bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional interplay between Mediator and RSC chromatin remodeling complex controls nucleosome-depleted region maintenance at promoters
Authors: André Kévin M. , Aiach Nathalie Giordanengo , Martinez-Fernandez Veronica , Zeitler Leo , Goldar Arach , Werner Michel , Wilkes Cyril Denby , Soutourina Julie 
Published: September 2022

SummaryChromatin organization is crucial for the transcriptional regulation in eukaryotes. Mediator is an essential and conserved coactivator thought to act in concert with chromatin regulators. However, it remains largely unknown how their functions are coordinated. Here, we provide evidence in the yeast Saccharomyces cerevisiae that Mediator establishes physical contact with RSC (Remodels the Structure of Chromatin), a conserved and essential chromatin remodeling complex that is crucial for nucleosome-depleted region (NDR) formation. We determined the role of Mediator-RSC interaction in their recruitment, nucleosome occupancy and transcription on a genomic scale. Mediator and RSC co-localize on wide NDRs of promoter regions, and specific Mediator mutations affect nucleosome eviction and TSS-associated +1 nucleosome stability. This work shows that Mediator contributes to RSC remodeling function to shape NDRs and maintain chromatin organization on promoter regions. It will help in our understanding of transcriptional regulation in the chromatin context relevant for severe diseases.
Deficiency in the cell-adhesion moleculedscaml1impairs hypothalamic CRH neuron development and perturbs normal neuroendocrine stress axis function
Authors: Ma Manxiu , Brunal Alyssa A. , Clark Kareem C. , Studtmann Carleigh , Stebbins Katelyn , Higashijima Shin-ichi , Pan Y. Albert 
Published: September 2022

ABSTRACTThe corticotropin-releasing hormone (CRH)-expressing neurons in the hypothalamus are critical regulators of the neuroendocrine stress response pathway, known as the hypothalamic-pituitary-adrenal (HPA) axis. As developmental vulnerabilities of CRH neurons contribute to stress-associated neurological and behavioral dysfunctions, it is critical to identify the mechanisms underlying normal and abnormal CRH neuron development. Using zebrafish, we identifiedDown syndrome cell adhesion molecule like-1 (dscaml1) as an integral mediator of CRH neuron development and necessary for establishing normal stress axis function. Indscaml1mutant animals, hypothalamic CRH neurons had highercrhb(the CRH homolog in fish) expression, increased cell number, and reduced cell death compared to wild-type controls. Physiologically,dscaml1mutant animals had higher baseline stress hormone (cortisol) levels and attenuated responses to acute stressors. Together, these findings identifydscaml1as an essential factor for stress axis development and suggest that HPA axis dysregulation may contribute to the etiology of humanDSCAML1-linked neuropsychiatric disorders.
Germ-stem cells and oocyte production in the Honeybee Queen Ovary
Authors: Cullen Georgia , Gilligan Joshua B. , Guhlin Joseph G. , Dearden Peter K. 
Published: September 2022

AbstractUnderstanding the reproduction of honeybee queens is crucial to support populations of this economically important insect. Here we examine the structure of the honeybee ovary to determine the nature of the germ-stem cells in the ovary. Using a panel of marker genes that mark somatic or germ-line tissue in other insects we determine which cells in the honeybee ovary are somatic and which germline. We examine patterns of cell division, and demonstrate that, unlike Drosophila, there are no single germ-line stem cells that provide the germ-line in honeybees. Germ-line stem cells are clustered in groups of 8 cells, joined by a polyfusome, and collections of these, in each ovariole, maintain the germ-line during reproduction. We also show that these 8-cell clusters can divide, and that their division occurs such that the numbers of germ-line stem cells are relatively constant over the reproductive life of queen honeybees. This information helps us to understand the diversity of structures in insects reproduction, and provide information to better support honeybee reproduction.
Loss of hepatic phosphoenolpyruvate carboxykinase 1 dysregulates metabolic responses to acute exercise but enhances adaptations to exercise training in mice
Authors: Rome Ferrol I. , Shobert Gregory L. , Voigt William C. , Stagg David B. , Puchalska Patrycja , Burgess Shawn C. , Crawford Peter A. , Hughey Curtis C. 
Published: September 2022

