bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the zebrafishgabra1sa43718/sa43718germline loss of function allele confirms a function for Gabra1 in motility and nervous system development
Authors: Paz David , Reyes-Nava Nayeli G. , Pinales Briana E. , Perez Isaiah , Gil Claudia B. , Gonzales Annalise V. , Grajeda Brian , Estevao Igor L. , Ellis Cameron C. , Castro Victoria L. , Quintana Anita M. 
Published: January 2023

SummaryMutation of theGABRA1gene is associated with neurodevelopmental defects and epilepsy.GABRA1encodes for the α1 subunit of the gamma-aminobutyric acid type A receptor (GABAAR), which regulates the fast inhibitory impulses of the nervous system. Multiple model systems have previously been developed to understand the function ofGABRA1during development, but these models have produced complex and at times incongruent data. Thus, additional model systems are required to validate and substantiate previously published results. We investigated the behavioral swim patterns associated with a nonsense mutation of the zebrafishgabra1(sa43718allele) gene. Thesa43718allele causes a decrease ingabra1mRNA expression, which is associated with light induced hypermotility, one phenotype associated with seizure like behavior in zebrafish. Mutation ofgabra1was accompanied by decreased mRNA expression ofgabra2, gabra3, and gabra5,indicating a reduction in the expression of additional alpha sub-units of the GABAAR. Although multiple sub-units were decreased in total expression, larvae continued to respond to pentylenetetrazole (PTZ) indicating that a residual GABAAR exists in thesa43718allele. Proteomics analysis demonstrated that nonsense mutation ofgabra1is associated with abnormal expression of proteins that regulate proton transport, ion homeostasis, vesicle transport, and mitochondrial protein complexes. These data support previous studies performed in a zebrafish nonsense allele created by CRISPR/Cas9 and validate that loss of function mutations in thegabra1gene result in seizure like phenotypes with abnormal function of inhibitory synapses.
Anillin Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study
Authors: Hall Aaron R. , Choi Yeol Kyo , Im Wonpil , Vavylonis Dimitrios 
Published: January 2023

AbstractThe organization of the cytokinetic ring at the cell equator of dividing animal and fungi cells depends crucially on the anillin scaffold proteins. In fission yeast, anillin related Mid1 binds to the plasma membrane and helps anchor and organize a medial broad band of cytokinetic nodes, which are the precursors of the contractile ring. Similar to other anillins, Mid1 contains a C terminal globular domain with two potential regions for membrane binding, the Pleckstrin Homology (PH) and C2 domains, and an N terminal intrinsically disordered region that is strongly regulated by phosphorylation. Previous studies have shown that both PH and C2 domains can associate with the membrane, preferring phosphatidylinositol-(4,5)-bisphosphate (PIP2) lipids. However, it is unclear if they can simultaneously bind to the membrane in a way that allows dimerization or oligomerization of Mid1, and if one domain plays a dominant role. To elucidate Mid1’s membrane binding mechanism, we used the available structural information of the C terminal region of Mid1 in all-atom molecular dynamics (MD) near a membrane with a lipid composition based on experimental measurements (including PIP2lipids). The disordered L3 loop of C2, as well as the PH domain, separately bind the membrane through charged lipid contacts. In simulations with the full C terminal region started away from the membrane, Mid1 binds through the L3 loop and is stabilized in a vertical orientation with the PH domain away from the membrane. However, a configuration with both C2 and PH initially bound to the membrane remains associated with the membrane. These multiple modes of binding may reflect Mid1’s multiple interactions with membranes and other node proteins, and ability to sustain mechanical forces.
Dysregulated CD38 expression in blood and skin immune cells of patients with hidradenitis suppurativa
Authors: Dimitrion Peter , Hamzavi Iltefat , Yin Congcong , Loveless Ian , Toor Jugmohit , Subedi Kalpana , Khalasawi Namir , Miller Angela , Huggins Richard , Adrianto Indra , Veenstra Jesse , Vellaichamy Gautham , Hans Aakash , Daveluy Steven , Athar Mohammad , Liao Wilson , Lim Henry , Ozog David , Zhou Li , Mi Qing-Sheng 
Published: January 2023

