bluuebunny/crossref_metadata_2025_split huggingface dataset:
Live-cell imaging and physical modeling reveal control of chromosome folding dynamics by cohesin and CTCF
Authors: Mach Pia , Kos Pavel I. , Zhan Yinxiu , Cramard Julie , Gaudin Simon , Tünnermann Jana , Marchi Edoardo , Eglinger Jan , Zuin Jessica , Kryzhanovska Mariya , Smallwood Sebastien , Gelman Laurent , Roth Gregory , Nora Elphège P. , Tiana Guido , Giorgetti Luca 
Published: March 2022

AbstractPhysical proximity between genomic sequences in mammalian chromosomes controls key biological processes such as transcriptional regulation and DNA repair. Yet it is currently unknown if chromosomal contacts are rare and stable or instead frequent and dynamic, and how they depend on the loop extrusion activity of cohesin or barriers such as CTCF. By imaging chromosomal locations at high spatial and temporal resolution over several hours in living cells, we show that sequences within topological associating domains (TADs) frequently come into physical proximity during the course of a cell cycle and remain close to each other only for a few minutes. Such contacts become nonetheless substantially longer and more frequent in the presence of convergent CTCF sites, resulting in a suppression of variability in chromosome folding in single cells across time. Supported by physical models of chromosome dynamics, our data additionally suggests that individual CTCF-anchored loops last around 10 minutes. The estimates of chromosomal contact dynamics in our study provide a novel quantitative framework to link chromosome structure to function and show that cohesin and CTCF stabilize otherwise highly dynamic chromosome structures to facilitate selected subsets of chromosomal interactions.
Cardiac cycle affects the asymmetric value updating in instrumental reward learning
Authors: Kimura Kenta , Kanayama Noriaki , Toyama Asako , Katahira Kentaro 
Published: March 2022

AbstractThis study aimed to investigate whether instrumental reward learning is affected by the cardiac cycle. To this end, we examined the effects of the cardiac cycle (systole or diastole) on the computational processes underlying the participants’ choices in the instrumental learning task. In the instrumental learning task, participants were required to select one of two discriminative stimuli (neutral visual stimuli) and immediately receive reward/punishment feedback depending on the probability assigned to the chosen stimuli. To manipulate the cardiac cycle, the presentation of discriminative stimuli was timed to coincide with either cardiac systole or diastole. We fitted the participants’ choices in the task with reinforcement learning (RL) models and estimated parameters involving instrumental learning (i.e., learning rate and inverse temperature) separately in the systole and diastole trials. Model-based analysis revealed that the learning rate for positive prediction errors was higher than that for negative prediction errors in the systole trials; however, learning rates did not differ between positive and negative prediction errors in the diastole trials. These results demonstrate that the natural fluctuation of cardiac afferent signals can affect asymmetric value updating in instrumental reward learning.
p73 is required for vessel integrity controlling endothelial junctional dynamics through Angiomotin
Authors: Maeso-Alonso Laura , Alonso-Olivares Hugo , Martínez-García Nicole , Lopez-Ferreras Lorena , Villoch-Fernández Javier , Puente-Santamaría Laura , Colas-Algora Natalia , Fernández-Corona Alfonso , Lorenzo-Marcos María Elena , Jiménez Benilde , Holmgren Lars , Wilhelm Margareta , Millan Jaime , Peso Luis del , Claesson-Welsh Lena , Marques Margarita M. , Marin Maria C. 
Published: March 2022

