bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rab11 suppresses neuronal stress signaling by localizing Dual leucine zipper kinase to axon terminals for protein turnover
Authors: Kim Seungmi , Quagraine Yaw , Singh Monika , Kim Jung Hwan 
Published: April 2023

SummaryDual Leucine Zipper Kinase (DLK) mediates multiple neuronal stress responses, and its expression levels are constantly suppressed to prevent excessive stress signaling. We found that Wallenda (Wnd), theDrosophilaortholog of DLK, is highly enriched in the axon terminals ofDrosophilasensory neurons in vivo and that this subcellular localization is necessary for Highwire-mediated Wnd protein turnover under normal conditions. Our structure-function analysis found that Wnd palmitoylation is essential for its axon terminal localization. Palmitoylation-defective Wnd accumulated in neuronal cell bodies, exhibited dramatically increased protein expression levels, and triggered excessive neuronal stress responses. Defective intracellular transport is implicated in neurodegenerative conditions. Comprehensive dominant-negative Rab protein screening identified Rab11 as an essential factor for Wnd localization in axon terminals. Consequently,Rab11loss-of-function increased the protein levels of Wnd and induced neuronal stress responses. Inhibiting Wnd activity significantly ameliorated neuronal loss and c-Jun N-terminal kinase signaling triggered byRab11loss-of-function. Taken together, these suggest that DLK proteins are constantly transported to axon terminals for protein turnover and a failure of such transport can lead to neuronal loss. Our study demonstrates how subcellular protein localization is coupled to protein turnover for neuronal stress signaling.HighlightsWnd is highly enriched in axon terminals.Wnd protein turnover by Hiw is restricted in the axon terminals.Protein palmitoylation of Wnd and Rab11 activity is essential for Wnd axonal localization.Rab11mutations and defective Wnd palmitoylation impair Wnd protein turnover leading to increased Wnd protein levels and neuronal loss.Inhibiting Wnd activity mitigates neuronal stress response caused byRab11loss-of-function.
An efficient induction method for human spinal lower motor neurons and high-throughput image analysis at the single cell level
Authors: Setsu Selena , Morimoto Satoru , Nakamura Shiho , Ozawa Fumiko , Tomari Yukihide , Okano Hideyuki 
Published: April 2023

SummaryThis study presents a newly developed method to rapidly and efficiently induce human spinal lower motor neurons (LMNs) from induced pluripotent stem cells (iPSCs) for elucidation of the amyotrophic lateral sclerosis (ALS) pathomechanism and drug screening. Previous methods had several limitations such as poor efficiency and low purity of LMN induction and labor intensiveness of the induction and evaluation procedures. Our new protocol achieved nearly 80% induction efficiency in only 2 weeks by combining a small molecule-based approach and transduction of transcription factors. To overcome cellular heterogeneity, we analyzed morphology and viability of iPSC-derived LMNs on a cell-by-cell basis using time-lapse microscopy and machine learning, thus establishing a highly accurate pathophysiological evaluation system. Our rapid, efficient, and simplified protocol and single cell-based evaluation method allow the conduct of large-scale analysis and drug screening using iPSC-derived motor neurons.
DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements
Authors: Chandrashekar Pramod Bharadwaj , Chen Hai , Lee Matthew , Ahmadinejad Navid , Liu Li 
Published: April 2023

AbstractGene transcription is an essential process involved in all aspects of cellular functions with significant impact on biological traits and diseases. This process is tightly regulated by multiple elements that co-operate to jointly modulate the transcription levels of target genes. To decipher the complicated regulatory network, we present a novel multi-view attention-based deep neural network that models the relationship between genetic, epigenetic, and transcriptional patterns and identifies co-operative regulatory elements (COREs). We applied this new method, named DeepCORE, to predict transcriptomes in 25 different cell lines, which outperformed the state-of-the-art algorithms. Furthermore, DeepCORE translates the attention values embedded in the neural network into interpretable information, including locations of putative regulatory elements and their correlations, which collectively implies COREs. These COREs are significantly enriched with known promoters and enhancers. Novel regulatory elements discovered by DeepCORE showed epigenetic signatures consistent with the status of histone modification marks.
Dietary fibers benefits on glucose homeostasis require type 2 conventional dendritic cells in mice fed a high-fat diet
Authors: Gélineau Adélaïde , Marcelin Geneviève , Ouhachi Melissa , Dussaud Sébastien , Voland Lise , Baba Ines , Rouault Christine , Yvan-Charvet Laurent , Clément Karine , Tussiwand Roxane , Huby Thierry , Gautier Emmanuel L. 
Published: April 2023