2.ABSTRACTBackgroundHidradenitis suppurativa (HS) is a multifactorial, inflammatory skin disease. Increased systemic inflammatory comorbidities and serum cytokines highlight systemic inflammation as a feature of HS. However, the specific immune cell subsets contributing to systemic and cutaneous inflammation have not been resolved.ObjectiveIdentify features of peripheral and cutaneous immune dysregulation.MethodsHere, we generated whole-blood immunomes by mass cytometry. We performed a meta-analysis of RNA-seq data, immunohistochemistry, and imaging mass cytometry to characterize the immunological landscape of skin lesions and perilesions from patients with HS.ResultsBlood from patients with HS exhibited lower frequencies of natural killer cells, dendritic cells, and classical (CD14+CD16-) and nonclassical (CD14-CD16+) monocytes, as well as higher frequencies of Th17 cells and intermediate (CD14+CD16+) monocytes than blood from healthy controls. Classical and intermediate monocytes from patients with HS had increased expression of skin-homing chemokine receptors. Furthermore, we identified a CD38+ intermediate monocyte subpopulation that was more abundant in the immunome of blood from patients with HS. Meta-analysis of RNA-seq data found higher CD38 expression in lesional HS skin than in perilesional skin, and markers of classical monocyte infiltration. Imaging mass cytometry showed that CD38+ classical monocytes and CD38+ monocyte-derived macrophages were more abundant in lesional HS skin.ConclusionOverall, we report targeting CD38 may be worth pursuing in clinical trials.3.Key MessagesMonocyte subsets express markers of activation in circulation and HS lesionsTargeting CD38 may be a viable strategy for treating systemic and cutaneous inflammation in patients with HS4.Capsule SummaryDysregulated immune cells in patients with HS express CD38 and may be targeting by anti-CD38 immunotherapy.
Joint tensor modeling of single cell 3D genome and epigenetic data with Muscle
Authors: Park Kwangmoon , Keleş Sündüz 
Published: January 2023

AbstractEmerging single cell technologies that simultaneously capture long-range interactions of genomic loci together with their DNA methylation levels are advancing our understanding of three-dimensional genome structure and its interplay with the epigenome at the single cell level. While methods to analyze data from single cell high throughput chromatin conformation capture (scHi-C) experiments are maturing, methods that can jointly analyze multiple single cell modalities with scHi-C data are lacking. Here, we introduce Muscle, a semi-nonnegative joint decomposition ofMultiplesinglecelltensors, to jointly analyze 3D conformation and DNA methylation data at the single cell level. Muscle takes advantage of the inherent tensor structure of the scHi-C data, and integrates this modality with DNA methylation. We developed an alternating least squares algorithm for estimating Muscle parameters and established its optimality properties. Parameters estimated by Muscle directly align with the key components of the downstream analysis of scHi-C data in a cell type specific manner. Evaluations with data-driven experiments and simulations demonstrate the advantages of the joint modeling framework of Muscle over single modality modeling or a baseline multi modality modeling for cell type delineation and elucidating associations between modalities. Muscle is publicly available athttps://github.com/keleslab/muscle.
Pleistocene dispersion supports a unique native diversity in the Colombian avocado germplasm
Authors: Berdugo-Cely J.A. , Cortés A.J. , López-Hernández F. , Delgadillo P. , Cerón-Souza I. , Reyes-Herrera P. , Navas A. , Yockteng R 
Published: January 2023

AbstractGenomic characterization of ex-situ collections optimizes the utilization of genetic resources, identifies redundancies among accessions, captures cryptic variation, establishes reference collections, and ultimately assists pre-breeding and breeding efforts. However, the integration of population genomic analyses is often lacking when studying the biodiversity of crop gene pools. Here, we present modern classification and machine learning approaches to characterize and harness the genebank of an agrobiodiversity hotspot onPersea americanaMill., an iconic American fruit tree crop that has seen an unprecedented expansion worldwide. We selected 144 accessions from the Colombian National genebank and 240 materials from local plantations in the Colombian Northwest Andes. We genotyped them using a strategy based on reduced representation sequencing. We included available sequences of genotypes from known avocado races, Mexican, Guatemalan, and West Indian, to discover SNPs, analyze the population structure and identify possible new genetic groups in Colombian germplasm. We detected a population structure suggestive of a new fourth race in Colombia, with a possible genetic substructure related to geographical origin (Andean and Caribbean). Hybrid determination and ABC modeling suggested rampant inter-race geneflow. They supported the hypothesis of the high mobility of native avocado trees from Central America to Northern South America starting in the Pleistocene. Our study supports that Colombia might be a new diversity center forP. americana.Genotypes of the two newly identified Colombian groups can be used as parents in plant breeding strategies to generate cultivars adapted to specific ecogeographical regions of Colombia.
Biflavonoid quercetin protects against cyclophosphamide–induced organ toxicities via modulation of inflammatory cytokines, brain neurotransmitters, and astrocyte immunoreactivity
Authors: Onaolapo Adejoke Y. , Ojo Foluso O , Onaolapo Olakunle J. 
Published: January 2023