AbstractPreservation of blood vessels integrity, which is critical for normal physiology and organ function, is controlled at multiple levels, including endothelial junctions. However, the mechanism that controls the adequate assembly of endothelial cell junctions is not fully defined. Here we uncover TAp73 transcription factor as a vascular architect that orchestrates transcriptional programs involved in cell junction establishment and developmental blood vessel morphogenesis and identify Angiomotin (AMOT) as a TAp73 direct transcriptional target. Knockdown of p73 in endothelial cells not only results in decreased Angiomotin expression and localization at intercellular junctions, but also affects its downstream function regarding Yes-Associated Protein (YAP) cytoplasmic sequestration upon cell-cell contact. Analysis of adherens junctional morphology after p73-knockdown in human endothelial cells revealed striking alterations, particularly a sharp increase in serrated junctions and actin bundles appearing as stress fibers, both features associated with enhanced barrier permeability. In turn, stabilization of Angiomotin levels rescued those junctional defects, confirming that TAp73 controls endothelial junction dynamics, at least in part, through the regulation of Angiomotin. The observed defects in monolayer integrity were linked to hyperpermeability and reduced transendothelial electric resistance. Moreover, p73-knockout retinas showed a defective sprout morphology coupled to hemorrhages, highlighting the physiological relevance of p73 regulation in the maintenance of vessel integrity in vivo. We propose a new model in which TAp73 acts as a vascular architect integrating transcriptional programs that will impinge with Angiomotin/YAP signaling to maintain junctional dynamics and integrity, whilst balancing endothelial cell rearrangements in angiogenic vessels.
Reconstructed human pigmented skin/epidermis models achieve epidermal pigmentation through melanocore transfer
Authors: Hall Michael J. , Lopes-Ventura Sara , Neto Matilde V. , Charneca João , Zoio Patricia , Seabra Miguel C. , Oliva Abel , Barral Duarte C. 
Published: March 2022

AbstractThe skin acts as a barrier to environmental insults and provides many vital functions. One of these is to shield DNA from harmful UV radiation, which is achieved by skin pigmentation arising as melanin is produced and dispersed within the epidermal layer. This is a crucial defence against DNA damage, photo-ageing and skin cancer. The mechanisms and regulation of melanogenesis and melanin transfer involve extensive crosstalk between melanocytes and keratinocytes in the epidermis, as well as fibroblasts in the dermal layer. Although the predominant mechanism of melanin transfer continues to be debated and several plausible models have been proposed, we and others previously provided evidence for a coupled exo/phagocytosis of melanocore model. Herein, we performed histology and immunohistochemistry analyses and demonstrated that a newly developed full-thickness 3D reconstructed human pigmented skin model and an epidermis-only model exhibit dispersed pigment throughout keratinocytes in the epidermis. Transmission electron microscopy revealed melanocores between melanocytes and keratinocytes, suggesting that melanin is transferred through coupled exocytosis/phagocytosis of the melanosome core similar to our previous observations in human skin biopsies. We therefore present evidence that our in vitro models of pigmented human skin show epidermal pigmentation comparable to human skin. These findings have a high value for studies of skin pigmentation mechanisms and pigmentary disorders, whilst reducing the reliance on animal models and human skin biopsies.SignificanceCurrently, many approaches to study skin pigmentation and pigmentary disorders use 2D cultures or co-culture of melanocytes and/or keratinocytes, as well as skin biopsies obtained from consenting donors. However, challenges are faced when it is necessary to mimic the tissue microenvironment as there is a limited availability of skin biopsies, especially for the case of rare pigmentary disorders. Through this study, we show the potential of 3D in vitro reconstructed pigmented skin/epidermis models for both general and specific pigmentary research questions, which could reduce reliance on animal models and human skin biopsies.
Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins
Authors: Davidson Phillip L , Guo Haobing , Swart Jane S , Massri Abdull J , Edgar Allison , Wang Lingyu , Berrio Alejandro , Devens Hannah R , Koop Demian , Cisternas Paula , Zhang He , Zhang Yaolei , Byrne Maria , Fan Guangyi , Wray Gregory A 
Published: March 2022

