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomes and transcriptomes help unravel the complex life cycle of the blastoclad fungus,Coelomomyces lativittatus,an obligate parasite of mosquitoes and microcrustaceans
Authors: Ettinger Cassandra L. , Ostovar Talieh , Yacoub Mark , Ahrendt Steven , Hice Robert H. , Federici Brian A. , Stajich Jason E. 
Published: January 2023

ABSTRACTSpecies of the phylum Blastocladiomycota, early diverging zoosporic (flagellated) lineages of fungi, are vastly understudied. This phylum includes the genusCoelomomyceswhich consists of more than 80 fungal species that are obligate parasites of arthropods. KnownCoelomomycesspecies lack a complete asexual life cycle, instead surviving through an obligate heteroecious alternation of generations life cycle. Despite their global distribution and interesting life cycle, little is known about the genomics of anyCoelomomycesspecies. To address this, we generated three draft-level genomes and annotations forC. lativittatusrepresenting its haploid meiospore, orange gamete, and amber gamete life stages. These draft genome assemblies ranged in size from 5002 to 5799 contigs with a total length of 19.8-22.8 Mb and a mean of 7416 protein-coding genes. We then demonstrated the utility of these genomes by combining the draft annotations as a reference for analysis ofC. lativittatustranscriptomes. We analyzed transcriptomes from across host-associated life stages including infection of larva and excised mature sporangia from the mosquito,Anopheles quadrimaculatus. We identified differentially expressed genes and enriched GO terms both across and within life stages and used these to make hypotheses aboutC. lativittatusbiology. Generally, we found theC. lativittatustranscriptome to be a complex and dynamic expression landscape; GO terms related to metabolism and transport processes were enriched during infection and terms related to dispersal were enriched during sporulation. We further identified five HMG box genes inC. lativittatus, three belonging to clades with mating type (MAT) loci from other fungi,as well as four ortholog expansions inC. lativittatuscompared to other fungi. TheC. lativittatusgenomes and transcriptomes reported here are a valuable resource and may be leveraged toward furthering understanding of the biology of these and other early diverging fungal lineages.
If it’s there, could it be a bear?
Authors: Foxon Floe 
Published: January 2023

AbstractIt has been suggested that the American black bear (Ursus americanus) may be responsible for a significant number of purported sightings of an alleged unknown species of hominid in North America. Previous analyses have identified correlation between ‘sasquatch’ or ‘bigfoot’ sightings and black bear populations in the Pacific Northwest using ecological niche models and simple models of expected animal sightings. The present study expands the analysis to the entire US and Canada by regressing sasquatch sightings on bear populations in each state/province while adjusting for human population and forest area in a generalized linear model. Sasquatch sightings were statistically significantly associated with bear populations such that, on the average, every 1, 000 bear increase in the bear population is associated with a 4% (95% CI: 1%–7%) increase in sasquatch sightings. Thus, as black bear populations increase, sasquatch sightings are expected to increase also. On the average, across all states and provinces in 2006, after controlling for human population and forest area, there were approximately 5, 000 bears per sasquatch sighting. Based on statistical considerations, it is likely that many supposed sasquatch are really misidentified known forms. If bigfoot is there, it may be a bear.
Dysregulated mammalian estrus cycle rescued by timed activation of VIP neurons in the circadian pacemaker and late afternoon light exposure
Authors: Kahan Anat , Coughlin Gerard M. , Borsos Máté , Brunton Bingni W. , Gradinaru Viviana 
Published: January 2023