AbstractBackgroundQuercetin’s antioxidative properties make it of potential benefit in many clinical conditions where oxidative stress is implicated in the pathological processes.ObjectivesTo investigate the possible protective effects of quercetin on neurobehaviour, brain oxidative status, markers of inflammation, neurotransmitter balance and astrocyte immunoreactivity in healthy rats administered cyclophosphamide.MethodsSixty rats were randomly assigned into six groups (n=10). Groups A and D served as normal and cyclophosphamide control respectively and were fed standard rat chow, groups B and E were fed quercetin supplemented diet (100 mg/kg of feed), while those in groups C and F were fed quercetin supplemented diet at 200 mg/kg of feed. Animals in group A-C also received intraperitoneal normal saline on days 1 and 2, while those in groups D-F got intraperitoneal cyclophosphamide (150 mg/kg/day on days 1 and 2). Standard diet and quercetin supplemented diet were administered daily for 21 days. At the end of the experimental period, behavioural tests were carried out, following which animals were sacrificed and blood taken for the assessment of biochemical parameters. Organs were either homogenised or processed for histological study.ResultsQuercetin mitigated CYP-induced weight loss and reduction in food consumption. It also improved total antioxidant capacity while reducing CYP-induced lipid peroxidation and biochemical markers of impaired liver function. A reduction in CYP-induced increase in urea and creatinine was also observed. Interleukin-10 increased, while the CYP-induced increase in interleukin-1 beta and TNF-α were also mitigated following quercetin administration. Open field exploratory activities and grooming increased with CYP and the lowest dose of quercetin. The anxiolytic effects of quercetin was demonstrable in the elevated plus maze; while its memory-enhancing effects were seen in the Y-maze and radial-arm maze. Finally, quercetin improved acetylcholine/dopamine levels and brain-derived neurotropic factor, while reducing serotonin levels and astrocyte immunoreactivity.ConclusionThe results show quercetin’s ability to protect against CYP-induced changes in rats. They also highlight the possible use of quercetin as a possible adjunct in cancer chemotherapy-induced tissue damage. However, further research will be needed to delineate its exact role in cancer chemotherapy.
Sexually Dimorphic Role for Insular Perineuronal Nets in Aversion-Resistant Ethanol Consumption
Authors: de Carvalho Luana Martins , Chen Hu , Sutter Mason , Lasek Amy W. 
Published: January 2023

AbstractCompulsive alcohol drinking is a key symptom of alcohol use disorder (AUD) that is particularly resistant to treatment. An understanding of the biological factors that underly compulsive drinking will allow for the development of new therapeutic targets for AUD. One animal model of compulsive alcohol drinking involves the addition of bitter-tasting quinine to an ethanol solution and measuring the willingness of the animal to consume ethanol despite the aversive taste. Previous studies have demonstrated that this type of aversion-resistant drinking is modulated in the insular cortex of male mice by specialized condensed extracellular matrix known as perineuronal nets (PNNs), which form a lattice-like structure around parvalbumin-expressing neurons in the cortex. Several laboratories have shown that female mice exhibit higher levels of aversion-resistant ethanol intake but the role of PNNs in females in this behavior has not been examined. Here we compared PNNs in the insula of male and female mice and determined if disrupting PNNs in female mice would alter aversion-resistant ethanol intake. PNNs were visualized in the insula by fluorescent labeling withWisteria floribundaagglutinin (WFA) and disrupted in the insula by microinjecting chondroitinase ABC, an enzyme that digests the chondroitin sulfate glycosaminoglycan component of PNNs. Mice were tested for aversion-resistant ethanol consumption by the addition of sequentially increasing concentrations of quinine to the ethanol in a two-bottle choice drinking in the dark procedure. PNN staining intensity was higher in the insula of female compared to male mice, suggesting that PNNs in females might contribute to elevated aversion-resistant drinking. However, disruption of PNNs had limited effect on aversion-resistant drinking in females. In addition, activation of the insula during aversion-resistant drinking, as measured by c-fos immunohistochemistry, was lower in female mice than in males. Taken together, these results suggest that neural mechanisms underlying aversion-resistant ethanol consumption differ in males and females.
Anteromedial Thalamus Gates the Selection & Stabilization of Long-Term Memories
Authors: Toader Andrew C. , Regalado Josue M. , Li Yan Ran , Terceros Andrea , Yadav Nakul , Kumar Suraj , Satow Sloane , Hollunder Florian , Bonito-Oliva Alessandra , Rajasethupathy Priya 
Published: January 2023