ABSTRACTChanges in developmental gene regulatory networks (dGRNs) underlie much of the diversity of life1, but the evolutionary mechanisms that operate on interactions with these networks remain poorly understood. Closely related species with extreme phenotypic divergence provide a valuable window into the genetic and molecular basis for changes in dGRNs and their relationship to adaptive changes in organismal traits. Here we analyze genomes, epigenomes, and transcriptomes during early development in two sea urchin species in the genus Heliocidaris that exhibit highly divergent life histories and in an outgroup species. Signatures of positive selection and changes in chromatin status within putative gene regulatory elements are both enriched on the branch leading to the derived life history, and particularly so near dGRN genes; in contrast, positive selection within protein-coding regions have at most a modest enrichment in branch and function. Single-cell transcriptomes reveal a dramatic delay in cell fate specification in the derived state, which also has far fewer open chromatin regions, especially near dGRN genes with conserved roles in cell fate specification. Experimentally perturbing the function of three key transcription factors reveals profound evolutionary changes in the earliest events that pattern the embryo, disrupting regulatory interactions previously conserved for ∼225 million years. Together, these results demonstrate that natural selection can rapidly reshape developmental gene expression on a broad scale when selective regimes abruptly change and that even highly conserved dGRNs and patterning mechanisms in the early embryo remain evolvable under appropriate ecological circumstances.
Impact of fungal hyphae on growth and dispersal of obligate anaerobic bacteria in aerated habitats
Authors: Xiong Bi-Jing , Kleinsteuber Sabine , Sträuber Heike , Dusny Christian , Harms Hauke , Wick Lukas Y. 
Published: March 2022

AbstractAnoxic microsites arising in fungal biofilms may foster the presence of obligate anaerobes even in well-areated environments. Here, we analyzed whether and to which degree fractal hyphae of Coprinopsis cinerea thriving in oxic habitats enable the germination, growth, and dispersal of obligate anaerobic soil bacterium Clostridium acetobutylicum. Time-resolved optical oxygen mapping, microscopy and metabolite analysis revealed the formation and persistence of anoxic circum hyphal niches allowing for spore germination, growth and fermentative activity of the obligate anaerobe in an otherwise oxic environment. Hypoxic liquid films containing 80 ± 10% of atmospheric oxygen saturation around single air-exposed hyphae thereby allowed for efficient clostridial dispersal amid spatially separated (>0.5 cm) anoxic sites. Our results suggest that fungal biomass typical in soil (<550 μg g-1soil) may create anoxic microniches and enable activity as well as dispersal of obligate anaerobes near hyphae in an otherwise inhabitable environment.
Development of a mouse salivary gland-derived mesenchymal cell line for immunological studies of murine cytomegalovirus
Authors: White Timothy M. , Stanfield Brent A. , Bonavita Cassandra M. , Rudd Jared S. , Cardin Rhonda D. 
Published: March 2022

AbstractThe salivary glands are a crucial site of replication for human cytomegalovirus (HCMV) and its murine counterpart, murine cytomegalovirus (MCMV). Studies of MCMV often involve the use of BALB/c strain mice, but mostin vitroassays are carried out in the NIH 3T3 cell line, which is derived from Swiss Albino mice. This report describes a BALB/c-derived mouse salivary gland cell line immortalized using the SV40 large T antigen. Cells stained positive for PDGFR1 and negative for E-cadherin and PECAM-1, indicating mesenchymal origin. This cell line, which has been named murine salivary gland mesenchymal (mSGM), shows promise as a tool forex vivoimmunological assays due to its MHC haplotype match with the BALB/c mouse strain. In addition, plaque assays using mSGM rather than NIH 3T3 cells are significantly more sensitive for detecting low concentrations of MCMV particles. Finally, it is demonstrated that mSGM cells express all 3 BALB/c MHC class I isotypes and are susceptible to T cell-mediatedex vivocytotoxicity assays, leading to many possible uses in immunological studies of MCMV.
Modulation of the Biophysical and Biochemical Properties of Collagen by Glycation for Tissue Engineering Applications
Authors: Vaez Mina , Asgari Meisam , Hirvonen Liisa , Bakir Gorkem , Aguayo Sebastian , Schuh Christina M. , Gough Kathleen , Bozec Laurent 
Published: March 2022