ABSTRACTAcute exercise increases liver gluconeogenesis to supply glucose to working muscle. Concurrently, elevated liver lipid breakdown fuels the high energetic cost of gluconeogenesis. This functional coupling between liver gluconeogenesis and lipid oxidation has been proposed to underlie the ability of regular exercise to enhance liver mitochondrial oxidative metabolism and decrease liver steatosis in individuals with non-alcoholic fatty liver disease. Herein we tested whether repeated bouts of increased hepatic gluconeogenesis are necessary for exercise training to lower liver lipids. Experiments used diet-induced obese mice lacking hepatic phosphoenolpyruvate carboxykinase 1 (KO) to inhibit gluconeogenesis and wild type (WT) littermates. 2H/13C metabolic flux analysis quantified glucose and mitochondrial oxidative fluxes in untrained mice at rest and during acute exercise. Circulating and tissue metabolite levels were determined during sedentary conditions, acute exercise, and refeeding post-exercise. Mice also underwent six weeks of treadmill running protocols to define hepatic and extrahepatic adaptations to exercise training. Untrained KO mice were unable to maintain euglycemia during acute exercise resulting from an inability to increase gluconeogenesis. Liver triacylglycerides were elevated following acute exercise and circulating β-hydroxybutyrate was higher during post-exercise refeeding in untrained KO mice. In contrast, exercise training prevented liver triacylglyceride accumulation in KO mice. This was accompanied by pronounced increases in indices of skeletal muscle mitochondrial oxidative metabolism in KO mice. Together, these results show that hepatic gluconeogenesis is dispensable for exercise training to reduce liver lipids. This may be due to responses in ketone body metabolism and/or metabolic adaptations in skeletal muscle to exercise.
Post-Cyclase Skeletal Rearrangements in Plant Triterpenoid Biosynthesis by a Pair of Branchpoint Isomerases
Authors: Chuang Ling , Liu Shenyu , Franke Jakob 
Published: September 2022

AbstractTriterpenoids possess potent biological activities, but their polycyclic skeletons are challenging to synthesise. In biochemistry, the skeletal diversity of plant triterpenoids is normally generated by oxidosqualene cyclases and remains unaltered during subsequent tailoring steps. In contrast, we report here enzyme-mediated skeletal rearrangements after the initial cyclisation, controlling the pathway bifurcation between different plant triterpenoid classes. Using a combination of bioinformatics, heterologous expression in plants and chemical analyses, we identified a cytochrome P450 monooxygenase and two isomerases for this process. The two isomerases share one epoxide substrate but generate two different rearrangement products, one containing a cyclopropane ring. Our findings reveal a new strategy how triterpenoid skeletal diversity is generated in Nature and are crucial for the biotechnological production of limonoid, quassinoid, isoprotolimonoid and glabretane triterpenoids.
Proteome dynamics during transition from exponential to stationary phase under aerobic and anaerobic conditions in yeast
Authors: den Ridder Maxime , van den Brandeler Wiebeke , Altiner Meryem , Daran-Lapujade Pascale , Pabst Martin 
Published: September 2022

ABSTRACTThe yeast Saccharomyces cerevisiae is a widely used eukaryotic model organism and a promising cell factory for industry. However, despite decades of research, the regulation of its metabolism is not yet fully understood, and its complexity represents a major challenge for engineering and optimising biosynthetic routes. Recent studies have demonstrated the potential of resource and proteomic allocation data in enhancing models for metabolic processes. However, comprehensive and accurate proteome dynamics data that can be used for such approaches are still very limited. Therefore, we performed a quantitative proteome dynamics study to comprehensively cover the transition from exponential to stationary phase for both aerobically and anaerobically grown yeast cells. The combination of highly controlled reactor experiments, biological replicates and standardised sample preparation procedures ensured reproducibility and accuracy. Additionally, we selected the CEN.PK lineage for our experiments because of its relevance for both fundamental and applied research. Together with the prototrophic, standard haploid strain CEN.PK113-7D, we also investigated an engineered strain with genetic minimisation of the glycolytic pathway, resulting in the quantitative assessment of over 1700 proteins across 54 proteomes. These proteins account for nearly 40% of the overall yeast proteome and approximately 99% of the total protein biomass. The anaerobic cultures showed remarkably less proteome-level changes compared to the aerobic cultures, during transition from the exponential to the stationary phase as a consequence of the lack of the diauxic shift in the absence of oxygen. These results support the notion that anaerobically growing cells lack time and resources to adapt to changes in the environment. This proteome dynamics study constitutes an important step towards better understanding of the impact of glucose exhaustion and oxygen on the complex proteome allocation process in yeast. Finally, the established proteome dynamics data provide a valuable resource for the development of resource allocation models as well as for metabolic engineering efforts.
Conformational dynamics and target-dependent myristoyl switch of calcineurin B homologous protein 3
Authors: Becker Florian , Fuchs Simon , Refisch Lukas , Drepper Friedel , Bildl Wolfgang , Schulte Uwe , Liang Shuo , Heinicke Jonas Immanuel , Hansen Sierra C. , Kreutz Clemens , Warscheid Bettina , Fakler Bernd , Mymrikov Evgeny V. , Hunte Carola 
Published: September 2022

