bluuebunny/crossref_metadata_2025_split huggingface dataset:
A kinetic basis for curvature sensing by septins
Authors: Shi Wenzheng , Cannon Kevin S. , Curtis Brandy N. , Edelmaier Christopher , Gladfelter Amy S. , Nazockdast Ehssan 
Published: May 2022

The ability of cells to sense and communicate their shape is central to many of their functions. Much is known about how cells generate complex shapes, yet how they sense and respond to geometric cues remains poorly understood. Septins are GTP-binding proteins that localize to sites of micron-scale membrane curvature. Assembly of septins is a multi-step and multi-scale process but it is unknown how these discrete steps lead to curvature sensing. Here we experimentally examine the time-dependent binding of septins at different curvatures and septin bulk concentrations. These experiments unexpectedly indicated that the curvature preference of septins is not absolute but rather is sensitive to the combinations of membrane curvatures present in a reaction, suggesting there is competition between different curvatures for septin binding. To understand the basis of this result, we developed a kinetic model that connects septins’ self-assembly and curvature sensing properties. Our experimental and modeling results are consistent with curvature-sensitive assembly being driven by cooperative associations of septin oligomers in solution with the bound septins. When combined, the work indicates septin curvature sensing is kinetically determined, sensitive to bulk concentration, and the available membrane curvatures. While much geometry-sensitive assembly in biology is thought to be guided by intrinsic material properties of molecules, this is an important example of how kinetics can drive mesoscale curvature-sensitive assembly of polymers.Significance StatementCells use their membrane curvature to coordinate the activation and spatiotemporal compartmentalization of molecules during key cellular processes. Recent works have identified different proteins that can sense or induce membrane curvature from nano- to micron-scale. Septins are nanoscopic cytoskeletal proteins that preferentially bind to membranes with a narrow range of micron-scale curvatures. Yet the sensing mechanism remains ambiguous. Using a combination of microscopy and kinetic modeling, we show that, unlike most proteins that sense curvature in a single protein scale, curvature sensing in septins is determined kinetically through their multi-step hierarchical assembly on the membrane. This introduces a novel kinetic basis of fidelity, where the same protein can be deployed for differential binding sensitivities in different cellular contexts.
Cachd1 is a novel Frizzled- and LRP6-interacting protein required for neurons to acquire left-right asymmetric character
Authors: Powell Gareth T. , Faro Ana , Zhao Yuguang , Stickney Heather , Novellasdemunt Laura , Henriques Pedro , Gestri Gaia , White Esther Redhouse , Ren Jingshan , Lu Weixian , Young Rodrigo M. , Hawkins Thomas A. , Cavodeassi Florencia , Schwarz Quenten , Dreosti Elena , Raible David W. , Li Vivian S. W. , Wright Gavin J. , Jones E. Yvonne , Wilson Stephen W. 
Published: May 2022

AbstractNeurons on left and right sides of the nervous system frequently show asymmetric properties but how these differences arise is poorly understood. Through a forward genetic screen in zebrafish, we find that loss of function of the transmembrane protein Cachd1 results in right-sided habenula neurons adopting left-sided character. Cachd1 is expressed in habenula neuron progenitors, functions symmetrically downstream of asymmetric environmental signals that determine laterality and influences timing of the normally left-right asymmetric patterns of neurogenesis. Unbiased screening for Cachd1 partners identified the Wnt co-receptor Frizzled7 and further biochemical and structural analysis revealed Cachd1 can bind simultaneously to Fzd proteins and Lrp6, bridging between these two Wnt co-receptors. Consistent with these structural studies, lrp6 mutant zebrafish show symmetric habenulae with left-sided character and epistasis experiments with other Wnt pathway genes support an in vivo role for Cachd1 in modulating Wnt pathway activity in the brain. Together, these studies identify Cachd1 as a conserved novel Wnt-receptor interacting protein with roles in regulating neurogenesis and neuronal identity.
Quantitative analysis of three-dimensional cell organisation and concentration profiles within curved epithelial tissues
Authors: Prabhakara Chaitra , Iyer Krishnan Swaminathan , Rao Madan , Saunders Timothy E , Mayor Satyajit 
Published: May 2022

