bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hippocampal place cells use vector computations to navigate
Authors: Ormond Jake , O’Keefe John 
Published: June 2021

SUMMARYOne function of the Hippocampal Cognitive Map is to provide information about salient locations in familiar environments such as those containing reward or danger, and to support navigation towards or away from those locations1. Although much is known about how the hippocampus encodes location in world-centred coordinates, how it supports flexible navigation is less well understood. We recorded from CA1 place cells while rats navigated to a goal or freely foraged on the honeycomb maze2. The maze tests the animal’s ability to navigate using indirect as well as direct paths to the goal and allows the directionality of place cells to be assessed at each choice point during traversal to the goal. Place fields showed strong directional polarization in the navigation task, and to a lesser extent during random foraging. This polarization was characterized by vector fields which converged to sinks distributed throughout the environment. The distribution of these convergence sinks was centred near the goal location, and the population vector field converged on the goal, providing a strong navigational signal. Changing the goal location led to the movement of ConSinks and vector fields towards the new goal and within-days, the ConSink distance to the goal decreased with continued training. The honeycomb maze allows the independent assessment of spatial representation and spatial action in place cell activity and shows how the latter depends on the former. The results suggest a vector-based model of how the hippocampus supports flexible navigation, allowing animals to select optimal paths to destinations from any location in the environment.
Modular, Cascade-like Transcriptional Program of Regeneration inStentor
Authors: Sood Pranidhi , Lin Athena , Yan Connie , McGillivary Rebecca , Diaz Ulises , Makushok Tatyana , Marshall Wallace F. 
Published: June 2021

AbstractThe giant ciliateStentor coeruleusis a classical model system for studying regeneration and morphogenesis at the level of a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. If a cell is cut in half, each half will regenerate an intact cell, including a new oral apparatus in the posterior half. We used RNAseq to assay the dynamic changes inStentor’s transcriptome during regeneration, after both oral apparatus shedding and bisection, allowing us to identify distinct temporal waves of gene expression including kinases, RNA binding proteins, centriole biogenesis factors, and orthologs of human ciliopathy genes implicated in Meckel and Joubert syndromes. By comparing transcriptional profiles of different regeneration events in the same species, we were able to identify distinct modules of gene expression corresponding to oral apparatus regeneration, posterior holdfast regeneration, and recovery after wounding. By measuring gene expression in cells in which translation is blocked, we show that the sequential waves of gene expression involve a cascade mechanism in which later waves of expression are triggered by translation products of early-expressed genes. Among the early-expressed genes, we identified an E2F transcription factor and the conserved RNA binding protein Pumilio as potential regulators of regeneration based on the expression pattern of their predicted target genes. RNAi mediated knockdown experiments indicate that Pumilio is required for regenerating oral structures of the correct size. We show that E2F is involved in the completion of regeneration but is dispensable for earlier steps. This work allows us to classify regeneration genes into groups based on their potential role for regeneration in distinct cell regeneration paradigms, and provides insight into how a single cell can coordinate complex morphogenetic pathways to regenerate missing structures.
E484K and N501Y SARS-CoV 2 Spike Mutants Increase ACE2 Recognition but Reduce Affinity for Neutralizing Antibody
Authors: Chakraborty Sandipan 
Published: June 2021

AbstractSARS-CoV2 mutants emerge as variants of concern (VOC) due to altered selection pressure and rapid replication kinetics. Among them, lineages B.1.1.7, B.1.351, and P.1 contain a key mutation N501Y. B.1.135 and P.1 lineages have another mutation, E484K. Here, we decode the effect of these two mutations on the host receptor, ACE2, and neutralizing antibody (B38) recognition. The gain in binding affinity for the N501Y RBD mutant to the ACE2 is attributed to improved π-π stacking and π-cation interactions. The enhanced receptor affinity of the E484K mutant is caused due to the formation of a specific hydrogen bond and salt-bridge interaction with Glu75 of ACE2. Notably, both the mutations reduce the binding affinity for B38 due to the loss of several hydrogen-bonding interactions. The insights obtained from the study are crucial to interpret the increased transmissibility and reduction in the neutralization efficacy of rapidly emerging SARS-CoV2 VOCs.
A Multi-omics Method Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem Cell-derived Cardiomyocytes
Authors: Bayne Elizabeth F. , Simmons Aaron D. , Roberts David S. , Zhu Yanlong , Aballo Timothy J. , Wancewicz Benjamin , Palecek Sean P. , Ge Ying 
Published: June 2021

