bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of PARP1 in oligodendrocyte differentiation during developmental myelination and remyelination after myelin damage
Authors: Wang Yan , Zhang Sheng , Kim Bokyung , Hull Vanessa L. , Xu Jie , Prabhu Preeti , Gregory Maria , Martinez-Cerdeno Veronica , Zhan Xinhua , Deng Wenbin , Guo Fuzheng 
Published: April 2021

AbstractThe function of poly(ADP-ribosyl) polymerase 1 (PARP1) in myelination and remyelination of the central nervous system (CNS) remain enigmatic. Here we report that PARP1 is an intrinsic driver for oligodendroglial development and myelination. Genetic PARP1 depletion impairs the differentiation of oligodendrocyte progenitor cells (OPCs) into oligodendrocytes and impedes CNS myelination. Mechanistically, PARP1-mediated PARylation activity is not only necessary but also sufficient for OPC differentiation. At the molecular level, we identify the RNA-binding protein Myef2 as a novel PARylated target which we show controls OPC differentiation through PARylation-modulated de-repression of myelin protein expression. Furthermore, PARP1’s enzymatic activity is necessary for oligodendrocyte and myelin regeneration after demyelination. Together, our findings suggest that PARP1-mediated PARylation activity may be a potential therapeutic target for promoting OPC differentiation and remyelination in neurological disorders characterized by arrested OPC differentiation and remyelination failure such as multiple sclerosis.
Does cellular adaptation to force loading rate determine the biphasic vs monotonic response of actin retrograde flow with substrate rigidity?
Authors: Sakha De Partho , De Rumi 
Published: April 2021

AbstractThe transmission of cytoskeletal forces to the extracellular matrix through focal adhesion complexes is essential for a multitude of biological processes such as cell migration, differentiation, tissue development, cancer progression, among others. During migration, focal adhesions arrest the actin retrograde flow towards the cell interior, allowing the cell front to move forward. Here, we address a puzzling observation of the existence of two distinct phenomena: a biphasic relationship of the retrograde flow and cell traction force with increasing substrate rigidity, with maximum traction force and minimum retrograde flow velocity being present at an optimal substrate stiffness; in contrast, a monotonic relationship between them where the retrograde flow decreases and traction force increases with substrate stiffness. We propose a theoretical model for cell-matrix adhesions at the leading edge of a migrating cell, incorporating a novel approach in force loading rate sensitive binding and reinforcement of focal adhesions assembly and the subsequent force-induced slowing down of actin flow. Our model unravels both biphasic and monotonic responses of the retrograde flow and cell traction force with increasing substrate rigidity, owing to the cell’s ability to sense and adapt to the fast-growing forces. Moreover, we also elucidate how the viscoelastic properties of the substrate regulate these nonlinear responses and alter cellular behaviours.
Action selection based on multiple-stimulus aspects in the wind-elicited escape behavior of crickets
Authors: Sato Nodoka , Shidara Hisashi , Ogawa Hiroto 
Published: April 2021

ABSTRACTAnimals detect approaching predators via sensory inputs through various modalities and immediately show an appropriate behavioral response to survive. Escape behavior is essential to avoid the predator’s attack and is more frequently observed than other defensive behaviors. In some species, multiple escape responses are exhibited with different movements. It has been reported that the approaching speed of a predator is important in choosing which escape action to take among the multiple responses. However, it is unknown whether other aspects of sensory stimuli, that indicate the predator’s approach, affect the selection of escape responses. We focused on two distinct escape responses (running and jumping) to a stimulus (short airflow) in crickets and examined the effects of multiple stimulus aspects (including the angle, velocity, and duration) on the choice between these escape responses. We found that the faster and longer the airflow, the more frequently the crickets jumped, meaning that they could choose their escape response depending on both velocity and duration of the stimulus. This result suggests that the neural basis for choosing escape responses includes the integration process of multiple stimulus parameters. It was also found that the moving speed and distance changed depending on the stimulus velocity and duration during running but not during jumping, suggesting higher adaptability of the running escape. In contrast, the movement direction was accurately controlled regardless of the stimulus parameters in both responses. The escape direction depended only on stimulus orientation, but not on velocity and duration.Summary statementWhen air currents triggering escape are faster and longer, crickets more frequently jump than run. Running speed and distance depend on stimulus velocity and duration, but direction control is independent.
A chromosome-scale strawberry genome assembly of a Japanese variety, Reikou
Authors: Shirasawa Kenta , Hirakawa Hideki , Nakayama Shinobu , Sasamoto Shigemi , Tsuruoka Hisano , Minami Chiharu , Watanabe Akiko , Kishida Yoshie , Kohara Mitsuyo , Yamada Manabu , Fujishiro Tsunakazu , Komaki Akiko , Isobe Sachiko N 
Published: April 2021