ABSTRACTDiet composition impacts metabolic health and is now recognized to shape the immune system, especially in the intestinal tract. Nutritional imbalance and increased caloric intake are induced by high-fat diet (HFD) in which lipids are enriched at the expense of dietary fibers. Such nutritional challenge alters glucose homeostasis as well as intestinal immunity. Here, we observed that short-term HFD induced dysbiosis, glucose intolerance and decreased intestinal RORγt+CD4 T cells, including peripherally-induced Tregs and IL17-producing (Th17) T cells. However, dietary fiber supplementation of HFD-fed animals was sufficient to maintain RORγt+CD4 T cell subsets and microbial species known to induce them, alongside having a beneficial impact on glucose tolerance. Dietary fiber-mediated normalization of Th17 cells and amelioration of glucose handling required the cDC2 dendritic cell subset in HFD-fed animals, while IL-17 neutralization limited fibers impact on glucose tolerance. Overall, we uncover a novel and pivotal role of cDC2 in the control of the immune and metabolic effects of dietary fibers in the context of HFD feeding.
Radical fringe facilitates NOTCH1 and JAG1cisinteractions to sustain Hematopoietic stem cell fate
Authors: Thambyrajah Roshana , Maqueda Maria , Neo Wen Hao , Imbach Kathleen , Guillen Yolanda , Grases Daniela , Fadlullah Zaki , Gambera Stefano , Matteini Francesca , Wang Xiaonan , Calero-Nieto Fernando J. , Esteller Manel , Florian Maria Carolina , Porta Eduard , Benedito Rui , Göttgens Berthold , Lacaud Georges , Espinosa Lluis , Bigas Anna 
Published: April 2023

SummaryHematopoietic stem cells (HSCs) develop within a short time window from the hemogenic endothelium in the aorta- gonads-and mesonephros (AGM) region during embryonic development. The first HSCs reside within Intra-aortic hematopoietic clusters (IAHC) along with hematopoietic progenitors (HPC). The signalling mechanisms that divert HSCs from HPCs are unknown. Notch signaling is essential for arterial specification, IAHC formation and HSC activity, but current studies on how Notch drives these different fates are inconsistent. To determine the role of Notch in the specification of hemogenic endothelium, HSC and/or HPCs, we extensively analyzed Notch dynamics in the period of HSC generation. We defined the expression pattern of Notch signalling molecules at the gene and protein level and established a molecular mechanism that reconcile previous studies demonstrating the loss of HSC activity in NOTCH1, JAG1 and RBPJ null mutants, the enhanced HSC generation by blocking specific Notch activities or the abrogation of emerging HSCs by high Notch activation. We now demonstrate that Notch activity is highest in a subset of Gfi1+ hemogenic endothelial cells and is gradually lost with HSC maturation. We uncover that the HSC phenotype is maintained through loss of Notch activity due to increasing levels of NOTCH1 and JAG1 interactions on the surface of the same cell (cis) that renders the NOTCH1 receptor from being activated. Forcing activation of the NOTCH1 receptor in IAHC cells activates a hematopoietic differentiation program and supports acis-inhibitory function for JAG1 and NOTCH1. Furthermore, we demonstrate that thiscis-inhibitory interaction is enabled by RADICAL FRINGE (RFNG), a glycosyltransferase that enhances the affinity of NOTCH1 to JAG1 incis. Finally, our results indicate that NOTCH1-JAG1cis-inhibition is necessary for preserving the HSC phenotype in the hematopoietic clusters of the aorta.
Pharmacological inhibition of CLK2 activates YAP by promoting alternative splicing of AMOTL2
Authors: Bulos Maya L. , Grzelak Edyta M. , Li-Ma Chloris , Chen Emily , Hull Mitchell , Johnson Kristen A. , Bollong Michael J. 
Published: April 2023