AbstractHuman pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) show immense promise for patient-specific disease modeling, cardiotoxicity screening, and regenerative therapy development. However, hPSC-CMs in culture have not recapitulated the structural or functional properties of adult CMs in vivo thus far. To gain global insight into hPSC-CM biology, we established a multi-omics method for analyzing the hPSC-CM metabolome and proteome from the same cell culture, creating multi-dimensional profiles of hPSC-CMs. Specifically, we developed a sequential extraction to capture metabolites and proteins from the same hPSC-CM monolayer cultures, and analyzed these extracts using high-resolution mass spectrometry (MS). Using this method, we annotated 205 metabolites/lipids and 4,008 proteins from 106 cells with high reproducibility. We further integrated the proteome and metabolome measurements to create network profiles of molecular phenotypes for hPSC-CMs. Out of 310 pathways identified using metabolomics and proteomics, 40 pathways were considered significantly overrepresented (FDR-corrected p ≤ 0.05). Highly populated pathways included those involved in protein synthesis (ribosome, spliceosome), ATP generation (oxidative phosphorylation), and cardiac muscle contraction. This multi-omics method achieves deep coverage of metabolites and proteins, creating a multidimensional view of the hPSC-CM phenotype, which provides a strong technological foundation to advance the understanding of hPSC-CM biology.
Bioaffinity-based surface-immobilization of antibodies to capture endothelial colony-forming cells
Authors: Boulanger Mariève D. , Elkhodiry Mohamed A. , Bashth Omar S. , Laroche Gaétan , Hoesli Corinne A. 
Published: June 2021

AbstractMaximizing the re-endothelialization of vascular implants such as prostheses or stents has the potential to significantly improve their long-term performance. Endothelial progenitor cell capture stents with surface-immobilized antibodies show significantly improved endothelialization in the clinic. However, most current antibody-based stent surface modification strategies rely on antibody adsorption or direct conjugation via amino or carboxyl groups which leads to poor control over antibody surface concentration and/or molecular orientation, and ultimately bioavailability for cell capture. Here, we assess the utility of a bioaffinity-based surface modification strategy consisting of a surface-conjugated cysteine-tagged protein G molecules that immobilize Immunoglobulin G (IgG) antibodies via the Fc domain to capture circulating endothelial colony-forming cells (ECFCs). The cysteine-tagged protein G was grafted onto aminated substrates at different concentrations as detected by an enzyme-linked immunosorbent assay and fluorescence imaging. Different IgG antibodies were successfully immobilized on the protein G-modified surfaces and higher antibody surface concentrations were achieved compared to passive adsorption methods. Surfaces with immobilized antibodies targeting endothelial surface proteins, such as CD144, significantly enhanced the capture of circulating ECFCsin vitrocompared to surfaces with non-endothelial specific antibodies such as anti-CD14. This work presents a potential avenue for enhancing the clinical performance of vascular implants by using covalent grafting of protein G to immobilize IgG antibodies more effectively.Table of ContentsAntibody immobilization via surface-conjugated recombinant cysteine-protein G provides an effective approach to capture circulating therapeutic cells.
Genetic Loci and Metabolic States Associated With Murine Epigenetic Aging
Authors: Mozhui Khyobeni , Lu Ake T. , Li Caesar Z , Haghani Amin , Sandoval-Sierra Jose Vladimir , Wu Yibo , Williams Robert W. , Horvath Steve 
Published: June 2021

