bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fifty generations of amitosis: tracing asymmetric allele segregation in polyploid cells with single-cell DNA sequencing
Authors: Vitali Valerio , Rothering Rebecca , Catania Francesco 
Published: March 2021

AbstractAmitosis is a widespread form of unbalanced nuclear division whose biomedical and evolutionary significance remain unclear. Traditionally, insights into the genetics of amitosis are acquired by assessing the rate of phenotypic assortment. The phenotypic diversification of heterozygous clones during successive cell divisions reveals the random segregation of alleles to daughter nuclei. Though powerful, this experimental approach relies on the availability of phenotypic markers. Here, we present an approach that overcomes the requirement for phenotypic assortment. LeveragingParamecium tetraurelia, a unicellular eukaryote with nuclear dimorphism and a highly polyploid somatic nucleus, we use single-cell whole-genome sequencing to track the assortment of developmentally acquired somatic DNA variants. Accounting for genome representation biases, we measure the effect of amitosis on allele segregation across the first ∼50 amitotic divisions post self-fertilization and compare our empirical findings with theoretical predictions estimated via mathematical modeling. In line with our simulations, we show that amitosis inP. tetraureliaproduces measurable but modest levels ofsomatic assortment. In forgoing the requirement for phenotypic assortment and employing developmental, environmentally induced somatic variation as molecular markers, our work provides a new powerful approach to investigate the consequences of amitosis in polyploid cells.
COVID-19 and the abrupt shift to remote learning: Impact on grades and perceived learning for undergraduate biology students
Authors: Supriya K. , Mead Chris , Anbar Ariel D. , Caulkins Joshua L. , Collins James P. , Cooper Katelyn M. , LePore Paul C. , Lewis Tiffany , Pate Amy , Scott Rachel A. , Brownell Sara E. 
Published: March 2021

AbstractInstitutions across the world transitioned abruptly to remote learning in 2020 due to the COVID-19 pandemic. This rapid transition to remote learning has generally been predicted to negatively affect students, particularly those marginalized due to their race, socioeconomic class, or gender identity. In this study, we examined the impact of this transition in the Spring 2020 semester on the grades of students enrolled in the in-person biology program at a large university in Southwestern United States as compared to the grades earned by students in the fully online biology program at the same institution. We also surveyed in-person instructors to understand changes in assessment practices as a result of the transition to remote learning during the pandemic. Finally, we surveyed students in the in-person program to learn about their perceptions of the impacts of this transition. We found that both online and in-person students received a similar small increase in grades in Spring 2020 compared to Spring 2018 and 2019. We also found no evidence of disproportionately negative impacts on grades received by students marginalized due to their race, socioeconomic class, or gender in either modality. Focusing on in-person courses, we documented that instructors made changes to their courses when they transitioned to remote learning, which may have offset some of the potential negative impacts on course grades. However, despite receiving higher grades, in-person students reported negative impacts on their learning, interactions with peers and instructors, feeling part of the campus community, and career preparation. Women reported a more negative impact on their learning and career preparation compared to men. This work provides insights into students’ perceptions of how they were disadvantaged as a result of the transition to remote instruction and illuminates potential actions that instructors can take to create more inclusive education moving forward.
Mass recalibration for desorption electrospray ionization mass spectrometry imaging using endogenous reference ions
Authors: Inglese Paolo , Huang Helen Xuexia , Wu Vincen , Lewis Matthew R , Takats Zoltan 
Published: March 2021