AbstractJet lag and shift work disrupt the menstrual cycle and decrease fertility. The circadian pacemaker, the suprachiasmatic nucleus (SCN), is known to modulate ovulation, but the mechanism is unclear. Here we explore this connection by tracking the dynamics of vasoactive intestinal peptide (VIP)-expressing neurons in the SCN in freely-behaving mice. We show that SCNVIPactivity is time-of-day- and sex-dependent, and estrous-state-dependent in late afternoon, gating downstream activation of GnRH neurons. Afternoon light, as well as specific activation of SCNVIPneurons, rescues estrous cycle regularity and egg release in animals in altered light conditions, emphasizing the role of SCNVIPneurons as a time-dependent light-responsive switch. Our results reveal the dynamic mechanism by which SCNVIPneurons mediate light responses to regulate estrous states and demonstrate light-induced fertility rescue.One Sentence SummaryModulating and recording the activity of suprachiasmatic VIP neurons in freely behaving mice reveals their regulation of fertility by mediating the response to late afternoon light.
scRNAseq_KNIME workflow: A Customizable, Locally Executable, Interactive and Automated KNIME workflow for single-cell RNA seq
Authors: Kausar Samina , Asif Muhammad , Baudot Anaïs 
Published: January 2023

AbstractSummarySingle-cell RNA sequencing (scRNA-seq) is nowadays widely used to measure gene expression in individual cells, but meaningful biological interpretation of the generated scRNA-seq data remains a complicated task. Indeed, expertise in both the biological domain under study, statistics, and computer programming are prerequisite for thorough analysis of scRNA-seq data. However, biological experts may lack data science expertise, and bioinformatician’s limited understanding of the biology may lead to time-consuming iterations.A user-friendly and automated workflow with possibility for customization is hence of a wide interest for both the biological and bioinformatics communities, and for their fruitful collaborations. Here, we propose a locally installable, user-friendly, interactive, and automated workflow that allows the users to perform the main steps of scRNA-seq data analysis. The interface is composed of graphical entities dedicated to specific and modifiable tasks. It can easily be used by biologists and can also serve as a customizable basis for bioinformaticians.Availability and implementationThe workflow is developed in KNIME; its tasks were defined by R scripts using KNIME R nodes. The workflow is publicly available athttps://github.com/Saminakausar/scRNAseq_KNIME.Contact:anais.baudot@univ-amu.fr;muhasif123@gmail.com
Histone acetylation insulator SET orchestrates PP2A inhibition and super-enhancer activation
Authors: Xu He , Wu Di , Xu Jin , Lei Yubin , Lei Yalan , Yu Xianjun , Shi Si 
Published: January 2023

SummaryWide-spread growth-essential genes are hyper-transcribed in the pancreatic cancer cells. Searching for the factors that reprogram this abnormal transcription, we identified the nuclear oncogene SET that supported CDK9-induced and Pol II-mediated transcription. SET disrupted PP2A-A/C interaction via its C-terminal domains. Through blocking PP2A activity, SET assisted CDK9 to maintain Pol II CTD phosphorylation and activated mRNA transcription. Meanwhile, as a histone acetylation insulator, SET mainly suppressed histone acetylation in the gene promoters but evaded enhancers. Massive super-enhancer associated genes, including the oncogeneMET, were hence permitted to be transcribed by SET over-expression. Our findings position SET as a key factor that bridges histone acetylation and PP2A related transcription in cancer cells.
Gastrodin ameliorates synaptic impairment, reestablishes mitochondrial membrane potential and reduces oxidative stress in N2a/APP cells through ERK1/2 and GSK-3β pathways
Authors: Tang Zhi , Peng Yaqian , Wang Li , Guo Min , Chen Zhuyi , Zhang Ting , Xiao Yan , Ni Ruiqing , Qi Xiaolan 
Published: January 2023