AbstractChanges in DNA methylation (DNAm) are linked to aging. Here, we profile highly conserved CpGs in 339 predominantly female mice belonging to the BXD family for which we have deep longevity and genomic data. We use a ‘pan-mammalian’ microarray that provides a common platform for assaying the methylome across mammalian clades. We computed epigenetic clocks and tested associations with DNAm entropy, diet, weight, metabolic traits, and genetic variation. We describe the multifactorial variance of methylation at these CpGs, and show that high fat diet augments the age-associated changes. Entropy increases with age. The progression to disorder, particularly at CpGs that gain methylation over time, was predictive of genotype-dependent life expectancy. The longer-lived BXD strains had comparatively lower entropy at a given age. We identified two genetic loci that modulate rates of epigenetic age acceleration (EAA): one on chromosome (Chr) 11 that encompasses the Erbb2/Her2 oncogenic region, and a second on Chr19 that contains a cytochrome P450 cluster. Both loci harbor genes associated with EAA in humans including STXBP4, NKX2-3, and CUTC. Transcriptome and proteome analyses revealed associations with oxidation-reduction, metabolic, and immune response pathways. Our results highlight concordant loci for EAA in humans and mice, and demonstrate a tight coupling between the metabolic state and epigenetic aging.
Parallel Evaluation of Nucleophilic and Electrophilic Chemical Probes for Sulfenic Acid: Reactivity, Selectivity and Biocompatibility
Authors: Shi Yunlong , Carroll Kate S. 
Published: June 2021

AbstractS-sulfenylation of cysteine thiols (Cys-SOH) is a regulatory posttranslational modification in redox signaling and an important intermediate to other cysteine chemotypes. Owing to the dual chemical nature of the sulfur in sulfenic acid, both nucleophilic and electrophilic chemical probes have been developed to react with and detect Cys-SOH; however, the efficiency of existing probes has not been evaluated in a side-by-side comparison. Here, we employ small-molecule and protein models of Cys-SOH and compare the chemical probe reactivity. These data clearly show that 1,3-diketone-based nucleophilic probes react more efficiently with sulfenic acid as compared to strained alkene/alkyne electrophilic probes. Kinetic experiments that rigorously address the selectivity of the 1,3-diketone-based probes are also reported. Consideration of these data alongside relative cellular abundance, indicates that biological electrophiles, including cyclic sulfenamides, aldehydes, disulfides and hydrogen peroxide, are not meaningful targets of 1,3-diketone-based nucleophilic probes, which still remain the most viable tools for the bioorthogonal detection of Cys-SOH.
Repertoire analyses reveal TCR sequence features that influence T cell fate
Authors: Lagattuta Kaitlyn A. , Kang Joyce B. , Nathan Aparna , Pauken Kristen E. , Jonsson Anna Helena , Rao Deepak A. , Ishigaki Kazuyoshi , Raychaudhuri Soumya 
Published: June 2021

ABSTRACTT cells acquire a regulatory phenotype when their T cell receptors (TCRs) experience an intermediate-high affinity interaction with a self-peptide presented on MHC. Using TCR sequences from FACS-sorted human cells, we identified TCR features that shape affinity to these self-peptide-MHC complexes, finding that 1) CDR3β hydrophobicity and 2) certain TRBV genes promote Treg fate. We developed a scoring system for TCR-intrinsic regulatory potential (TiRP) and found that within the tumor microenvironment clones exhibiting Treg-Tconv plasticity had higher TiRP than expanded clones maintaining the Tconv phenotype. To elucidate drivers of these predictive TCR features, we examined the two elements of the Treg TCR ligand separately: the self-peptide via murine Tregs, and the human MHC II molecule via human memory Tconvs. These analyses revealed that CDR3β hydrophobicity promotes reactivity to self-peptides, while TRBV gene usage shapes the TCR’s general propensity for MHC II-restricted activation.
Why are SNAREpins rod-shaped?
Authors: Zeng Jin , McDargh Zachary , An Dong , O’Shaughnessy Ben 
Published: June 2021