1AbstractBackgroundMass spectrometry imaging (MSI) data often consist of tens of thousands of mass spectra collected from a sample surface. During the time necessary to perform a single acquisition, it is likely that uncontrollable factors alter the validity of the initial mass calibration of the instrument, resulting in mass errors of magnitude significantly larger than their expected values. This phenomenon has a two-fold detrimental effect: a) it reduces the ability to interpret the results based on the observed signals, b) it can affect the quality of the observed signal spatial distributions.ResultsWe present a post-acquisition computational method capable of reducing the observed mass drift by up to 60 ppm in biological samples, exploiting the presence of typical molecules with a known mass-to-charge ratio. The procedure, tested on time-of-flight (TOF) and Orbitrap mass spectrometry analyzers interfaced to a desorption electrospray ionization (DESI) source, improves the molecular annotation quality and the spatial distributions of the detected ions.ConclusionThe presented method represents a robust and accurate tool for performing post-acquisition mass recalibration of DESI-MSI datasets and can help to increase the reliability of the molecular assignment and the data quality.
Lysophosphatidyl-choline 16:0 mediates persistent joint pain through Acid-Sensing Ion Channel 3: preclinical and clinical evidences
Authors: Jacquot Florian , Khoury Spiro , Labrum Bonnie , Delanoe Kévin , Pidoux Ludivine , Barbier Julie , Delay Lauriane , Bayle Agathe , Aissouni Youssef , Barriere David A. , Kultima Kim , Freyhult Eva , Hugo Anders , Kosek Eva , Ahmed Aisha S. , Jurczak Alexandra , Lingueglia Eric , Svensson Camilla I. , Breuil Véronique , Ferreira Thierry , Marchand Fabien , Deval Emmanuel 
Published: March 2021

AbstractRheumatic diseases are often associated to debilitating chronic joint pain, which remains difficult to treat and requires new therapeutic strategies. Here, we describe increased content of lysophosphatidyl-choline (LPC) 16:0 in the knee synovial fluids of two independent cohorts of patients with painful joint diseases. If LPC16:0 levels correlated with pain in patients with osteoarthritis (OA), they do not appear to be the hallmark of a particular joint disease. We found that intra-articular injections of LPC16:0 in mouse produce chronic pain and anxiety-like behaviors in both males and females with no apparent inflammation, peripheral nerve sprouting and damage, nor bone alterations. LPC16:0-induced persistent pain state is dependent on peripheral Acid-Sensing Ion Channel 3 (ASIC3), ultimately leading to central sensitization. LPC16:0 and ASIC3 thus appear as key players of chronic joint pain with potential implications in OA and possibly across others rheumatic diseases.
Conjugative plasmid transfer is limited by prophages but can be overcome by high conjugation rates
Authors: Igler Claudia , Schwyter Lukas , Gehrig Daniel , Wendling Carolin Charlotte 
Published: March 2021

AbstractAntibiotic resistance spread via plasmids is a serious threat to successfully fight infections and makes understanding plasmid transfer in nature crucial to prevent the rise of antibiotic resistance. Studies addressing the dynamics of plasmid conjugation have yet neglected one omnipresent factor: prophages (viruses integrated into bacterial genomes), whose activation can kill host and surrounding bacterial cells. To investigate the impact of prophages on conjugation, we combined experiments and mathematical modelling. UsingE. coli, prophageλand the multidrug-resistant plasmid RP4 we find that prophages can substantially limit the spread of conjugative plasmids. This inhibitory effect was strongly dependent on environmental conditions and bacterial genetic background. Our empirically parameterized model reproduced experimental dynamics of cells acquiring either the prophage or the plasmid well but could only reproduce the number of cells acquiring both elements by assuming complex interactions between conjugative plasmids and prophages in sequential infections. Varying phage and plasmid infection parameters over empirically realistic ranges revealed that plasmids can overcome the negative impact of prophages through high conjugation rates. Overall, the presence of prophages introduces an additional death rate for plasmid carriers, the magnitude of which is determined in non-trivial ways by the environment, the phage and the plasmid.
Mechanically Activated Extracellular Vesicle Functionalised Melt Electrowritten Materials for Bone Regeneration: A Mechano-Biomimetic Scaffold
Authors: Eichholz Kian F. , Federici Angelica , Riffault Mathieu , Woods Ian , Mahon Olwyn R. , O’Driscoll Lorraine , Hoey David A. 
Published: March 2021