AbstractOrganogenesis involves folding of flat epithelial tissues into three-dimensional (3D) shapes. Quantitative analysis in 3D of the concentration gradients of biochemical and mechano-chemical cues that shape the tissue has remained a challenge, due to the complex tissue geometries. Towards addressing this, we present a methodology that transforms the cartesian images acquired by high-resolution confocal microscopy of curved tissues into a laminar organisation from the outer-most tissue surface. We further detail a data-based intensity correction method to account for the intensity variations that arise as a consequence of the global geometry. Applying our approach to the dome-shaped Drosophila wing disc, we quantitatively estimate the concentration profiles of different biochemical signals, including the Wingless morphogen gradient. The laminar data-organisation method also enabled visualisation of apical and basal layers facilitating an accurate 3D reconstruction of cell shapes within the pseudostratified epithelium. We find that the columnar disc proper cells have irregular 3D shapes and undergo frequent apico-basal cell intercalations, concomitantly leading to cell neighbour exchanges along the apico-basal axis. The workflow of image processing described here may be employed to quantify 3D concentration gradients and 3D cellular organisation in any layered curved tissue, provided a marker describing the reference surface manifold is available.
A curated human cellular microRNAome based on 196 primary cell types
Authors: Patil Arun H. , Baran Andrea , Brehm Zachary P. , McCall Matthew N. , Halushka Marc K. 
Published: May 2022

AbstractBackgroundAn incomplete picture of the expression distribution of microRNAs (miRNAs) across human cell types has long hindered our understanding of this important regulatory class of RNA. With the continued increase in available public small RNA sequencing datasets, there is an opportunity to more fully understand the general distribution of miRNAs at the cell level.ResultsFrom the NCBI Sequence Read Archive, we obtained 6,054 human primary cell datasets and processed 4,184 of them through the miRge3.0 small RNA-seq alignment software. This dataset was curated down, through shared miRNA expression patterns, to 2,077 samples from 196 unique cell types derived from 175 separate studies. Of 2,731 putative miRNAs listed in miRBase (v22.1), 2,452 (89.8%) were detected. Among reasonably expressed miRNAs, 108 were designated as cell specific/near specific, 59 as infrequent, 52 as frequent, 54 as near ubiquitous and 50 as ubiquitous. The complexity of cellular microRNA expression estimates recapitulates tissue expression patterns and informs on the miRNA composition of plasma.ConclusionsThis study represents the most complete reference, to date, of miRNA expression patterns by primary cell type. The data is available through the human cellular microRNAome track at the UCSC Genome Browser (https://genome.ucsc.edu/cgi-bin/hgHubConnect) and an R/Bioconductor package (https://bioconductor.org/packages/microRNAome/).
Membrane stretching activates calcium-permeability of a putative channel Pkd2 during fission yeast cytokinesis
Authors: Poddar Abhishek , Hsu Yen-Yu , Zhang Faith , Shamma Abeda , Kreais Zachary , Muller Clare , Malla Mamata , Ray Aniruddha , Liu Allen , Chen Qian 
Published: May 2022

AbstractPkd2 is the fission yeast homolog of polycystins. This putative ion channel localizes to the plasma membrane. It is required for the expansion of cell volume during interphase growth and cytokinesis, the last step of cell division. However, the channel activity of Pkd2 remains untested. Here, we examined the calcium permeability and mechanosensitivity of Pkd2 through in vitro reconstitution and calcium imaging of the pkd2 mutant cells. Pkd2 was translated and inserted into the lipid bilayer of giant unilamellar vesicles using a cell-free expression system. The reconstituted Pkd2 permeated calcium when the membrane was stretched via hypo-osmotic shock. In vivo, inactivation of Pkd2 through a temperature-sensitive mutation pkd2-B42 reduced the average intracellular calcium level by 34%. Compared to the wild type, the hypomorphic mutation pkd2-81KD reduced the amplitude of hypo-osmotic shock-triggered calcium spikes by 59%. During cytokinesis, mutations of pkd2 reduced by 60% the calcium spikes that accompany the cell separation and the ensuing membrane stretching. We concluded that fission yeast polycystin Pkd2 allows calcium influx when activated by membrane stretching, representing a likely mechanosensitive channel that contributes to the cytokinetic calcium spikes.
Toxic effects of elevated bile acid levels on fetal myocardium in intrahepatic cholestasis of pregnancy, a retrospective study from a neonatal perspective
Authors: Wang Junnai , Shi Wei , Lun Weiwei 
Published: May 2022