AbstractYes-associated protein (YAP), the downstream effector of the evolutionarily conserved Hippo pathway, promotes cellular proliferation and coordinates certain regenerative responses in mammals. Small molecule activators of YAP may therefore display therapeutic utility in treating disease states involving insufficient proliferative repair. From a high-throughput chemical screen of the comprehensive drug repurposing library ReFRAME, here we report the identification of SM04690, a clinical stage inhibitor of CLK2, as a potent activator of YAP driven transcriptional activity in cells. CLK2 inhibition promotes alternative splicing of the Hippo pathway protein AMOTL2, producing an exon-skipped gene product that can no longer associate with membrane-bound proteins, resulting in decreased phosphorylation and membrane localization of YAP. This study reveals a novel mechanism by which pharmacological perturbation of alternative splicing inactivates the Hippo pathway and promotes YAP dependent cellular growth.
Selective Inhibition of Facilitative Glucose Transporter 1 Improves Ultrafiltration Efficiency in Experimental Peritoneal Dialysis
Authors: Martus Giedre , Siddhuraj Premkumar , Erjefält Jonas S. , Lindström Martin , Bergling Karin , Öberg Carl M. 
Published: April 2023

AbstractLocal and systemic side-effects of glucose remain major limitations of peritoneal dialysis (PD). Glucose transport during PD is thought to occur via inter-endothelial pathways, but recent data indicated that some glucose is transferred via facilitative glucose channels. Here we used BAY-876, a potent and highly selective blocker of facilitative glucose channel 1 (GLUT1), in an experimental rat model of PD using either 1.5% or 2.3% glucose fluid in a 1-h dwell. We also sought to elucidate whether diffusion of radiolabeled [18F]-deoxyglucose in the opposite direction (plasma → dialysate) is also lowered by selective/non-selective GLUT inhibition. Results show that selective GLUT1 inhibition markedly improved UF and enhanced the sodium dip, but no alterations in glucose transport or [18F]-deoxyglucose diffusion could be detected. Non-selective GLUT-inhibition using phloretin showed similar improvements on water and sodium transport, but also markedly decreased diffusion capacity for [18F]-deoxyglucose. We conclude that selective GLUT1 inhibition improved the UF efficiency in terms of mL of water removed per gram glucose absorbed by almost 70% for 1.5% glucose, implicating a role for GLUT1 in glucose mediated osmotic water transport in PD. Selective inhibitors of facilitative glucose transporter 1 may be promising agents to improve UF efficacy in patients treated with PD.Translational StatementPeritoneal dialysis (PD) is limited by systemic and local glucose toxicity. Here we used a highly selective inhibitor of facilitative glucose channel 1 (GLUT1) in a rat model of PD, and show marked, direct improvements in osmotic water removal (UF) per gram glucose absorbed. Inhibitors of GLUT1 may provide marked improvements in UF in patients on PD.
Plant genome evolution in the genusEucalyptusdriven by structural rearrangements that promote sequence divergence
Authors: ferguson Scott , Jones Ashley , Murray Kevin , Andrew Rose , Schwessinger Benjamin , Borevitz Justin 
Published: April 2023

AbstractGenomes have a highly organised architecture (non-random organisation of functional and non-functional genetic elements within chromosomes) that is essential for many biological functions, particularly, gene expression and reproduction. Despite the need to conserve genome architecture, a surprisingly high level of structural variation has been observed within species. As species separate and diverge, genome architecture also diverges, becoming increasingly poorly conserved as divergence time increases. However, within plant genomes, the processes of genome architecture divergence are not well described. Here we use long-read sequencing andde novoassembly of 33 phylogenetically diverse, wild and naturally evolvingEucalyptusspecies, covering 1-50 million years of diverging genome evolution to measure genome architectural conservation and describe architectural divergence. The investigation of these genomes revealed that following lineage divergence genome architecture is highly fragmented by rearrangements. As genomes continue to diverge, the accumulation of mutations and subsequent divergence beyond recognition of rearrangements becomes the primary driver of genome divergence. The loss of syntenic regions also contribute to genome divergence, but at a slower pace than rearrangements. We hypothesise that duplications and translocations are potentially the greatest contributors toEucalyptusgenome divergence.
Effects of Repeat Test Exposure on Gait Parameters in Naïve Lewis Rats
Authors: Thurlow Nat A. , Chan Kiara M. , Yeater Taylor D. , Allen Kyle D. 
Published: April 2023