SUMMARYMemories initially formed in hippocampus gradually stabilize to cortex, over weeks-to-months, for long-term storage. The mechanistic details of this brain re-organization process remain poorly understood. In this study, we developed a virtual-reality based behavioral task and observed neural activity patterns associated with memory reorganization and stabilization over weeks-long timescales. Initial photometry recordings in circuits that link hippocampus and cortex revealed a unique and prominent neural correlate of memory in anterior thalamus that emerged in training and persisted for several weeks. Inhibition of the anteromedial thalamus-to-anterior cingulate cortex projections during training resulted in substantial memory consolidation deficits, and gain amplification more strikingly, was sufficient to enhance consolidation of otherwise unconsolidated memories. To provide mechanistic insights, we developed a new behavioral task where mice form two memories, of which only the more salient memory is consolidated, and also a technology for simultaneous and longitudinal cellular resolution imaging of hippocampus, thalamus, and cortex throughout the consolidation window. We found that whereas hippocampus equally encodes multiple memories, the anteromedial thalamus forms preferential tuning to salient memories, and establishes inter-regional correlations with cortex, that are critical for synchronizing and stabilizing cortical representations at remote time. Indeed, inhibition of this thalamo-cortical circuit while imaging in cortex reveals loss of contextual tuning and ensemble synchrony in anterior cingulate, together with behavioral deficits in remote memory retrieval. We thus identify a thalamo-cortical circuit that gates memory consolidation and propose a mechanism suitable for the selection and stabilization of hippocampal memories into longer term cortical storage.
The RPA complex orchestrates K63-linked deubiquitination via ZUP1
Authors: Foster Benjamin , Attwood Martin , Chong Kay , Drake Matthew , Gilroy Ryan , Fournier Marjorie , Gibbs-Seymour Ian 
Published: January 2023

AbstractUbiquitin signaling is regulated by deubiquitinating enzymes (DUBs), which can edit or remove ubiquitin from substrates. Recently, ZUP1 was discovered as the founding and only member of a novel DUB class that cleaves long K63-linked ubiquitin chains, with a putative role in DNA repair. However, ZUP1 has poor activity on its own, suggesting additional mechanisms exist to promote its activity in cells. Here, using a range of cellular, biochemical, and structural proteomics approaches, we show that ZUP1 directly interacts with the RPA complex, a single-stranded DNA binding protein complex involved in DNA replication and multiple DNA repair processes. Functionally, the ZUP1-RPA complex interaction dramatically stimulates ZUP1 K63-linked DUB activity, which occurs through S1 and S1’ site communication. Collectively, our results suggest a mechanism that couples sensing of ssDNA to the activation of K63-linked deubiquitination via the ZUP1-RPA complex.
A Fully Defined Synthetic Medium Mimicking Sugar Cane Molasses
Authors: Eliodório Kevy Pontes , de Gois e Cunha Gabriel Caetano , de Oliveira Lino Felipe Senne , Sommer Morten Otto Alexander , Gombert Andreas Karoly , Giudici Reinaldo , Basso Thiago Olitta 
Published: January 2023