AbstractIntroductionIntrahepatic cholestasis of pregnancy (ICP) is a liver disease which may lead to a sudden fetal death. Previous studies have suggested that the fetal accident may be related to their cardiac dysfunction. However, the relationship between fetal cardiac dysfunction and their maternal bile acid levels is not clear. The objective was to clarify the relationship from a neonatal perspective and to furtherly make clear the after-effect by analysing the cardiac parameters of the older neonates.Materials and methodsIn this case-control study, patients and their neonates, managed between 10 September 2018 and 30 June 2021 at a Chinese university hospital center, were divided into severe ICP group, mild ICP group and control gestational group. The maternal bile acid levels and the cardiac paramerers of one-day-old neonates and five-day-old neonates were analysed, respectively.ResultsThe specific-myocardial enzyme(CK-MB) and left ventricular fraction shortening(FS) of neonates showed significant differences between ICP group and control group, and were meaningfully correlated with maternal bile acid levels. However, There was no significant difference in cardiac injury parameters of older neonates between the ICP and control groups.ConclusionsThe elevated maternal bile acid levels can lead to fetal myocardial injury and the injury can be recovered after removel from high concentrations of bile acid.
Identification of CD133+Intercellsomes in Intercellular Communication to Offset Intracellular Signal Deficit
Authors: Kaneko Kota , Liang Yan , Liu Qing , Zhang Shuo , Scheiter Alexander , Song Dan , Feng Gen-Sheng 
Published: May 2022

AbstractCD133 (prominin 1) is widely viewed as a cancer stem cell marker in association with drug resistance and cancer recurrence. Herein we report that with impaired RTK-Shp2 Ras-Erk signaling, heterogenous hepatocytes form clusters that manage to divide during liver regeneration. These hepatocytes are characterized by upregulated CD133 while negative for other progenitor cell markers. Pharmaceutical inhibition of proliferative signaling also induced CD133 expression in various cancer cell types, suggesting an inherent and common mechanism of stress response. Super-resolution and electron microscopy localize CD133 on intracellular vesicles that apparently migrate between cells, which we name “intercellsome”. Isolated CD133+intercellsomes are enriched with mRNAs rather than miRNAs. Single-cell RNA sequencing reveals lower intracellular diversity (entropy) of mitogenic mRNAs in Shp2-deficient cells, which may be remedied by intercellular mRNA exchanges between CD133+cells. CD133-deficient cells are more sensitive to proliferative signal inhibition in livers and intestinal organoids. These data suggest a mechanism of intercellular communication to compensate intracellular signal deficit in various cell types.
Characterization of protein isoform diversity in human umbilical vein endothelial cells (HUVECs) via long-read proteogenomics
Authors: Mehlferber Madison M. , Jordan Ben T. , Jeffery Erin D. , Sheynkman Leon , Saquing Jamie , Acharya Bipul R. , Hirschi Karen K. , Sheynkman Gloria M. 
Published: May 2022

AbstractEndothelial cells (ECs) comprise the lumenal lining of all blood vessels and are critical for the functioning of the cardiovascular system. Their phenotypes can be modulated by protein isoforms. To characterize the isoform landscape within ECs, we applied a long read proteogenomics approach to analyze human umbilical vein endothelial cells (HUVECs). Transcripts delineated from PacBio sequencing serve as the basis for a sample-specific protein database used for downstream MS analysis to infer protein isoform expression. We detected 53,836 transcript isoforms from 10,426 genes, with 22,195 of those transcripts being novel. Furthermore, the predominant isoform in HUVECs does not correspond with the accepted “reference isoform” 25% of the time, with vascular pathway-related genes among this group. We found 2,597 protein isoforms supported through unique peptides, with an additional 2,280 isoforms nominated upon incorporation of long-read transcript evidence. We characterized a novel alternative acceptor for endothelial-related geneCDH5, suggesting potential changes in its associated signaling pathways. Finally, we identified novel protein isoforms arising from a diversity of splicing mechanisms supported by uniquely mapped novel peptides. Our results represent a high resolution atlas of known and novel isoforms of potential relevance to endothelial phenotypes and function.Graphical Abstract
Domestication of different varieties in the cheese-making fungusGeotrichum candidum
Authors: Bennetot Bastien , Vernadet Jean-Philippe , Perkins Vincent , Hautefeuille Sophie , Rodríguez de la Vega Ricardo C. , O’Donnell Samuel , Snirc Alodie , Grondin Cécile , Lessard Marie-Hélène , Peron Anne-Claire , Labrie Steve , Landaud Sophie , Giraud Tatiana , Ropars Jeanne 
Published: May 2022