AbstractAlzheimer’s disease (AD) is featured by abnormal β-amyloid (Aβ) deposition, neurofibrillary tangle formation, downstream mitochondrial dysfunction, oxidative stress, and synaptic loss. Gastrodin, a phenolic glycoside, has shown neuroprotective effect and used in the treatment of a range of brain diseases. Here we aim to assess the mechanisms and signaling pathways involved in the neuroprotective effect of gastrodin in murine neuroblastoma N2a cells expressing human Swedish mutant amyloid precursor protein (N2a/APP). The levels of pre- and postsynaptic proteins, amyloid precursor protein C-terminal fragments (APP-CTFs), levels of tau, glycogen synthase kinase-3 β (GSK-3β), extracellular regulated kinase (ERK), and c-Jun N-terminal Kinase (JNK) were assessed by Western blotting. Flow cytometry assays for mitochondrial membrane potential (JC1) and reactive oxidative stress, as well as immunofluorescence staining for lipid peroxidation (4◻hydroxynonenal) and DNA oxidation (8◻hydroxy◻2’◻deoxyguanosine), were performed. We found that gastrodin treatment increased the levels of presynaptic SNAP25, synaptophysin, and postsynaptic PSD95, reduced phosphorylated tau protein Ser396, and APP-CTFs in N2a/APP cells. In addition, gastrodin reduced the levels of reactive oxygen species generation, lipid peroxidation, and DNA oxidation, reestablished mitochondrial membrane potential. Upregulated levels of phosphorylated-GSK-3β, reduced levels of phosphorylated-ERK, and phosphorylated-JNK were involved the protective effect of gastrodin. In conclusion, we demonstrated a neuroprotective effect of gastrodin in N2a/APP cell line.
Reliable genetic correlation estimation via multiple sample splitting and smoothing
Authors: Mai The Tien 
Published: January 2023

AbstractIn this paper, we aim to investigate the problem of estimating the genetic correlation between two traits. Instead of making assumptions about the distribution of effect sizes of the genetic factors, we propose the use of a high-dimensional linear model to relate a trait to genetic factors. To estimate the genetic correlation, we develop a generic strategy that combines the use of sparse penalization methods and multiple sample splitting approaches. The final estimate is determined by taking the median of the calculations, resulting in a smoothed and reliable estimate. Through simulations, we demonstrate that our proposed approach is reliable and accurate in comparison to naive plug-in methods. To further illustrate the advantages of our method, we apply it to a real-world example of a bacterial GWAS dataset, specifically to estimate the genetic correlation between antibiotic resistant traits inStreptococus pneumoniae. This application not only validates the effectiveness of our method but also highlights its potential in real-world applications.
The phospho-regulated amphiphysin/endophilin interaction is required for synaptic vesicle endocytosis
Authors: Kontaxi Christiana , Cousin Michael A. 
Published: January 2023

AbstractThe multidomain adaptor protein amphiphysin-1 (Amph1) is an important coordinator of clathrin-mediated endocytosis in non-neuronal cells and synaptic vesicle (SV) endocytosis at central nerve terminals. Amph1 contains a lipid-binding N-BAR (Bin/Amphiphysin/Rvs) domain, central proline-rich (PRD) and clathrin/AP2 (CLAP) domains, and a C-terminal SH3 domain. All domains interact with either lipids or SV endocytosis proteins, with all of these interactions required for SV endocytosis, apart from the Amph1 PRD. In this study, we determined this role and confirmed requirements for established Amph1 interactions in SV endocytosis at typical small central synapses. Domain-specific interactions of Amph1 were validated usingin vitroGST pull-down assays, with the role of these interactions in SV endocytosis determined in molecular replacement experiments in primary neuronal culture. Using this approach, we confirmed important roles for CLAP and SH3 domain interactions in the control of SV endocytosis. Furthermore, we identified an interaction site for the endocytosis protein endophilin A1 in the Amph1 PRD and revealed a key role for this interaction in SV endocytosis. Finally, we discovered that the phosphorylation status of Amph1-S293 within the PRD dictates the formation of the Amph1-endophilin A1 complex and is essential for efficient SV regeneration. This work therefore identifies an activity-dependent dephosphorylation-dependent interaction that is key for efficient SV endocytosis.
Cultivation ofUlvasp. offshore the Eastern Mediterranean Sea in experimental bioreactors: seasonal growth dynamics and environmental effects
Authors: Zollmann Meiron , Liberzon Alexander , Palatnik Ruslana R. , Zilberman David , Golberg Alexander 
Published: January 2023