AbstractSNARE proteins are the core components of the cellular machineries that fuse membranes for neurotransmitter or hormone release and other fundamental processes. Fusion is accomplished when SNARE proteins hosted by apposing membranes form SNARE complexes called SNAREpins, but the mechanism of fusion remains unclear. Computational simulations of SNARE-mediated membrane fusion are challenging due to the millisecond timescales of physiological membrane fusion. Here we used ultra-coarse-grained (UCG) simulations to investigate the minimal requirements for a molecular intracellular fusogen, and to elucidate the mechanisms of SNARE-mediated fusion. We find fusion by simple body forces that push vesicles together is highly inefficient. Inter-vesicle fusogens with different aspect ratios can fuse vesicles only if they are rodlike, of sufficient length to clear the fusogens from the fusion site by entropic forces. Simulations with rod-shaped SNAREpin-like fusogens fused 50-nm vesicles on ms timescales, driven by entropic forces along a reproducible fusion pathway. SNARE-SNARE and SNARE-membrane entropic forces cleared the fusion site and pressed the vesicles into an extended contact zone (ECZ), drove stalk nucleation at the high curvature ECZ boundary, and expanded the stalk into a long-lived hemifusion diaphragm in which a simple pore completed fusion. Our results provide strong support for the entropic hypothesis of SNARE-mediated membrane fusion, and implicate the rodlike structure of the SNAREpin complex as a necessity for entropic force production and fusion.
Cardiovascular disease causes proinflammatory microvascular changes in the human right atrium
Authors: Linna-Kuosmanen Suvi , Schmauch Eloi , Galani Kyriakitsa , Ojanen Johannes , Boix Carles A. , Örd Tiit , Toropainen Anu , Singha Prosanta K. , Moreau Pierre R. , Harju Kristiina , Blazeski Adriana , Segerstolpe Åsa , Lahtinen Veikko , Hou Lei , Kang Kai , Meibalan Elamaran , Agudelo Leandro Z. , Kokki Hannu , Halonen Jari , Jalkanen Juho , Gunn Jarmo , MacRae Calum A. , Hollmén Maija , Hartikainen Juha , Kaikkonen Minna U. , García-Cardeña Guillermo , Tavi Pasi , Kiviniemi Tuomas , Kellis Manolis 
Published: June 2021

AbstractIschemic heart disease is globally the leading cause of death. It plays a central role in the electrical and structural remodeling of the right atrium, predisposing to arrhythmias, heart failure, and sudden death. Here, we provide the first dissection of the gene expression changes in the live right atrial tissue, using single-nuclei RNA-seq and spatial transcriptomics. We investigate matched samples of the tissue and pericardial fluid and reveal substantial differences in disease- associated gene expression in all cell types, leading to inflammatory microvascular dysfunction and changes in the tissue composition. Our study demonstrates the importance of creating high- resolution cellular maps and partitioning disease signals beyond epicardial coronary arteries and ischemic left ventricle to identify candidate mechanisms leading to more severe types of human cardiovascular disease.One-Sentence SummarySingle-cell dissection ofex vivoheart biopsies and pericardial fluid in ischemic heart disease and heart failure
Dynamic aspects of plant water potential revealed by a microtensiometer
Authors: Pagay Vinay 
Published: June 2021

AbstractWater potential is a fundamental thermodynamic parameter that describes the activity of water. In this paper, we describe the continuous measurement of plant water potential, a reliable indicator of its water status, using a novelin situsensor known as a ‘microtensiometer’ in mature grapevines under field conditions. The microtensiometer operates on the principle of equilibration of water potentials of internal liquid water with an external vapour or liquid phase. We characterised the seasonal and diurnal dynamics of trunk water potentials (Ψtrunk) obtained from microtensiometers installed in two grapevine cultivars, Shiraz and Cabernet Sauvignon, and compared these values to pressure chamber-derived stem (Ψstem) and leaf (Ψleaf) water potentials as well as leaf stomatal conductance. Diurnal patterns of Ψtrunkmatched those of Ψstemand Ψleafunder low vapour pressure deficit (VPD) conditions, but diverged under high VPD conditions. The highest diurnal values of Ψtrunkwere observed shortly after dawn, while the lowest values were typically observed in the late afternoon. Differential responses of Ψtrunkto VPD were observed between cultivars, with Shiraz more sensitive than Cabernet to increasing VPD over long time scales, and both cultivars had a stronger VPD response than soil moisture response. On a diurnal basis, however, time cross correlation analysis revealed that Shiraz Ψtrunklagged Cabernet Ψtrunkin response to changing VPD. Microtensiometers were shown to operate reliably under field conditions over several months. To be useful for irrigation scheduling of woody crops, new thresholds of Ψtrunkneed to be developed.
Multiple mechanisms impact fluconazole resistance of mutant Erg11 proteins in Candida glabrata
Authors: Vu Bao Gia , Moye-Rowley W. Scott 
Published: June 2021