AbstractCultivated strawberry (Fragaria×ananassa) is an octoploid species (2n = 8x= 56) that is widely consumed around the world as both fresh and processed fruit. In this study, we report a chromosome-scale strawberry genome assembly of a Japanese variety, Reikou. The Illumina short reads derived from paired-end, mate-pair, and 10X Genomics libraries were assembled using Denovo MAGIC 3.0. The generated phased scaffolds consisted of 32,715 sequences with a total length of 1.4 Gb and an N50 length of 3.9 Mb. A total of 63 pseudomolecules including chr0 were created by aligning the scaffolds onto the Reikou S1 linkage maps with the IStraw90 Axiom SNP array and ddRAD-Seq. Meanwhile, genomes of diploidFragariaspecies were resequenced and compared with the most similar chromosome-scale scaffolds to investigate the possible progenitor of each subgenome. Clustering analysis suggested that the most likely progenitors wereF. vescaandF. iinumae. The phased pseudomolecules were assigned the scaffolds names with Av, Bi, and X, representing sequence similarity withF. vesca(Av),F. iinumae(Bi), and others (X), respectively. The result of a comparison with the Camerosa genome suggested the possibility of subgenome structure differences between the two varieties.
Coordination of two opposite flagella allows high-speed swimming and active turning of individual zoospores
Authors: Tran Quang D. , Galiana Eric , Thomen Philippe , Cohen Céline , Orange François , Peruani Fernando , Noblin Xavier 
Published: April 2021

AbstractPhytophthoraspecies cause diseases in a large variety of plants and represent a serious agricultural threat, leading, every year, to multibillion dollar losses. Infection occurs when these biflagellated zoospores move across the soil at their characteristic high speed and reach the roots of a host plant. Despite the relevance of zoospore spreading in the epidemics of plant diseases, characteristics of individual swimming of zoospores have not been fully investigated. It remains unknown about the characteristics of two opposite beating flagella during translation and turning, and the roles of each flagellum on zoospore swimming. Here, combining experiments and modeling, we show how these two flagella contribute to generate thrust when beating together, and identify the mastigonemes-attached anterior flagellum as the main source of thrust. Furthermore, we find that turning involves a complex active process, in which the posterior flagellum temporarily stops, while the anterior flagellum keeps on beating and changes its pattern from sinusoidal waves to power and recovery strokes, similar toChlamydomonas’s breaststroke, to reorient its body to a new direction. Our study is a fundamental step towards a better understanding of the spreading of plant pathogens’ motile forms, and shows that the motility pattern of these biflagellated zoospores represents a distinct eukaryotic version of the celebrated “run-and-tumble” motility class exhibited by peritrichous bacteria.
Integrative Omics Reveals Subtle Molecular Perturbations Following Ischemic Conditioning in a Porcine Kidney Transplant Model
Authors: O’Brien Darragh P. , Thorne Adam M. , Huang Honglei , Pappalardo Elisa , Yao Xuan , Thyrrestrup Peter Søndergaard , Ravlo Kristian , Secher Niels , Norregaard Rikke , Ploeg Rutger J. , Jespersen Bente , Kessler Benedikt M. 
Published: April 2021

ABSTRACTBackgroundRemote Ischemic Conditioning (RIC) has been proposed as a therapeutic intervention to circumvent the ischemia/reperfusion injury (IRI) that is inherent to organ transplantation. Using a porcine kidney transplant model, we aimed to decipher the subclinical molecular effects of a RIC regime, compared to non-RIC controls.MethodsKidney pairs (n = 8+8) were extracted from brain dead donor pigs and transplanted in juvenile recipient pigs following a period of cold ischemia. One of the two kidney recipients in each pair was subjected to RIC prior to kidney graft reperfusion, while the other served as non-RIC control. We designed a modern integrative Omics strategy combining transcriptomics, proteomics, and phosphoproteomics to deduce molecular signatures in kidney tissue that could be attributed to RIC.ResultsIn kidney grafts taken out 10 h after transplantation we detected minimal molecular perturbations following RIC compared to non-RIC at the transcriptome level, which was mirrored at the proteome level. In particular, we noted that RIC resulted in suppression of tissue inflammatory profiles. Furthermore, an accumulation of muscle extracellular matrix assembly proteins in kidney tissues was detected at the protein level, which may be in response to muscle tissue damage and/or fibrosis. However, the majority of these protein changes did not reach significance (p<0.05).ConclusionsOur data identifies subtle molecular phenotypes in porcine kidneys following RIC and this knowledge could potentially aid optimization of remote ischemic conditioning protocols in renal transplantation.
Gene co-expression networks identify novel candidate genes for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)
Authors: Zhou Zhaoran , Eichner Christiane , Nilsen Frank , Jonassen Inge , Dondrup Michael 
Published: April 2021

