bluuebunny/crossref_metadata_2025_split huggingface dataset:
LXR-inducible host E3 ligase IDOL targets a human cytomegalovirus reactivation determinant
Authors: Mlera Luwanika , Collins-McMillen Donna , Zeltzer Sebastian , Buehler Jason C. , Moy Melissa , Zarrella Kristen , Caviness Katie , Cicchini Louis , Tafoya David J. , Goodrum Felicia 
Published: November 2022

SummaryLiver X receptor (LXR) signaling broadly restricts virus replication; however, the mechanisms of restriction are poorly defined. Here, we demonstrate that the LXR-inducible cellular E3 ligase IDOL (inducible degrader of low-density lipoprotein receptor, LDLR) targets the human cytomegalovirus (HMCV) UL136p33 protein for turnover.UL136encodes multiple proteins that differentially impact latency and reactivation. UL136p33 is a determinant of reactivation. UL136p33 is targeted for rapid turnover by the proteasome and its stabilization by mutation of lysine residues to arginine results in a failure to quiet replication for latency. We show that IDOL targets UL136p33 for turnover, but not the stabilized variant. IDOL is highly expressed in undifferentiated hematopoietic cells where HCMV establishes latency, but is sharply downregulated upon differentiation, a stimulus for reactivation. We hypothesize that IDOL maintains low levels of UL136p33 for the establishment of latency. Consistent with this, knockdown of IDOL impacts viral gene expression in WT HCMV infection, but not in infection where UL136p33 has been stabilized. Further, induction of LXR signaling restricts WT HCMV reactivation from latency, but does not affect replication of a recombinant virus expressing a stabilized variant of UL136p33. This work establishes the UL136p33-IDOL interaction as a key regulator of the bistable switch between latency and reactivation. It further suggests a model whereby a key viral determinant of HCMV reactivation is regulated by a host E3 ligase and acts as a sensor at the tipping point between the decision to maintain the latent state or exit latency for reactivation.ImportanceHerpesviruses establish life-long latent infections, which pose an important risk for disease particularly in the immunocompromised. Our work is focused on the beta-herpesvirus, human cytomegalovirus (HCMV) that latently infects the majority of the population worldwide. Defining the mechanisms by which HCMV establishes latency or reactivates from latency is important to controlling viral disease. Here, we demonstrate that the cellular inducible degrader of low-density lipoprotein receptor, IDOL, targets a HCMV determinant of reactivation for degradation. The instability of this determinant is important for the establishment of latency. This work defines a pivotal virus-host interaction that allows HCMV to sense changes in host biology to navigate decisions to establish latency or replicate.
The CWI pathway is activated through high hydrostatic pressure, enhancing glycerol efflux via the aquaglyceroporin Fps1 inSaccharomyces cerevisiae
Authors: Mochizuki Takahiro , Tanigawa Toshiki , Shindo Seiya , Suematsu Momoka , Oguchi Yuki , Mioka Tetsuo , Kato Yusuke , Fujiyama Mina , Hatano Eri , Yamaguchi Masashi , Chibana Hiroji , Abe Fumiyoshi 
Published: November 2022

AbstractThe fungal cell wall is the initial barrier for the fungi against diverse external stresses, such as osmolarity changes, harmful drugs, and mechanical injuries. This study explores the roles of osmoregulation and the cell wall integrity (CWI) pathway in response to high hydrostatic pressure in the yeastSaccharomyces cerevisiae. We demonstrate the roles of the transmembrane mechanosensor Wsc1 and aquaglyceroporin Fps1 in a general mechanism to maintain cell growth under high-pressure regimes. The promotion of water influx into cells at 25 MPa, as evident by an increase in cell volume and a loss of the plasma membrane eisosome structure, promotes the activation of Wsc1, an activator of the CWI pathway. The downstream mitogen-activated protein kinase Slt2 was hyperphosphorylated at 25 MPa. Glycerol efflux increases via Fps1 phosphorylation, which is initiated by downstream components of the CWI pathway and contributes to the reduction in intracellular osmolarity under high pressure. The elucidation of the mechanisms underlying adaption to high pressure through the well-established CWI pathway could potentially translate to mammalian cells and provide novel insights into cellular mechanosensation.
Feeling lucky? Prospective and retrospective cues for sensorimotor confidence
Authors: Fassold Marissa E. , Locke Shannon M. , Landy Michael S. 
Published: November 2022