AbstractAzoles, the most commonly used antifungal drugs, specifically inhibit the fungal lanosterol α-14 demethylase enzyme, which is referred to as Erg11. Inhibition of Erg11 ultimately leads to a reduction in ergosterol production, an essential fungal membrane sterol. Many Candida species, such as Candida albicans, develop mutations in this enzyme which reduces the azole binding affinity and results in increased resistance. Candida glabrata is also a pathogenic yeast that has low intrinsic susceptibility to azole drugs and easily develops elevated resistance. These azole resistant mutations typically cause hyperactivity of the Pdr1 transcription factor and rarely lie within the ERG11 gene. Here, we generated C. glabrata ERG11 mutations that were analogous to azole resistance alleles from C. albicans ERG11. Three different Erg11 forms (Y141H, S410F, and the corresponding double mutant (DM)) conferred azole resistance in C. glabrata with the DM Erg11 form causing the strongest phenotype. The DM Erg11 also induced cross-resistance to amphotericin B and caspofungin. Resistance caused by the DM allele of ERG11 imposed a fitness cost that was not observed with hyperactive PDR1 alleles. Crucially, the presence of the DM ERG11 allele was sufficient to activate the Pdr1 transcription factor in the absence of azole drugs. Our data indicate that azole resistance linked to changes in ERG11 activity can involve cellular effects beyond an alteration in this key azole target enzyme. Understanding the physiology linking ergosterol biosynthesis with Pdr1-mediated regulation of azole resistance is crucial for ensuring the continued efficacy of azole drugs against C. glabrata.ImportanceAzole drugs target the Erg11 enzyme and lead to a reduction in fungal ergosterol, a vital sterol in yeast. Mutations in Erg11 are common among azole resistant Candida albicans clinical isolates, but not in C. glabrata, a major human pathogen. In this study, we showed that ERG11 mutations were tolerated in C. glabrata, and these mutations could confer azole resistance. We found that the strongest azole-resistant allele of ERG11 led to induction of the Pdr1 transcription factor and Cdr1 ATP-binding cassette transporter protein in the absence of drug. ERG11 mutations can cause azole resistance via altered enzymatic properties but also by triggering induction of other resistance systems owing to impacts on ergosterol biosynthesis. These data illustrate the deep connections between ergosterol biosynthesis and regulation of membrane transporter proteins via Pdr1 and the ergosterol-responsive transcription factor Upc2A.
An Open-Source Modular Framework for Automated Pipetting and Imaging Applications
Authors: Ouyang Wei , Bowman Richard , Wang Haoran , Bumke Kaspar E , Collins Joel T , Spjuth Ola , Carreras-Puigvert Jordi , Diederich Benedict 
Published: June 2021

The number of samples in biological experiments are continuously increasing, but complex protocols and human experimentation in many cases lead to suboptimal data quality and hence difficulties in reproducing scientific findings. Laboratory automation can alleviate many of these problems by precisely reproducing machine-readable protocols. These instruments generally require high up-front investments and due to lack of open APIs they are notoriously difficult for scientists to customize and control outside of the vendor-supplied software.Here, we demonstrate automated, high-throughput experiments for interdisciplinary research in life science that can be replicated on a modest budget, using open tools to ensure reproducibility by combining the tools Openflexure, Opentrons, ImJoy and UC2. Our automated sample preparation and imaging pipeline can easily be replicated and established in many laboratories as well as in educational contexts through easy-to-understand algorithms and easy-to-build microscopes. Additionally, the creation of feedback loops, with later pipetting or imaging steps depending on analysis of previously acquired images, enables the realization of smart microscopy experiments, featuring completely autonomously performed experiments. All documents and source-files are publicly available (https://beniroquai.github.io/Hi2) to prove the concept of smart lab automation using inexpensive, open tools. We believe this democratizes access to the power and repeatability of automated experiments.