1AbstractMechanobiological cues arising directly via tissue/scaffold mechanics or indirectly via mechanically activated cell secretomes represent potent stimuli that mediate cell behaviour and tissue adaptation. Exploiting these cues in regeneration strategies holds great promise for tissue repair. In this study, we harness indirect biophysical cues originating from osteocytes in a combination with direct biophysical cues from Melt ElectroWritten (MEW) scaffolds to form a single engineered construct with the aim of synergistically enhancing osteogenesis. The secretome of mechanically activated osteocytes was collected within conditioned media (CM) and extracellular vesicles (EV) were subsequently isolated. Building on MEW micro-fibrous scaffolds with controlled microarchitecture and mineral nanotopography optimised for bone repair, a protocol was developed to functionalise these materials with CM or EVs. Human MSC proliferation was enhanced in both CM and EV functionalised scaffolds. EV functionalised scaffolds were further found to significantly enhance MSC osteogenesis, with enhanced alkaline phosphatase expression, collagen production, and mineralisation compared to control scaffolds. Furthermore, enhanced formation of mineralised nodules was identified in EV functionalised materials. Combining direct biophysical cues provided by the fibrous architecture/mineral nanotopography with the indirect cues provided by EVs, these constructs hold great promise to enhance the repair of damaged bone in a physiologically relevant manner.
Whole-Genome Sequencing on 220 Alfalfa (Medicago sativa L.) Accessions Identified Association of DREB1C Gene with Fall Dormancy Height
Authors: Zhang Fan , Kang Junmei , Long Ruicai , Li Mingna , Sun Yan , Wang Zhen , Zhang Zhiwu , Yang Qingchuan 
Published: March 2021

AbstractFall dormancy (FD) is one of the most important traits of alfalfa (Medicago sativa) for cultivar selection to overcome winter stress. Although transcriptomics, proteomics analysis, and QTL mapping have revealed some important genes correlated with FD, the genetic architecture of this trait is still unclear. There are no applicable genes or markers for selection, which hinders progress in the genetic research and molecular breeding for the trait. We conducted whole-genome sequencing (WGS) on 220 alfalfa accessions at 10x depth. Among the 875,023 SNPs, four of them were associated with FD height using GWAS. One SNP located on chromosome 6 is in linkage disequilibrium with dehydration-responsive element-binding protein 1C (DREB1C). Furthermore, seven DREB genes are clustered in this region, one of which has previously been shown to enhance freezing tolerance in the model plant Medicago truncatula. The candidate genes uncovered by our research will benefit the transgenic and CRISPR-Cas9 research of FD in alfalfa. This gene will also be useful for molecular marker development and marker-associated breeding of FD for alfalfa.
Untangling the complexity of priority effects in multispecies communities
Authors: Song Chuliang , Fukami Tadashi , Saavedra Serguei 
Published: March 2021

AbstractThe history of species immigration can dictate how species interact in local communities, thereby causing historical contingency in community assembly. Since immigration history is rarely known, these historical influences, or priority effects, pose a major challenge in predicting community assembly. Here, we provide a graph-based, non-parametric, theoretical framework for understanding the predictability of community assembly as affected by priority effects. To develop this frame-work, we first show that the diversity of possible priority effects increases super-exponentially with the number of species. We then point out that, despite this diversity, the consequences of priority effects for multispecies communities can be classified into four basic types, each of which reduces community predictability: alternative stable states, alternative transient paths, compositional cycles, and the lack of escapes from compositional cycles to stable states. Using a neural network, we show that this classification of priority effects enables accurate explanation of community predictability, particularly when each species immigrates repeatedly. We also demonstrate the empirical utility of our theoretical framework by applying it to two experimentally derived assembly graphs of algal and ciliate communities. Based on these analyses, we discuss how the framework proposed here can help guide experimental investigation of the predictability of history-dependent community assembly.
Disruption of the microphysiological niche alters matrix deposition and causes loss of mitochondrial Ca2+control in skeletal muscle fibers
Authors: Gineste Charlotte , Youhanna Sonia , Vorrink Sabine U. , Henriksson Sara , Hernández Andrés , Cheng Arthur J. , Chaillou Thomas , Buttgereit Andreas , Schneidereit Dominik , Friedrich Oliver , Hultenby Kjell , Bruton Joseph D. , Ivarsson Niklas , Sandblad Linda , Lauschke Volker M. , Westerblad Håkan 
Published: March 2021