AbstractRodent gait analysis has emerged as a powerful, quantitative behavioral assay to characterize the pain and disability associated with movement-related disorders. In other behavioral assays, the importance of acclimation and the effect of repeated testing have been evaluated. However, for rodent gait analysis, the effects of repeated gait testing and other environmental factors have not been thoroughly characterized. In this study, fifty-two naïve male Lewis rats ages 8 to 42 weeks completed gait testing at semi-random intervals for 31 weeks. Gait videos and force plate data were collected and processed using a custom MATLAB suite to calculate velocity, stride length, step width, percentage stance time (duty factor), and peak vertical force data. Exposure was quantified as the number of gait testing sessions. Linear mixed effects models were used to evaluate the effects of velocity, exposure, age, and weight on animal gait patterns. Relative to age and weight, repeated exposure was the dominant parameter affecting gait variables with significant effects on walking velocity, stride length, fore and hind limb step width, fore limb duty factor, and peak vertical force. From exposure 1 to 7, average velocity increased by approximately 15 cm/s. Together, these data indicate arena exposure had large effects on gait parameters and should be considered in acclimation protocols, experimental design, and subsequent data analysis of rodent gait data.
Dextromethorphan inhibits collagen transport in the endoplasmic reticulum eliciting an anti-fibrotic response inex-vivoandin vitromodels of pulmonary fibrosis
Authors: Khan Muzamil M , Zukowska Joanna , Jung Juan , Galea George , Tuechler Nadine , Halavatyi Aliaksandr , Tischer Christian , Haberkant Per , Stein Frank , Jung Ferris , Landry Jonathan , Khan Arif M. , Oorschot Viola , Becher Isabelle , Neumann Beate , Muley Thomas , Winter Hauke , Duerr Julia , Mall Marcus A , Savitski Mikhail , Pepperkok Rainer 
Published: April 2023

AbstractExcessive deposition of fibrillar collagen in the interstitial extracellular matrix (ECM) of human lung tissue causes fibrosis, which can ultimately lead to organ failure. Despite our understanding of the molecular mechanisms underlying the disease, a cure for pulmonary fibrosis has not yet been found. In this study, we screened an FDA-approved drug library containing 712 drugs and found that Dextromethorphan (DXM), a cough expectorant, significantly reduces the amount of excess fibrillar collagen deposited in the ECM inin-vitrocultured primary human lung fibroblasts (NHLF) andex-vivocultured human precision-cut lung slice (hPCLS) models of lung fibrosis. Reduced extracellular fibrillar collagen levels in the ECM upon DXM treatment are due to a reversible trafficking inhibition of collagen type I (COL1) in the endoplasmic reticulum (ER) in TANGO1 and HSP47 positive structures. Mass spectrometric analysis shows that DXM causes hyper-hydroxylation of proline and lysine residues on Collagen (COL1, COL3, COL4, COL5, COL7, COL12) and Latent-transforming growth factor beta-binding protein (LTBP1 and LTBP2) peptides coinciding with their secretion block. In addition, thermal proteome profiling of cells treated with DXM shows increased thermal stability of prolyl-hydroxylases such as P3H2, P3H3, P3H4, P4HA1 and P4HA2, suggesting a change in activity. Transcriptome analysis of pro-fibrotic stimulated NHLFs and hPCLS upon DXM treatment showed activation of an anti-fibrotic program via regulation of pathways such as those involved in the MMP-ADAMTS axis, WNT, and fibroblast-to-myofibroblast differentiation. Taken together, the data obtained from both in-vitro and ex-vivo models of fibrogenesis show that Dextromethorphan has potent anti-fibrotic activity by efficient inhibition of COL1 membrane trafficking in the ER.
S2′ cleavage site plays a decisive role in expansion of Vero cell tropism by infectious bronchitis virus HV80, with Q855H promoting cell-to-cell fusion
Authors: Jiang Yi , Cheng Xu , Gao Mingyan , Dou Xinhong , Yu Yan , Shen Haiyu , Tang Mengjun , Zhou Sheng , Peng Daxin 
Published: April 2023