AbstractOn a daily basis, humans interact with the outside world using judgments of sensorimotor confidence, constantly evaluating our actions for success. We ask, what sensory and motorexecution cues are used in making these judgements and when are they available? Two sources of temporally distinct information are prospective cues, available prior to the action (e.g., knowledge of motor noise and past performance), and retrospective cues specific to the action itself (e.g., proprioceptive measurements). We investigated the use of these two cues in two tasks, a secondary motor-awareness task and a main task in which participants reached toward a visual target with an unseen hand and then made a continuous judgment of confidence about the success of the reach. Confidence was reported by setting the size of a circle centered on the reach-target location, where a larger circle reflects lower confidence. Points were awarded if the confidence circle enclosed the true endpoint, with fewer points returned for larger circles. This incentivized accurate reaches and attentive reporting to maximize the score. We compared three Bayesian-inference models of sensorimotor confidence based on either prospective cues, retrospective cues, or both sources of information to maximize expected gain (i.e., an ideal-performance model). Our findings showed two distinct strategies: participants either performed as ideal observers, using both prospective and retrospective cues to make the confidence judgment, or relied solely on prospective information, ignoring retrospective cues. Thus, participants can make use of retrospective cues, evidenced by the behavior observed in our motorawareness task, but these cues are not always included in the computation of sensorimotor confidence.Author SummarySensorimotor confidence is a secondary judgment about how successful we feel a motor action was with relation to the goal. To make this judgment we can draw on information available before we execute an action such as our past experiences and knowledge of the environment, as well as after the action including visual feedback and proprioception, a sense of where our body is in space. In this study, we inquired as to how the information available before and after an action is weighted when considering the final feeling of sensorimotor confidence. To do so we asked participants to make reaches to visually cued targets in an unseen hand task, then report their confidence in how successful they were at hitting the target. We measured each participant’s reach accuracy and proprioceptive sensitivity in a separate task. Using mathematical models to fit our data we tested if a given participant depended more heavily on prior information or retrospective information when making their confidence judgment. We found that participants with high proprioceptive uncertainty were more likely to focus on prior knowledge while those with a more exact sense of proprioception incorporated information from both time points.
Gene Expression Detection in Developing Mouse Tissue Using In Situ Hybridization and µCT Imaging
Authors: Väänänen Vilma , Christensen Mona M. , Suhonen Heikki , Jernvall Jukka 
Published: November 2022

AbstractHigh resolution and noninvasiveness have made soft tissue X-ray microtomography (µCT) a widely applicable three-dimensional (3D) imaging method in studies of morphology and development. However, scarcity of molecular probes to visualize gene activity with µCT has remained a challenge. Here we apply horseradish peroxidase -assisted reduction of silver and catalytic gold enhancement of the silver deposit toin situhybridization in order to detect gene expression in developing tissues with µCT (here called GECT, Gene Expression CT). We show that GECT detects expression patterns ofcollagen type II alpha 1 (Col2a1) andsonic hedgehog (Shh) in developing mouse tissues comparably with an alkaline phosphatase-based detection method. After detection, expression patterns are visualized with laboratory µCT, demonstrating that GECT is compatible with varying levels of gene expression and varying sizes of expression regions. Additionally, we show that the method is compatible with prior phosphotungstic acid (PTA) staining, a conventional contrast staining approach in µCT imaging of soft tissues. Overall, GECT is a method that can be integrated with existing laboratory routines to obtain spatially accurate 3D detection of gene expression.
Evidence for a putative isoprene reductase inAcetobacterium wieringae
Authors: Kronen Miriam , Vázquez-Campos Xabier , Wilkins Marc R. , Lee Matthew , Manefield Michael J 
Published: November 2022

AbstractRecent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome assembled genome (MAG) of the most abundant (89% rel. abundance) lineage in the enrichment,Acetobacterium wieringae, was obtained. Comparative proteogenomics and RT-PCR identified a putative five-gene operon from theA. wieringaeMAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 x HypA-like, HypB-like) and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, FAD and two pairs of [4Fe-4S]-clusters. Other knownAcetobacteriumstrains do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase (∼47–49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across theFirmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, BacteroidetesandProteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons.ImportanceIsoprene was recently shown to act as an electron acceptor for a homoacetogenic bacterium. The focus of this study is the molecular basis for isoprene reduction. By comparing a genome from our isoprene reducing enrichment culture, dominated byAcetobacterium wieringae, with genomes of otherAcetobacteriumlineages that do not reduce isoprene, we shortlisted candidate genes for isoprene reduction. Using comparative proteogenomics and reverse transcription PCR we have identified a putative five-gene operon encoding an oxidoreductase referred to as putative isoprene reductase.
Emergence of division of labor in tissues through cell interactions and spatial cues
Authors: Adler Miri , Moriel Noa , Goeva Aleksandrina , Avraham-Davidi Inbal , Mages Simon , Adams Taylor S , Kaminski Naftali , Macosko Evan Z , Regev Aviv , Medzhitov Ruslan , Nitzan Mor 
Published: November 2022