SummaryCells rapidly lose their physiological phenotype upon disruption of their extracellular matrix (ECM)-intracellular cytoskeleton interactions. Here, we investigated acute effects of ECM disruption on cellular and mitochondrial morphology, transcriptomic signatures, and Ca2+handling in adult mouse skeletal muscle fibers. Adult skeletal muscle fibers were isolated from mouse toe muscle either by collagenase-induced dissociation of the ECM or by mechanical dissection that leaves the contiguous ECM intact. Experiments were generally performed four hours after cell isolation. At this time, there were striking differences in the gene expression patterns between fibers isolated with the two methods; 24h after cell isolation, enzymatically dissociated fibers had transcriptomic signatures resembling dystrophic phenotypes. Mitochondrial appearance was grossly similar in the two groups, but 3D electron microscopy revealed shorter and less branched mitochondria in enzymatically dissociated than in mechanically dissected fibers. Similar increases in free cytosolic [Ca2+] during repeated tetanic stimulation were accompanied by marked mitochondrial Ca2+uptake only in enzymatically dissociated muscle fibers. The aberrant mitochondrial Ca2+uptake was partially prevented by the mitochondrial Ca2+uniporter inhibitor Ru360 and by cyclosporine A and NV556, which inhibit the mitochondrial protein Ppif (also called cyclophilin D). Importantly, inhibition of Ppif with NV556 significantly improved survival of mice with mitochondrial myopathy in which muscle mitochondria take up excessive amounts of Ca2+even with an intact ECM. In conclusion, skeletal muscle fibers isolated by collagenase-induced dissociation of the ECM display aberrant mitochondrial Ca2+uptake, which involves a Ppif-dependent mitochondrial Ca2+influx resembling that observed in mitochondrial myopathies.
Evidence Graphs: Supporting Transparent and FAIR Computation, with Defeasible Reasoning on Data, Methods, and Results
Authors: Al Manir Sadnan , Niestroy Justin , Levinson Maxwell Adam , Clark Timothy 
Published: March 2021

AbstractIntroductionTransparency of computation is a requirement for assessing the validity of computed results and research claims based upon them; and it is essential for access to, assessment, and reuse of computational components. These components may be subject to methodological or other challenges over time. While reference to archived software and/or data is increasingly common in publications, a single machine-interpretable, integrative representation of how results were derived, that supports defeasible reasoning, has been absent.MethodsWe developed the Evidence Graph Ontology, EVI, in OWL 2, with a set of inference rules, to provide deep representations of supporting and challenging evidence for computations, services, software, data, and results, across arbitrarily deep networks of computations, in connected or fully distinct processes. EVI integrates FAIR practices on data and software, with important concepts from provenance models, and argumentation theory. It extends PROV for additional expressiveness, with support for defeasible reasoning. EVI treats any computational result or component of evidence as a defeasible assertion, supported by a DAG of the computations, software, data, and agents that produced it.ResultsWe have successfully deployed EVI for large-scale predictive analytics on clinical time-series data. Every result may reference its evidence graph as metadata, which can be extended when subsequent computations are executed.DiscussionEvidence graphs support transparency and defeasible reasoning on results. They are first-class computational objects and reference the datasets and software from which they are derived. They support fully transparent computation, with challenge and support propagation. The EVI approach may be extended to include instruments, animal models, and critical experimental reagents.
Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging
Authors: Yeo Robin W. , Zhou Olivia Y. , Zhong Brian L. , Sun Eric D. , Negredo Paloma Navarro , Nair Surag , Sharmin Mahfuza , Ruetz Tyson J. , Wilson Mikaela , Kundaje Anshul , Dunn Alexander R. , Brunet Anne 
Published: March 2021