ABSTRACTInfectious bronchitis virus (IBV) has restricted cell tropism. Apart from the Beaudette strain, other IBVs cannot infect mammalian cell lines. The limited cell tropism of other IBVs has hindered the development of IBV vaccines and research on mechanisms of IBV infection. In a previous study, a new Vero-cell-adapted strain HV80 was obtained via serial chicken embryo and cell passaging of strain H120 and 17 mutations leading to amino acid substitutions occurred in replication gene 1a, S gene and E gene. This study, we constructed recombinants that expressed chimeric S glycoprotein, S1 or S2 subunit of strain H120, and demonstrated that mutations in S2 subunit were related to the Vero cell adaption of strain HV80. With a genome backbone of strain HV80 or H120, and expression of chimeric S2′ cleavage site of H120 or HV80, two recombinants demonstrated that the RRRR690/S motif at the S2′ cleavage site played a key role in Vero cell adaption of strain HV80. Another six amino acid substitutions in the S2 subunit of the recombinants showed that F692V enhanced the capability of invasion of HV80 strain, and Q855H induced the formation of syncytia. A transient transfection assay demonstrated different mechanisms for virus-to-cell fusion and cell-to-cell fusion induced by S glycoprotein. The PRRR690/S motif at the S2′ cleavage site could be activated by proteases in the process of cell-to-cell fusion, while H855Q substitution did not affect the cell invasion of HV80, but hindered the cell-to-cell fusion by blocking activation of the S2′ cleavage site.IMPORTANCEInfectious bronchitis is an acute respiratory disease that has caused large economic losses to the poultry industry. As a member of the gamma-coronaviruses, the restricted cell tropism of infectious bronchitis virus (IBV) limits the development of cellular vaccines and research on infection mechanisms. As a strain that can replicate effectively in mammalian cell lines, studies of HV80’s adaptive mechanisms point a way for engineering other IBVs for adaptation in mammalian cell lines. In our study, different recombinants were constructed by reverse genetic techniques, and demonstrated the different mechanism between virus-to-cell and cell-to-cell fusion induced by HV80 S glycoprotein. The acquisition of a highly efficient S2′ cleavage site enabled the virus to invade Vero cells. The Q855H substitution played a key role in cell-to-cell fusion, and provided a more efficient model of infection in Vero cells. Our study provides new theoretical insights into mechanisms of IBV adaptation in mammalian cell lines.
Viral impacts on microbial activity and biogeochemical cycling in a seasonally anoxic freshwater lake
Authors: Tran Patricia Q. , Bachand Samantha C. , Peterson Benjamin , He Shaomei , McMahon Katherine , Anantharaman Karthik 
Published: April 2023

AbstractMicrobial biogeochemical cycling relies on alternative electron acceptors when oxygen is unavailable, yet the role of viruses (bacteriophages) in these processes is understudied. We investigated how seasonal anoxia impacts viral and microbial biogeochemical cycling, by using paired total metagenomes, viromes, and metatranscriptomes, that were collected weekly. Stratification and anoxia drove microbial community composition, but dataset origin impacted the interpretation of viral community structure, activity, and function. Importantly, taxa abundance did not correlate with activity for both microbes and viruses. We identified virus-host linkages for 116 phages across 55 distinct hosts, many of which expressed genes for aerobic methane oxidation, nitrogen fixation, denitrification, and sulfate reduction. Overall, this work demonstrates the breadth and dynamics of virus-host interactions in mediating biogeochemistry. Additionally, we propose that viral community detection, functional potential, and activity are sensitive to pre-sequencing decisions, which must be kept in mind when interpreting genomic data in a biologically meaningful way.
Characterization of self-dyed silk yarn with Rhodamine B dye for fashion applications
Authors: Tran Uyen Nguyen Tu , Phan Hung Ngoc , Hoang Thao Thanh , Le Nu Thi Hong , Bui Huong Mai 
Published: April 2023

PurposeThe textile industry has consumed large quantities of water and discharged large volumes of wastewater in the dyeing process. The study aims to characterize self-dyed silk with Rhodamine B (RhB) for fashion applications to reduce textile hazards to the environment and increase the added value of silk.Design/methodology/approachBombyx mori was fed with RhB-colored mulberry leaves (1500 ppm). The effects of self-dyeing were investigated via color strength K/S, Fourier-transform infrared spectroscopy (FT-IR), scanning electron microscope, X-ray diffraction, tensile strength, color fastness to washing, rubbing, perspiration and light.FindingsSelf-dyed silk possesses effective coloration and impressive color fastness (4–5/5), higher crystalline index (CrI) (73.26 ± 2.28%), less thermal stability and tenacity, slight change in amino acid composition compared with the pristine and no existence of harmful aromatic azo amines and arylamine salts.Practical implicationsThe application of self-dyed silk with RhB dye has expanded new technology into fashion industry, contributing partly to economic growth and adding value to silk in the global supply chain. Besides, the self-dyeing will yield practical values in the reduction of dyeing discharge in textile industry.Originality/valueSelf-dyed silk was characterized for textile applications in comparison with pristine silk in terms of color strength and fastness as well as determined its polymeric properties relating to crystallinity, morphology, chemical composition, tensile properties and thermal stability which have not been investigated before.