AbstractMost cell types in multicellular organisms can perform multiple functions. However, not all functions can be optimally performed simultaneously by the same cells. Functions incompatible at the level of individual cells can be performed at the cell population level, where cells divide labor and specialize in different functions. Division of labor can arise due to instruction by tissue environment or through self-organization. Here, we develop a computational framework to investigate the contribution of these mechanisms to division of labor within a cell-type population. By optimizing collective cellular task performance under trade-offs, we find that distinguishable expression patterns can emerge from cell-cell interactionsvs. instructive signals. We propose a method to construct ligand-receptor networks between specialist cells and use it to infer division-of-labor mechanisms from single-cell RNA-seq and spatial transcriptomics data of stromal, epithelial, and immune cells. Our framework can be used to characterize the complexity of cell interactions within tissues.
Insights into the structure-function relationship of the NorQ/NorD chaperones fromParacoccus denitrificansreveal shared principles of interacting MoxR AAA+/VWA domain proteins
Authors: Kahle Maximilian , Appelgren Sofia , Elofsson Arne , Carroni Marta , Ädelroth Pia 
Published: November 2022

AbstractNorQ, a member of the MoxR-class of AAA+ ATPases, and NorD, a protein containing a Von Willebrand Factor Type A (VWA) domain, are essential for non-heme iron (FeB) cofactor insertion into cytochromec-dependent nitric oxide reductase (cNOR).cNOR catalyzes the NO reduction, a key step of bacterial denitrification. This work aimed at elucidating the specific mechanism of NorQD-catalyzed FeBinsertion, and the general mechanism of the MoxR/VWA interacting protein families. We show that NorQ-catalyzed ATP hydrolysis, an intact VWA-domain in NorD and specific surface carboxylates oncNOR are all features required forcNOR activation. Supported by BN-PAGE, low-resolution cryo-EM structures of NorQ and the NorQD complex show that NorQ forms a circular hexamer with a monomer of NorD binding both to the side and to the central pore of the NorQ ring. Guided by AlphaFold predictions, we assign the density that ‘plugs’ the NorQ ring pore to the VWA domain of NorD with a protruding ‘finger’ inserting through the pore, and suggest this binding mode to be general for MoxR/VWA couples. We present a tentative model for the mechanism of NorQD-catalyzedcNOR remodelling and suggest many of its features to be applicable to the whole MoxR/VWA family.
Release site plasticity via Unc13A regulatory domains mediates synaptic short-term facilitation and homeostatic potentiation
Authors: Jusyte Meida , Blaum Natalie , Böhme Mathias A. , Berns Manon M. M. , Bonard Alix E. , Kobbersmed Janus R. L. , Walter Alexander M. 
Published: November 2022

AbstractChemical synaptic transmission relies on neurotransmitter release from presynaptic release sites and on transmitter-sensing by the postsynaptic cell. Presynaptic plasticity increasing neurotransmitter release achieves two fundamental nervous system functions: It tunes some synapses to be more responsive to millisecond repetitive activation and it maintains signals when postsynaptic transmitter sensitivity is reduced. How enhanced neurotransmitter release is achieved in these phenomena, termed short-term facilitation and homeostatic potentiation, remains unknown. We combine mathematical modeling and experimental analysis ofDrosophilaneuromuscular junction model synapses to elucidate the molecular mechanisms underlying these forms of plasticity. Our results indicate that both phenomena depend on a rapid increase in the participation of neurotransmitter release sites which is controlled by the regulatory domains of the evolutionarily conserved (M)Unc13A protein that bind Ca2+/Calmodulin and diacylglycerol. Mutation of the Calmodulin binding (CaM) domain increased baseline transmission and impaired both short-term facilitation and acute homeostatic potentiation. Mathematical modeling indicated that these defects result from too many release sites participating at rest combined with the inability to plastically further increase their number. Super-resolution microscopy revealed that this coincided with a redistribution of Unc13A’s functionally essential MUN domain closer to the synaptic plasma membrane, which may constitute the molecular switch to increase release site participation. Similar consequences (enhanced baseline transmission, block of both short-term facilitation and homeostatic potentiation) were caused by the acute pharmacological activation of the C1 domain of wildtype Unc13A using phorbol esters. This treatment had no effect on Unc13A CaM domain mutants, indicating that both the CaM and C1 domains activate a binary release site switch. Thus, our findings indicate that Unc13A regulatory domains are tuned to integrate a multitude of signals on various timescales to switch release site participation for synaptic plasticity.
Inferring the distributions of fitness effects and proportions of strongly deleterious mutations
Authors: Charmouh Anders P. , Bocedi Greta , Hartfield Matthew 
Published: November 2022