AbstractBackgroundThe salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod, living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required.MethodsThree weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages.ResultsEight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with the RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like gene obtained highest scores in the regulatory impact factor calculation.ConclusionsWe propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirmed the effectiveness of our approach and demonstrated the indispensable role of RAB1A-like gene in the development of salmon louse. In addition to salmon louse, this approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.
Polycomb requires Tcp-1η chaperonin for maintaining gene silencing inDrosophila
Authors: Shaheen Najma , Akhtar Jawad , Umer Zain , Khan Muhammad Haider Farooq , Saleem Murtaza , Faisal Amir , Tariq Muhammad 
Published: April 2021

AbstractIn metazoans, heritable states of cell type specific gene expression patterns linked with specialization of various cell types constitute transcriptional cellular memory. Evolutionarily conserved Polycomb group (PcG) and trithorax group (trxG) proteins contribute to the transcriptional cellular memory by maintaining heritable patterns of repressed and active expression states, respectively. Although chromatin structure and modifications appear to play a fundamental role in maintenance of repression by PcG, the precise targeting mechanism and the specificity factors that bind PcG complexes to a defined region in chromosomes remain elusive. Here we report a serendipitous discovery that uncovers a direct molecular interaction between Polycomb (PC) and TCP-1 Ring Complex (TRiC) chaperonin subunit, Tcp-1η inDrosophila. Tcp-1η interacts with PC at chromatin to maintain repressed states of homeotic and non-homeotic targets of PcG, which supports a strong genetic interaction observed betweenPcandTcp-1ηmutants. Depletion of Tcp-1η results in dissociation of PC from chromatin and redistribution of an abundant amount of PC in cytoplasm. We propose that Tcp-1η is an important modulator of PC, which helps PC recruitment at chromatin and compromising Tcp-1η can directly influence an evolutionary highly conserved epigenetic network that supervises the appropriate cellular identities during development and homoeostasis of an organism.Significance StatementSilencing of key developmental genes, e.g, Hox genes, by PcG is a hallmark of differential gene expression patterns associated with cell fate determination. Here we describe a previously unknown molecular and genetic interaction of Polycomb (PC) with Tcp-1η subunit of TRiC chaperonin complex inDrosophila. Compromising Tcp-1η function results in de-repression of PcG targets and a concomitant loss of PC from chromatin. Moreover, depletion of Tcp-1η leads to redistribution of PC in cytoplasm. Molecular interaction of PC with Tcp-1η highlights a novel factor which helps PC recruitment at chromatin. We propose that Tcp-1η chaperonin is one of the specificity factors and part of the targeting mechanism that binds PC to specific regions on chromosomes.
Urgent Brain Vascular Regeneration Occurs via Lymphatic Transdifferentiation
Authors: Chen Jingying , Li Xiuhua , Ni Rui , Chen Qi , Yang Qifen , He Jianbo , Luo Lingfei 
Published: April 2021

SUMMARYAcute ischemic stroke damages regional brain blood vessel (BV) network. Urgent recovery of basic blood flows, which represents the earliest regenerated BVs, are critical to improve clinical outcomes and minimize lethality. Although the late-regenerated BVs have been implicated to form via growing along the meninge-derived lymphatic vessels (iLVs), mechanisms underlying the early, urgent BV regeneration remain elusive. Using zebrafish cerebrovascular injury models, we show that the earliest regenerated BVs come from lymphatic transdifferentiation, a hitherto unappreciated process in vertebrates. Mechanistically, LV-to-BV transdifferentiation occurs exclusively in the stand-alone iLVs through Notch activation. In the track iLVs adhered by nascent BVs, transdifferentiation never occurs because the BV-expressing EphrineB2a paracellularly activates the iLV-expressing EphB4a to inhibit Notch activation. Suppression of LV-to-BV transdifferentiation blocks early BV regeneration and becomes lethal. These results demonstrate that urgent BV regeneration occurs via lymphatic transdifferentiation, suggesting this process and key regulatory molecules EphrinB2a/EphB4a/Notch as new post-ischemic therapeutic targets.
Multilayer diffusion networks as a tool to assess the structure and functioning of fine grain sub-specific plant-pollinator networks
Authors: Allen-Perkins Alfonso , Hurtado María , García-Callejas David , Godoy Oscar , Bartomeus Ignasi 
Published: April 2021