AbstractAging is accompanied by a deterioration in the regenerative and repair potential of stem cell niches in the brain1–5. However, the mechanisms underlying this decline are largely unknown. Here we characterize genome-wide chromatin accessibility in young and old neurogenic niche cellsin vivo, revealing defects in neural stem cell (NSC) adhesion and migration during aging. Interestingly, chromatin accessibility at cell adhesion and migration genes decreases with age in quiescent NSCs but increases with age in activated (proliferative) NSCs, and this is accompanied by corresponding expression changes in these genes. We experimentally validate that quiescent and activated NSCs exhibit opposing adhesion and migration behaviors with age: quiescent NSCs become less adhesive (and more migratory) whereas activated NSCs and progeny become more adhesive (and less migratory) during aging. We also show that the ability of activated NSCs and progeny to mobilize out of the niche duringin vivoneurogenesis diminishes during aging. Using tension sensors with single molecule resolution, we find that one of the cellular mechanisms by which aging impairs the migration of old activated NSCs and progeny involves increased force-producing adhesions. We identify inhibition of the cytoskeletal-regulating kinase ROCK6, 7as a way to reduce force-producing adhesions and restore migration in old activated NSCsin vitro. Interestingly, inhibition of ROCK in the neurogenic niche of old mice boosts neurogenesis to the olfactory bulbin vivo. These results have important implications for restoring the migratory potential of NSCs and progeny and for improving neurogenesis in the aged brain.
Astrocytes are implicated in BDNF-mediated enhancement of hippocampal long-term potentiation
Authors: Gomes Joana I. , Jesus João , Macau Renata , Gonçalves-Ribeiro Joana , Pinto Sara , Pina Carolina Campos , Armada-Moreira Adam , Sebastião Ana Maria , Vaz Sandra H. 
Published: March 2021

AbstractIt is known that astrocytes, by the Ca2+-dependent release of gliotransmitters, which then act in pre- and post-synaptic receptors, modulate neuronal transmission and plasticity. Thus, hippocampal θ-burst long-term potentiation (LTP), which is a form of synaptic plasticity, can be modulated by astrocytes, since these cells release gliotransmitters that are crucial for the maintenance of LTP. Therefore, in this study, we hypothesized that the facilitatory action of BDNF upon LTP would involve astrocytes. To address that possibility, fEPSP recordings were performed in CA3-CA1 area of hippocampal slices from three different experimental models: Wistar rats where astrocytic metabolism was selectively reduced by a gliotoxin, the DL-fluoricitric acid (FC), IP3R2−/−mice, which lack IP3R2-mediated Ca2+-signaling in astrocytes and dn-SNARE transgenic mice, in which the SNARE-dependent release of gliotransmittersis impaired. For the three models we observed that the astrocytic impairment abolished the excitatory BDNF effect upon hippocampal LTP, only while inducing LTP with a mild θ-burst stimulation paradigm. The present data shows for the first time that astrocytes play an active role in the facilitatory action of BDNF upon LTP, depending on stimulation paradigm.
Up and to the light: intra- and interspecific variability of photo- and geo-tactic oviposition preferences in genusTrichogramma
Authors: Burte V. , Perez G. , Ayed F. , Groussier G. , Mailleret L. , van Oudenhove L. , Calcagno V. 
Published: March 2021

AbstractTrichogrammaare parasitic microwasps much used as biological control agents. The genus is known to harbor tremendous diversity, at both inter- and intra-specific levels. The successful selection ofTrichogrammastrains for biocontrol depends on characterizing the existing diversity in this group, especially regarding oviposition performance and behavior. Oviposition preferences in relation to environmental cues such as light and gravity have received little attention so far, although they are suspected to play an important role in microhabitat selection and parasitism patterns. The extent of their variability, and their potential correlated variations, is virtually unknown. Here we use a novel experimental approach relying on automatic image analysis to characterize the oviposition preferences in relation to light and gravity, as well as their interaction, in 25 populations ofTrichogrammafrom five species. We show that mostTrichogrammapopulations and species harbour preferences for light and preferences for elevated parts. However, the two traits harbor significant inter and intraspecific variation. The effects of light and gravity on oviposition patterns were found to be almost perfectly additive overall, with two exceptions. Oviposition preference patterns were not static but very plastic in time: preferences tended to relax over consecutive days, and the strongest preferences relaxed the fastest, presumably because of the density-dependent effect of resource depletion. A correlation of oviposition patterns with the vegetation stratum at which populations were sampled suggests that different species/populations may be associated with different strata with corresponding differentiation in light- and gravity-related oviposition preferences.This article has been peer-reviewed and recommended byPeer Communityin Zoology doi:https://doi.org/10.24072/pci.zool.100008