AbstractThe distribution of fitness effects is a key property in evolutionary genetics as it has implications for several evolutionary phenomena including the evolution of sex and mating systems, the rate of adaptive evolution, and the prevalence of deleterious mutations. Despite the distribution of fitness effects being extensively studied, the effects of strongly deleterious mutations are difficult to infer since such mutations are unlikely to be present in samples of haplotypes, so genetic data may contain very little information about them. Recent work has attempted to correct for this issue by expanding the classic gamma-distributed model to explicitly account for strongly deleterious mutations. Here, we use simulations to investigate one such method, adding a parameter (plth) to capture the proportion of strongly deleterious mutations. We show thatplthcan improve the model fit when applied to individual species but can underestimate the true proportion of strongly deleterious mutations. The parameter can also artificially maximize the likelihood when used to jointly infer a distribution of fitness effects from multiple species. Asplthand related parameters are used in current inference algorithms, our results are relevant with respect to avoiding model artifacts and improving future tools for inferring the distribution of fitness effects.
Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells
Authors: Dunjić Marko , Jonas Felix , Yaakov Gilad , More Roye , Mayshar Yoav , Rais Yoach , Barkai Naama , Stelzer Yonatan 
Published: November 2022

AbstractEviction of histones from nucleosomes and their exchange with newly synthesized or alternative variants is a central epigenetic determinant. Here, we define the genome-wide incorporation and exchange pattern of canonical and non-canonical histone variants in mouse embryonic stem cells by implementing a recently established, genetically encoded exchange sensor. While exchange of all measured variants scales with transcription, we describe variant-specific associations with transcription elongation and Polycomb binding. We found considerable exchange of H3.1 and H2B variants in heterochromatin and repeat elements, contrasting the stable incorporation and little exchange of H3.3 in these regions. This unexpected association between H3.3 incorporation and exchange of canonical variants is also evident in active promoters and enhancers, and further validated by reduced H3.1 dynamics following depletion of the HIRA H3.3-specific chaperone. The sensor system provides a powerful tool for studying regulation of histone dynamics toward understanding its role in shaping the epigenetic landscapein vivo.
Embryonic signals mediate extracellular vesicle biogenesis and trafficking at the embryo–maternal interface
Authors: Guzewska Maria M. , Myszczynski Kamil , Heifetz Yael , Kaczmarek Monika M. 
Published: November 2022

ABSTRACTExtracellular vesicles (EVs) are membrane-coated nanoparticles secreted by almost all cell types in living organisms. EVs, as paracrine mediators, are involved in intercellular communication, immune response, and several reproductive events, including the maintenance of pregnancy. Using a domestic animal model (Sus scrofa) with an epitheliochorial, superficial type of placentation, we focused on EV biogenesis pathway at the embryo–maternal interface, when the embryonic signaling occurs for maternal recognition and the maintenance of pregnancy. Transmission electron microscopy was used during early pregnancy to visualize different populations of EVs and apocrine and/or merocrine pathways of secretion. Immunofluorescent staining localized proteins responsible for EV biogenesis and cell polarization at the embryo–maternal interface. The expression profiles of genes involved in biogenesis and the secretion of EVs pointed at the possible modulation of endometrial expression by embryonic signals. Further in vitro studies showed that factors of embryonic origin can regulate the expression of the ESCRT-II complex and EV trafficking in luminal epithelial cells. Moreover, miRNA-mediated rapid negative regulation of gene expression was abolished by delivered embryonic signals. Our findings demonstrated that embryonic signals are potent modulators of EV-mediated secretory activity of the endometrium during the critical stages of early pregnancy.
Real-time library search increases cross-link identification depth across all levels of sample complexity
Authors: Ruwolt Max , He Yi , Lima Diogo Borges , Barshop William , Broichhagen Johannes , Huguet Romain , Viner Rosa , Liu Fan 
Published: November 2022

AbstractCross-linking mass spectrometry (XL-MS) is a universal tool for probing structural dynamics and protein-protein interactionsin vitroandin vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental advances improved cross-link identification by enriching the cross-linker modified peptides chemically with the use of enrichable cross-linkers. However, mono-links (i.e., peptides modified with a hydrolyzed cross-linker) still hinder efficient cross-link identification since a large proportion of measurement time is spent on their MS2 acquisition. Currently, cross-links and mono-links cannot be separated by sample preparation techniques or chromatography because they are chemically almost identical. Here, we found that based on the intensity ratios of four diagnostic peaks when using PhoX/tBu-PhoX cross-linkers, cross-links and mono-links can be partially distinguished. Harnessing their characteristic intensity ratios for real-time library search (RTLS)-based triggering of high-resolution MS2 scans increased the number of cross-link identifications from both single protein samples and intactE. colicells. Specifically, RTLS improves cross-link identification from unenriched samples and short gradients, emphasizing its advantages in high-throughput approaches and when instrument time or sample amount is limited.