AbstractOffshore macroalgae production could provide an alternative source of biomass for food, materials and energy. However, the offshore environment in general, and specifically the Eastern Mediterranean Sea (EMS) offshore, is a high energy and low nutrients environment and thus is challenging for macroalgae farming. This study aims to understand the effects of season, depth, and fertilization duration on growth rates and chemical composition in offshoreUlvabiomass production and develop a predictive model suitable to offshore conditions. We hypothesize that offshoreUlvagrowth rates and chemical composition will follow a seasonal trend and that applying rapid onshore fertilization could refill nutrient storages and enable continuous offshore cultivation. We test this hypothesis by measuringUlvabiomass and internal nitrogen in offshore experiments in the nitrogen-poor EMS a few kilometers offshore the Israeli coast. We construct a predictive cultivation model to estimate N concentrations in the sea during experiments. This study demonstrates the feasibility of growingUlvasp. offshore the EMS with an onshore nutrient supply and develops a better understanding of seasonal growth dynamics and environmental effects (nitrogen, waves, depth, etc.). Furthermore, the study showcases the applicability of the macroalgae cultivation model in the offshore environment and its potential contribution throughout the whole lifecycle of seaweed cultivation.
Biomimetic actin cortices shape cell-sized lipid vesicles
Authors: Baldauf Lucia , Frey Felix , Perez Marcos Arribas , Mladenov Miroslav , Way Michael , Idema Timon , Koenderink Gijsje H. 
Published: January 2023

AbstractAnimal cells are shaped by a thin layer of actin filaments underneath the plasma membrane known as the actin cortex. This cortex stiffens the cell surface and thus opposes cellular deformation, yet also actively generates membrane protrusions by exerting polymerization forces. It is unclear how the interplay between these two opposing mechanical functions plays out to shape the cell surface. To answer this question, we reconstitute biomimetic actin cortices nucleated by the Arp2/3 complex inside cell-sized lipid vesicles. We show that thin Arp2/3-nucleated actin cortices strongly deform and rigidify the shapes of giant unilamellar vesicles and impart a shape memory on time scales that exceeds the time of actin turnover. In addition, actin cortices can produce finger-like membrane protrusions, showing that Arp2/3-mediated actin polymerization forces alone are sufficient to initiate protrusions in the absence of actin bundling or membrane curving proteins. Combining mathematical modeling and our experimental results reveals that the concentration of actin nucleating proteins, rather than actin polymerization speed, is crucial for protrusion formation. This is because locally concentrated actin polymerization forces can drive a positive feedback loop between recruitment of actin and its nucleators to drive membrane deformation. Our work paints a picture where the actin cortex can either drive or inhibit deformations depending on the local distribution of nucleators.Significance StatementThe cells in our body must actively change shape in order to migrate, grow and divide, but they also need to maintain their shape to withstand external forces during tissue development. Cellular shape control results from an interplay between the plasma membrane and its underlying cortex, a shell composed of crosslinked actin filaments. Using cell-free reconstitution and mathematical modelling, we show that minimal biomimetic actin cortices can mechanically rigidify lipid vesicles while at the same time driving membrane protrusion formation. Our observations suggest that the spatial distribution of actin nucleation determines whether the actin cortex drives or inhibits membrane deformations.
A century of sampling at an ecological preserve reveals declining diversity of wild bees
Authors: Graham Kelsey K. , Glaum Paul , Hartert Joseph , Gibbs Jason , Tucker Erika , Isaacs Rufus , Valdovinos Fernanda S. 
Published: January 2023