AbstractInteraction networks are a widely used tool to understand the dynamics of plant-pollinator ecological communities. However, while most mutualistic networks have been defined at the species level, ecological processes such as pollination take place at different scales, including the individual or patch levels. Yet, current approaches studying fine-grain sub-specific plant-pollinator networks only account for interactions among nodes belonging to a single plant species due to the conceptual and mathematical limitations of modeling simultaneously several plant species each composed of several nodes. Here, we introduce a multilayer diffusion network framework that allows modeling simple diffusion processes between nodes pertaining to the same or different layers (i.e. species). It is designed to depict from the network structure the potential conspecific and heterospecific pollen flows among plant individuals or patches. This potential pollen flow is modeled as a transport-like system, in which pollen grain movements are represented as random-walkers that diffuse on an ensemble of bipartite layers of conspecific plants and their shared pollinators. We exemplify this physical conceptualization using a dataset of nine fine-grain sub-specific plant-pollinator networks from a Mediterranean grassland of annual plants, where plant nodes represent groups of conspecifics within patches of 1m2. The diffusion networks show pollinators effectively connecting sets of patches of the same and different plant species, forming a modular structure. Interestingly, different properties of the network structure, such as the conspecific pollen arrival probability and the number of conspecific subgraphs in which plants are embedded, are critical for the seed production of different plant species. We provide a simple but robust set of metrics to calculate potential pollen flow and scale down network ecology to functioning properties at the individual or patch level, where most ecological processes take place, hence moving forward the description and interpretation of species-rich communities across scales.
Beta-band desynchronization reflects uncertainty in effector selection during motor planning
Authors: van Helvert Milou J.L. , Wijdenes Leonie Oostwoud , Geerligs Linda , Medendorp W. Pieter 
Published: April 2021

AbstractWhile beta-band activity during motor planning is known to be modulated by uncertainty about where to act, less is known about its modulations to uncertainty about how to act. To investigate this issue, we recorded oscillatory brain activity with EEG while human participants (n = 17) performed a hand choice reaching task. The reaching hand was either predetermined or of participants’ choice, and the target was close to one of the two hands or at about equal distance from both. To measure neural activity in a motion-artifact-free time window, the location of the upcoming target was cued 1000-1500 ms before the presentation of the target, whereby the cue was valid in 50% of trials. As evidence for motor planning during the cueing phase, behavioral observations showed that the cue affected later hand choice. Furthermore, reaction times were longer in the choice than in the predetermined trials, supporting the notion of a competitive process for hand selection. Modulations of beta-band power over central cortical regions, but not alpha-band or theta-band power, were in line with these observations. During the cueing period, reaches in predetermined trials were preceded by larger decreases in beta-band power than reaches in choice trials. Cue direction did not affect reaction times or beta-band power, which may be due to the cue being invalid in 50% of trials, retaining effector uncertainty during motor planning. Our findings suggest that effector uncertainty, similar to target uncertainty, selectively modulates beta-band power during motor planning.New & NoteworthyWhile reach-related beta-band power in central cortical areas is known to modulate with the number of potential targets, here we show, using a cueing paradigm, that the power in this frequency band, but not in the alpha or theta-band, is also modulated by the uncertainty of which hand to use. This finding supports the notion that multiple possible effector-specific actions can be specified in parallel up to the level of motor preparation.
Wnt-dependent activation of ERK mediates repression of chondrocyte fate during calvarial development
Authors: Ibarra Beatriz , Machen Cody , Atit Radhika P. 
Published: April 2021

AbstractWnt signaling regulates cell fate decisions in diverse contexts during development, and loss of Wnt signaling in the cranial mesenchyme results in a robust and binary cell fate switch from cranial bone to ectopic cartilage. The Extracellular signal-regulated protein kinase 1 and 2 (ERK1/2) and Wnt signaling pathways are activated during calvarial osteoblast cell fate selection. Here, we test the hypothesis that ERK signaling is a mediator of Wnt-dependent cell fate decisions in the cranial mesenchyme. First, we show that loss ofErk1/2 in the cranial mesenchyme results in a diminished domain of osteoblast marker expression and increased expression of cartilage fate markers and ectopic cartilage formation in the frontal bone primordia. Second, we show that mesenchyme Wnt/β-catenin signaling andWntlessare required for ERK activation in calvarial osteoblasts. Third, we demonstrate that Wnt and ERK signaling pathways function together to repress Sox9 expression in mouse cranial mesenchyme. Our results demonstrate a link between the Wnt and ERK signaling pathways in regulating lineage selection in a subset of calvarial cells and provide new insights into Wnt-dependent cell fate decisions.