ABSTRACTBackgroundYeast research in the context of food/beverage production and industrial biotechnology faces a dilemma: to use real industrial media or to use fully defined laboratory media? While the former option might lead to experiments closer to industrial conditions, the latter has the advantage of allowing for reproducibility and comparability of results among different laboratories, as well as being suitable for the investigation of how different individual components affect microbial or process performance. It is undoubtable that the development of a synthetic must a few decades ago led to important advances in wine yeast research.ResultsWe developed a fully defined medium that mimics sugarcane molasses, a frequently used medium in different industrial processes where yeast is cultivated. The medium, named 2SMol, builds upon a previously published semi-defined formulation and is conveniently prepared from some stock solutions: C-source, organic N, inorganic N, organic acids, trace elements, vitamins, Mg+K, and Ca. We validated the 2SMol recipe in a scaled-down sugarcane biorefinery model, comparing the performance of different yeast strains in different real molasses-based media. We also showcase the flexibility of the medium by investigating the effect of nitrogen availability on the ethanol yield during fermentation.ConclusionsHere we present in detail the development of a fully defined synthetic molasses medium, and we hope the 2SMol formulation will be valuable to researchers both in academia and industry to obtain new insights and developments in industrial yeast biotechnology.
Measuring and Modeling Macrophage Growth using a Lab-on-CMOS Capacitance Sensing Microsystem
Authors: Smith Kyle , Lin Ching-Yi , Gilpin Yann , Wayne Elizabeth , Dandin Marc 
Published: January 2023

AbstractWe report on the use of a lab-on-CMOS biosensor platform for quantitatively tracking the growth of RAW 264.7 murine Balb/c macrophages. We show that macrophage growth over a wide sensing area correlates linearly with an average capacitance growth factor resulting from capacitance measurements at a plurality of electrodes dispersed in the sensing area. We further show a temporal model that captures the cell evolution in the area of interest over long periods (e.g., 30 hours). The model links the cell numbers and the average capacitance growth factor associated with the sensing area to describe the observed growth kinetics.
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations
Authors: Stadlbauer Petr , Mlýnský Vojtěch , Krepl Miroslav , Šponer Jiří 
Published: January 2023

ABSTRACTGuanine quadruplexes (GQs) are non-canonical nucleic acid structures involved in many biological processes. GQs formed in single-stranded regions often need to be unwound by cellular machinery, so their mechanochemical properties are important. Here, we performed steered molecular dynamics simulations of human telomeric GQs to study their unfolding. We examined four pulling regimes, including very slow setup with pulling velocity and force load accessible to high-speed atomic force microscopy. We identified multiple factors affecting the unfolding mechanism. The more the direction of force was perpendicular to the GQ channel axis (determined by GQ topology), the more the base unzipping mechanism happened. If the GQ had either all-antior all-synpattern in a strand, strand slippage mechanism was more likely to occur. Importantly, slower pulling velocity led to richer unfolding pathways including partial refolding attempts. We show that GQ may eventually unfold after force drop under forces smaller than those the GQ withstood before the drop. This suggests that proteinsin vivomight resolve GQs even if their stall forces are smaller than GQ rupture force. Finally, we found out that different unfolding intermediates may have very similar chain end-to-end distance, which reveals some limitations of structural interpretations of single-molecule spectroscopic data.
Structural characterization of HIV-1 Env heterotrimers bound to one or two CD4 receptors reveals intermediate Env conformations
Authors: Dam Kim-Marie A. , Fan Chengcheng , Yang Zhi , Bjorkman Pamela J. 
Published: January 2023

SummaryHIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120/gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated gp120s and coreceptor binding sites on gp120 V3 hidden by V1V2 loops, and in fully-saturated CD4-bound open Env conformations with changes including outwardly rotated gp120s and displaced V1V2 loops. To investigate changes resulting from sub-stoichiometric CD4 binding, we solved 3.4Å and 3.9Å single-particle cryo-EM structures of soluble, native-like Envs bound to one or two CD4 molecules. Env trimer bound to one CD4 adopted the closed, prefusion Env state. When bound to two CD4s, the CD4-bound gp120s exhibited an open Env conformation including a four-stranded gp120 bridging sheet and displaced gp120 V1V2 loops that expose the coreceptor sites on V3. The third gp120 adopted an intermediate, occluded-open state that included gp120 outward rotation but maintained the prefusion, three-stranded gp120 bridging sheet and showed only partial V1V2 displacement and V3 exposure. We conclude that engagement of one CD4 molecule was insufficient to stimulate CD4-induced conformational changes, while binding two CD4 molecules led to Env opening in CD4-bound protomers only. Together, these results illuminate HIV-1 Env intermediate conformations and illustrate the structural plasticity of HIV-1 Env.