AbstractWe analyzed the wild bee community from 1921 to 2018 at a nature preserve in southern Michigan, USA using museum records and found significant shifts in the bee community. Across the near century of records, species richness peaked in the 1970s and 1980s. There was an intensive bee survey completed by F.C. Evans in 1972 and 1973. We attempted to replicate his effort in 2017 and 2018, and again found a significant decline in species richness and evenness. There was also evidence of declining abundance in many of the more common species. We also conducted traits analyses using neural networks, revealing that oligolectic ground-nesting bees and cleptoparasitic bees were more likely to be extirpated whereas polylectic cavity-nesting bees were more likely to have persisted. Additionally, larger body size was associated with increased probability of local extirpation for polylectic cavity-nesting species. Larger phenological range was associated with increased chances of persistence for polylectic species, while it was associated with extirpation for oligolectic ground-nesting species. Species in the contemporary samples also had a more southerly overall distribution compared to the historic one.Open Research StatementData used for analyses in this manuscript, including Evans’ original dataset from 1972/1973 with updated species nomenclature, will be permanently archived at theUSDA Ag Data Commonsafter the acceptance of this manuscript and will be citable and accessible here:https://data.nal.usda.gov/dataset/century-sampling-ecological-preserve-reveals-declining-diversity-wild-bees. Complete instructions on how to access all data referenced in this manuscript can be found in Appendix S1.
Exposure to high-sugar diet induces transgenerational changes in sweet sensitivity and feeding behavior via H3K27me3 reprogramming
Authors: Yang Jie , Tang Ruijun , Chen Shiye , Chen Yinan , Zhang Liudeng , Yuan Kai , Huang Rui , Wang Liming 
Published: January 2023

ABSTRACTHuman health is facing a host of new threats linked to unbalanced diets, including high sugar diet (HSD), which contributes to the development of both metabolic and behavioral disorders. Studies have shown that diet-induced metabolic dysfunctions can transmit to multiple generations of offspring and exert long-lasting health burden. Meanwhile, whether and how diet-induced behavioral abnormalities can be transmitted to the offspring remain largely unclear. Here, we showed that ancestral HSD exposure suppressed sweet sensitivity and feeding behavior in the offspring inDrosophila. These behavioral deficits were transmitted through the maternal germline and companied by the enhancement of H3K27me3 modifications. PCL-PRC2 complex, a major driver of H3K27 trimethylation, was upregulated by ancestral HSD exposure, and disrupting its activity eliminated the transgenerational inheritance of sweet sensitivity and feeding behavior deficits. Elevated H3K27me3 inhibited the expression of a transcriptional factor Cad and suppressed sweet sensitivity of the sweet-sensing gustatory neurons, reshaping the sweet perception and feeding behavior of the offspring. Taken together, we uncovered a novel molecular mechanism underlying behavioral abnormalities across multiple generations of offspring upon ancestral HSD exposure, which would contribute to the further understanding of long-term health risk of unbalanced diet.
Increased mitochondrial surface area and cristae density in the skeletal muscle of strength athletes
Authors: Botella Javier , Schytz Camilla T. , Pehrson Thomas F. , Hokken Rune , Laugesen Simon , Aagaard Per , Suetta Charlotte , Christensen Britt , Ørtenblad Niels , Nielsen Joachim 
Published: January 2023

AbstractMitochondria are the cellular organelles responsible for resynthesising the majority of ATP. In skeletal muscle, there is an increased ATP turnover during resistance exercise to sustain the energetic demands of muscle contraction. Despite this, little is known regarding the mitochondrial characteristics of chronically strength-trained individuals and any potential pathways regulating the strength-specific mitochondrial remodelling. Here, we investigated the mitochondrial structural characteristics in skeletal muscle of strength athletes and age-matched untrained controls. The mitochondrial pool in strength athletes was characterised by increased mitochondrial cristae density, decreased mitochondrial size, and increased surface-to-volume ratio, despite similar mitochondrial volume density. We also provide a fibre-type and compartment specific assessment of mitochondria morphology in human skeletal muscle, which reveals across groups a compartment-specific influence on mitochondrial morphology that is largely independent of fibre-type. Furthermore, we show that resistance exercise leads to signs of mild mitochondrial stress, without an increase in the number of damaged mitochondria. Using publicly available transcriptomic data we show that acute resistance exercise increases the expression of markers of mitochondrial biogenesis, fission, and mitochondrial unfolded protein responses (UPRmt). Further, we observed an enrichment of the UPRmtin the basal transcriptome of strength-trained individuals. Together, these findings show that strength athletes possess a unique mitochondrial remodelling, which minimises the space required for mitochondria. We propose that the concurrent activation of markers of mitochondrial biogenesis and mitochondrial remodelling pathways (fission and UPRmt) with resistance exercise may be partially responsible for the observed mitochondrial phenotype of strength athletes.