AbstractThe structural and functional properties of collagen are modulated by the presence of intramolecular and intermolecular crosslinks. Advanced Glycation End-products (AGEs) can produce intermolecular crosslinks by bonding the free amino groups of neighboring proteins. In this research, the following hypothesis is explored: The accumulation of AGEs in collagen decreases its proteolytic degradation rates while increasing its stiffness. Fluorescence Lifetime Imaging (FLIM) and Fourier-transform infrared spectroscopy (FTIR) detect biochemical changes in collagen scaffolds during the glycation process. The accumulation of AGEs increases exponentially in the collagen scaffolds as a function of Methylglyoxal (MGO) concentration by performing autofluorescence measurement and competitive ELISA. Glycated scaffolds absorb water at a much higher rate confirming the direct affinity between AGEs and interstitial water within collagen fibrils. In addition, the topology of collagen fibrils as observed by Atomic Force Microscopy (AFM) is a lot more defined following glycation. The elastic modulus of collagen fibrils decreases as a function of glycation, whereas the elastic modulus of collagen scaffolds increases. Finally, the enzymatic degradation of collagen by bacterial collagenase shows a sigmoidal pattern with a much slower degradation rate in the glycated scaffolds. This study identifies unique variations in the properties of collagen following accumulation of AGEs.
CeSpGRN: Inferring cell-specific gene regulatory networks from single cell multi-omics and spatial data
Authors: Zhang Ziqi , Han Jongseok , Song Le , Zhang Xiuwei 
Published: March 2022

AbstractSingle cell profiling techniques including multi-omics and spatial-omics technologies allow researchers to study cell-cell variation within a cell population. These variations extend to biological networks within cells, in particular, the gene regulatory networks (GRNs). GRNs rewire as the cells evolve, and different cells can have different governing GRNs. However, existing GRN inference methods usually infer a single GRN for a population of cells, without exploring the cell-cell variation in terms of their regulatory mechanisms. Recently, jointly profiled single cell transcriptomics and chromatin accessibility data have been used to infer GRNs. Although methods based on such multi-omics data were shown to improve over the accuracy of methods using only single cell RNA-seq (scRNA-seq) data, they do not take full advantage of the single cell resolution chromatin accessibility data.We propose CeSpGRN (CellSpecificGeneRegulatoryNetwork inference), which infers cell-specific GRNs from scRNA-seq, single cell multi-omics, or single cell spatial-omics data. CeSpGRN uses a Gaussian weighted kernel that allows the GRN of a given cell to be learned from the sequencing profile of itself and its neighboring cells in the developmental process. The kernel is constructed from the similarity of gene expressions or spatial locations between cells. When the chromatin accessibility data is available, CeSpGRN constructs cell-specific prior networks which are used to further improve the inference accuracy.We applied CeSpGRN to various types of real-world datasets and inferred various regulation changes that were shown to be important in cell development. We also quantitatively measured the performance of CeSpGRN on simulated datasets and compared with baseline methods. The results show that CeSpGRN has a superior performance in reconstructing the GRN for each cell, as well as in detecting the regulatory interactions that differ between cells. CeSpGRN is available athttps://github.com/PeterZZQ/CeSpGRN.
Rapid single-molecule characterisation of nucleic-acid enzymes
Authors: Mueller Stefan H. , Fitschen Lucy J. , Shirbini Afnan , Hamdan Samir M. , Spenkelink Lisanne M. , van Oijen Antoine M. 
Published: March 2022

ABSTRACTThe activity of enzymes is traditionally characterised through bulk-phase biochemical methods that only report on population averages. Single-molecule methods are advantageous in elucidating kinetic and population heterogeneity but are often complicated, time consuming, and lacking statistical power. We present a highly generalisable and high-throughput single-molecule assay to rapidly characterise proteins involved in DNA metabolism. The assay exclusively relies on changes in total fluorescence intensity of surface-immobilised DNA templates as a result of DNA synthesis, unwinding or digestion. Combined with an automated data-analysis pipeline, our method provides enzymatic activity data of thousands of molecules in less than an hour. We demonstrate our method by characterising three fundamentally different nucleic-acid enzyme activities: digestion by the phage λ exonuclease, synthesis by the phage Phi29 polymerase, and unwinding by the E. coli UvrD helicase. We observe a previously unknown activity of the UvrD helicase to remove proteins tightly bound to the ends of DNA.
Structural basis of flagellar filament asymmetry and supercoil templating by Leptospira spirochete sheath proteins
Authors: Brady Megan R. , Martin Fabiana San , Debs Garrett E. , Gibson Kimberley H. , Rodríguez Azalia , Durán Rosario , Wunder Elsio A. , Ko Albert I. , Buschiazzo Alejandro , Sindelar Charles V. 
Published: March 2022