AbstractCalcineurin B homologous protein 3 (CHP3) is an EF-hand Ca2+-binding protein involved in regulation of cancerogenesis, cardiac hypertrophy and neuronal development via interactions with sodium/proton exchangers (NHEs) and signalling proteins. CHP3 binds Ca2+with micromolar affinity providing the basis to respond to intracellular Ca2+signals. Ca2+binding and myristoylation are important for CHP3 function but the underlying molecular mechanism remained elusive. Here, we show that Ca2+binding and myristoylation independently affect conformational dynamics and functions of human CHP3. Ca2+binding increased flexibility and hydrophobicity of CHP3 indicative of an open conformation. CHP3 in open Ca2+-bound conformation had higher affinity for NHE1 and associated stronger with lipid membranes compared to the closed Mg2+-bound conformation. Myristoylation enhanced flexibility of CHP3 and decreased its affinity to NHE1 independently of the bound ion, but did not affect its binding to lipid membranes. The data exclude the proposed Ca2+-myristoyl switch for CHP3. Instead, they document a Ca2+-independent exposure of the myristoyl moiety induced by binding of the target peptide to CHP3 enhancing its association to lipid membranes. We name this novel regulatory mechanism “target-dependent myristoyl switch”. Taken together, the interplay of Ca2+binding, myristoylation and target binding allows for a context-specific regulation of CHP3 functions.
DHHC3 mediated Cadm4 palmitoylation regulates myelination in CNS
Authors: Chang Yanli , Zhu Jiangli , Nie Chenchen , Lu Yajuan , Ren Fangjing , Cao Xize , Li Juanjuan , Wang Changhong , Yang Chenyu , Li Tianhan , Liang Yinming , Qi Shiqian , Kang Xiaohong , Kong Eryan 
Published: September 2022

AbstractCell adhesion molecule 4 (Cadm4) plays important roles on plasma membrane (PM) to regulate myelin formation and the downregulation of Cadm4 is a prominent feature in many demyelination diseases. However, how Cadm4 maintains its level on PM has been elusive. Here, we identify that Cadm4 is palmitoylated at cysteine-347 (C347) and palmitoylation regulates the stable localization of Cadm4 on PM, as blocking palmitoylation by mutating C347 into alanine (C347A) results in the dissociation of Cadm4 from PM and targeting for degradation. Intriguingly, blocking Cadm4 palmitoylation by introducing C347A (Cadm4-KI) causes myelin abnormalities in CNS, characterized by loss of myelination, myelin infoldings and hypermyelination. Moreover, it is uncovered that Cadm4 palmitoylation is catalyzed by DHHC3, reducing Cadm4 palmitoylation by the deletion of DHHC3 renders the redistribution of Cadm4 for degrading. Consistently, the genetic deletion of DHHC3 leads to downregulated Cadm4 palmitoylation and defects in CNS myelination, virtually phenocopies that of the Cadm4-KI mice. Our findings suggest a mechanism that the stable localization of Cadm4 on PM regulated by protein palmitoylation is vital for myelination in CNS.
IL-17 signalling is critical for controlling subcutaneous adipose tissue dynamics and parasite burden during chronic Trypanosoma brucei infection
Authors: Sinton Matthew C. , Chandrasegaran Praveena , Capewell Paul , Cooper Anneli , Girard Alex , Ogunsola John , Perona-Wright Georgia , Ngoyi Dieudonné M. , Kuispond Nono , Bucheton Bruno , Camara Mamadou , Kajimura Shingo , Bénézech Cécile , MacLeod Annette , Quintana Juan F. 
Published: September 2022