AbstractDomestication is an excellent model for studying adaptation processes, involving recent adaptation and diversification, convergence following adaptation to similar conditions, as well as degeneration of unused functions.Geotrichum candidumis a fungus used for cheese making and is also found in other environments such as soil and plants. By analyzing whole-genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. Within the cheese clade, we identified three genetically differentiated populations and we detected footprints of recombination and admixture. The genetic diversity in the cheese clade was similar as that in the wild clade, suggesting the lack of strong bottlenecks. Commercial starter strains were scattered across the cheese clade, thus not constituting a single clonal lineage. The cheese populations were phenotypically differentiated from other populations, with a slower growth on all media, even cheese, a prominent production of typical cheese volatiles and a lower proteolytic activity. One of the cheese clusters encompassed all soft goat cheese strains, suggesting an effect of cheese-making practices on differentiation. Another of the cheese populations seemed to represent a more advanced stage of domestication, with stronger phenotypic differentiation from the wild clade, harboring much lower genetic diversity, and phenotypes more typical of cheese fungi, with denser and fluffier colonies and a greater ability of excluding cheese spoiler fungi. Cheese populations lacked two beta lactamase-like genes present in the wild clade, involved in xenobiotic clearance, and displayed higher contents of transposable elements, likely due to relaxed selection. Our findings suggest the existence of genuine domestication inG. candidum, which led to diversification into different varieties with contrasted phenotypes. Some of the traits acquired by cheese strains indicate convergence with other, distantly related fungi used for cheese maturation.
YAP promotes cell-autonomous immune responses to tackle intracellularStaphylococcus aureus in vitro
Authors: Robin Caire , Estelle Audoux , Mireille Thomas , Elisa Dalix , Aurélien Peyron , Killian Rodriguez , Yann Dickerscheit , Hubert Marotte , François Vandenesch , Frédéric Laurent , Jérôme Josse , Verhoeven Paul. O 
Published: May 2022

ABSTRACTTranscriptional cofactors YAP/TAZ have recently been found to support autophagy and inflammation, which are part of cell autonomous immunity and are critical in antibacterial defense. Here, we studied the role of YAP againstStaphylococcus aureususing CRISPR/Cas9-mutated HEK293 cells and a primary cell-based organoid model. We found thatS. aureusinfection increases YAP transcriptional activity, which is required to reduce intracellularS. aureusreplication. A 770-gene targeted transcriptomic analysis revealed that YAP upregulates genes involved in autophagy/lysosome and inflammation pathways in both infected and uninfected conditions. The YAP/TEAD transcriptional activity promotes autophagic flux and lysosomal acidification, which are important for defense against intracellularS. aureus. Furthermore, the staphylococcal toxin C3 exoenzyme EDIN-B was found effective in preventing YAP-mediated cell-autonomous immune response. This study provides new insights on the anti-S. aureusactivity of YAP, which could be conserved for defense against other intracellular bacteria.GRAPHICAL ABSTRACT
Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting
Authors: Fulcher James M. , Markillie Lye Meng , Mitchell Hugh D. , Williams Sarah M. , Engbrecht Kristin M. , Degnan David J. , Bramer Lisa M. , Moore Ronald J. , Chrisler William B. , Cantlon-Bruce Joshua , Bagnoli Johannes W. , Qian Wei-Jun , Seth Anjali , Paša-Tolić Ljiljana , Zhu Ying 
Published: May 2022