AbstractSeveral Leptospira species are bacterial agents of leptospirosis, a neglected tropical disease responsible for ~1 million cases and 50,000 deaths each year worldwide. Leptospira, like other members of the Spirochaeta phylum, possess specially adapted flagella that remain confined within the periplasm. These appendages drive a unique, corkscrew-like swimming style that enables efficient motility and pathogenesis. However, the composition, function, and molecular architecture of spirochetal flagellar filaments remain poorly understood. We solved single-particle cryo-EM structures of isolated Leptospira flagellar filaments, comparing the wild-type form to two mutant forms with different missing components and abrogated motilities. The structures reveal a complex proteinaceous sheath surrounding a conserved core composed of the FlaB flagellin homolog. Sheath proteins were found to fall into two distinct categories, both of which are required for motility. Filament ‘coiling’ proteins, FcpA and FcpB, exert force on the filament when they bind its surface, causing the filament to stretch. In contrast, we identify sheath components FlaAP (newly discovered in this study) and FlaA2 as ‘template’ factors, which have little effect on filament shape by themselves, but partition the coiling proteins to one side of the filament. In this way, the two types of Leptospira sheath factors operate collectively on the flagellar filament to bend it from a ‘relaxed’ form associated with cell immobility, to a motility-competent shape that is tightly supercoiled. Our structures also indicate that core-sheath interactions are largely mediated by carbohydrate moieties from flagellin core side chain O-glycosylations. The supercoiling mechanism presented here provides a benchmark for studies with other bacteria, for which near-atomic resolution structures of flagellar filament in native supercoiled forms, are still lacking.
Towards enhancement in reliability and safety of construction projects: developing a hybrid multi-dimensional fuzzy-based approach
Authors: Mohandes Saeed Reza , Durdyev Serdar , Sadeghi Haleh , Mahdiyar Amir , Hosseini M. Reza , Banihashemi Saeed , Martek Igor 
Published: March 2022

PurposeIn the study, a five-dimensional-safety risk assessment model (5D-SRAM) is developed to improve the construction safety risk assessment approaches available in the literature. To that purpose, a hybrid multi-dimensional fuzzy-based model is proposed, which provides a comprehensive ranking system for the safety risks existing in a project by considering the contextualization of the construction-related activities resulting in an accident.Design/methodology/approachThe developed 5D-SRAM is based on an amalgamation of different fuzzy-based techniques. Through the proposed fuzzy analytic hierarchy process (AHP) method, the importance weights of essential risk dimensions playing role in defining the magnitude of the construction-related risks are obtained, while a precise prioritized ranking system for the identified safety risks is acquired using the proposed fuzzy technique of order preference similarity to the ideal solution (FTOPSIS).FindingsThrough the application of the proposed 5D-SRAM to a real-life case study – which is the case of green building construction projects located in Hong Kong – contributions are realized as follows: (1) determination of a more complete range of risk dimensions, (2) calculation of importance weightings for each risk dimension and (3) obtainment of a precise and inclusive ranking system for safety risks. Additionally, the supremacy of the developed 5D-SRAM against the other safety assessment approaches that are commonly adopted in the construction industry is proved.Research limitations/implicationsThe developed 5D-SRAM provides the concerned safety decision-makers with not only all the crucial dimensions that play roles toward the magnitude of safety risks posing threats to the workers involved in construction activities, but also they are given hindsight regarding the importance weights of these dimensions. Additionally, the concerned parties are embellished with the final ranking of safety risks in a more comprehensive way than those of existing assessment methods, leading to sagacious adoption of future prudent strategies for dealing with such risks occurring on construction sites.Originality/valueNumerous studies have documented the safety risks faced by construction workers including proposals for risk assessment models. However, the dimensions considered by such models are limited, generally constrained to risk event probability combined with risk impact severity. Overlooking other dimensions that are essential towards the calculation of safety risks' magnitude culminates in overshadowing the further adoption of fruitful mitigative actions. To overcome this shortcoming, this study proposes a novel 5D-SRAM.