AbstractSingle-cell multiomics provides comprehensive insights into gene regulatory networks, cellular diversity, and temporal dynamics. Here, we introduce nanoSPLITS (nanodroplet SPlitting for Linked-multimodal Investigations of Trace Samples), an integrated platform that enables global profiling of the transcriptome and proteome from same single cells using RNA sequencing and mass spectrometry-based proteomics, respectively. Benchmarking of nanoSPLITS demonstrated excellent measurement precision, with deep proteomic and transcriptomic profiling of single-cells. We applied nanoSPLITS to cyclin-dependent kinase 1 inhibited cells and found phospho-signaling events could be quantified alongside global protein and mRNA measurements, providing new insights into cell cycle regulation. We also extended nanoSPLITS to single-cells isolated from human pancreatic islets, introducing an efficient approach for facile identification of unknown cell types, and detecting their protein markers by mapping transcriptomic data to existing large-scale single-cell RNA sequencing reference databases. Herein, we establish nanoSPLITS as a new multiomic technology incorporating global proteomics and anticipate the approach will be critical to furthering our understanding of single-cell systems.
Enterococcus faecalisandStaphylococcus aureusmixed species infection attenuates pathogen-specific neutrophil responses and impairs bacterial clearance
Authors: Kao Patrick Hien-Neng , Ch’ng Jun-Hong , Chong Kelvin K.L. , Wong Siu Ling , Kline Kimberly A. 
Published: May 2022

AbstractEnterococcus faecalisis an opportunistic pathogen that is frequently co-isolated with other microbes in catheterized urinary tract infections and chronically infected wounds. WhileE. faecaliscan subvert the host immune response and promote the survival of other microbes via interbacterial synergy, little is known about the impact of immune suppression mediated byE. faecalisand howE. faecalisimpacts the survival of co-infecting microbes. We hypothesized thatE. faecaliscan attenuate neutrophil-mediated responses in mixed-species infection to promote survival of the co-infecting species. Here, we show thatE. faecalisandStaphylococcus aureusmono-species infection activates intracellular ROS production and NET formation, respectively, enabling effective neutrophil-mediated control of the microbial infection. Growth of both bacterial species was enhanced during co-infection in neutrophilsin vitroand in woundsin vivo. E. faecalisreducedS. aureus-induced NET formation andS. aureussuppressedE. faecalis-induced intracellular ROS production. When the species ratios were skewed, the neutrophil reaction profile resembled that elicited by the more abundant species, favoring enhanced survival of the less abundant species. These findings highlight the complexity of the immune response to polymicrobial infections and show that attenuated pathogen-specific immune responses contribute to microbial survival in the mammalian host.
MAGScoT - a fast, lightweight, and accurate bin-refinement software
Authors: Rühlemann Malte Christoph , Wacker Eike Matthias , Ellinghaus David , Franke Andre 
Published: May 2022

AbstractWe introduce MAGScoT, a fast, lightweight and accurate implementation for the reconstruction of highest-quality metagenome-assembled genomes (MAGs) from the output of multiple genome-binning softwares. MAGScoT outperforms popular bin-refinement solutions in terms of quality and quantity of MAGs as well as computation time and resource consumption. MAGScoT is available via GitHub (https://github.com/ikmb/MAGScoT) and as an easy-to-use Docker container (https://hub.docker.com/repository/docker/ikmb/magscot).
Faunal remains from the Upper Paleolithic site of Nahal Rahaf 2 in the southern Judean Desert, Israel
Authors: Marom Nimrod , Gnezdilov Dariya Lokshin , Shafir Roee , Barzilai Omry , Shemer Maayan 
Published: May 2022

AbstractNahal Rahaf 2 (NR2) is an Early Upper Paleolithic (ca. 35 kya) rock shelter in the southern Judean Desert in Israel. Two excavation seasons in 2019 and 2020 revealed a stratigraphical sequence composed of intact archaeological surfaces attributed to the ‘Arkov-Divshon’ cultural entity of the arid southern Levant. We present the faunal assemblages from the site, which are rare among the desert sites due to preservation problems. Our results suggest that the residents of the site exploited prime adult caprines (Capra cf. Capra ibex), but were also engaged in hunting of gazelles (Gazella cf. Gazella gazella), whose carcasses were selectively transported to the site and processed for within-bone nutrients. Long-range hunting trips are suggested by the body-part selection in relatively small bovids, and by the presence of species representing wetter habitat patches 20-30 km north of the site. The bi-focal emphasis on generalized gazelle and age-specific caprine hunting, is unique among Late Pleistocene sites from the Levant. The proportion of caprines increases through the stratigraphic sequence, suggesting more specialized economy through time and in inverse relations to site use intensity.