SummaryIn the skin,Trypanosoma bruceicolonises the subcutaneous white adipose tissue (scWAT) and harbours a pool of parasites that are proposed to be competent for forward transmission. The interaction between parasites, adipose tissue, and the local immune system is likely to drive the adipose tissue wasting and weight loss observed in cattle and humans infected withT. brucei. However, mechanistically, the events leading to scWAT wasting are not fully understood. Here, using several complementary approaches, including mass cytometry by time of flight, bulk and single cell transcriptomics, andin vivogenetic models, we found thatT. bruceiinfection drives local expansion of several IL-17A-producing cells in the murine WAT, including TH17 and Vγ6+T cells. We also found that global IL-17 deficiency, or mice lacking IL-17 receptor expression exclusively in adipocytes, were protected from infection-induced WAT wasting and weight loss. Unexpectedly, we found that abrogation of IL-17 signalling in adipocytes results in a significant accumulation ofDpp4+Pi16+interstitial preadipocytes and a higher burden of extravascular parasites in the WAT, highlighting a critical role for IL-17 signalling in controlling preadipocyte fate, scWAT tissue dynamics, and local parasite burden. Taken together, our study highlights the central role of adipocyte IL-17 signalling in controlling WAT responses to infection, suggesting that adipocytes are a critical coordinator of the tissue dynamics and immune responses toT. bruceiinfection.
Higher levels of narrativity lead to similar patterns of posterior EEG activity across individuals
Authors: Dini Hossein , Simonetti Aline , Bigne Enrique , Bruni Luis Emilio 
Published: September 2022

AbstractThe focus of cognitive and psychological approaches to narrative has not so much been on the elucidation of important aspects of narrative, but rather on using narratives as tools for the investigation of higher order cognitive processes elicited by narratives (e.g., understanding, empathy, etc.). In this study, we work toward a scalar model of narrativity, which can provide testable criteria for selecting and classifying communication forms in their level of narrativity. We investigated whether being exposed to videos with different levels of narrativity modulates shared neural responses, measured by inter-subject correlation, and engagement levels. Thirty-two participants watched video advertisements with high-level and low-level of narrativity while their neural responses were measured through electroencephalogram. Additionally, participants’ engagement levels were calculated based on the composite of their self-reported attention and immersion scores. Results demonstrated that both calculated inter-subject correlation and engagement scores for high-level video ads were significantly higher than those for low-level, suggesting that narrativity levels modulate inter-subject correlation and engagement. We believe that these findings are a step toward the elucidation of the viewers’ way of processing and understanding a given communication artifact as a function of the narrative qualities expressed by the level of narrativity.
Flexible and open-source programs for quantitative image analysis in microbial ecology
Authors: Pasulka Alexis L. , Hood Jonathan F. , Michels Dana E. , Wright Mason D. 
Published: September 2022

AbstractEpifluorescence microscopy is an essential tool for obtaining reliable estimates of the abundance of marine microorganisms including viruses. However, computational analysis is required to gain consistent and quantitative data from digital microscopy images. Many imaging programs are proprietary and cost-prohibitive. The currently available free imaging programs are often platform specific and/or lack the flexibility to analyze microscopy images from natural samples, such as the planktonic environment, which can contain challenges such as debris and high background signals. Here we describe two MATLAB-based open-source image analysis programs that work across computer platforms and provide the tools to analyze a range of image types and cell sizes with a user-friendly interface. The Microbial Image Analysis (MiA) program aims to provide flexibility for the selection, identification, and quantification of cells that vary in size and fluorescence intensity within natural microbial communities. The Viral Image Analysis (ViA) program aims to provide an effective means for quantifying viral abundances from epifluorescence images as well as enumerating the intensity of a primary and secondary stain. In this paper, we provide an overview of the functionality of the MiA and ViA programs and highlight specific program features through several microbial image case studies.
Multi-scale observations of mangrove blue carbon fluxes; the NASA Carbon Monitoring System BlueFlux field campaign
Authors: Poulter Benjamin , Adams Frannie , Amaral Cibele , Barenblitt Abigail , Campbell Anthony , Charles Sean P. , Roman-Cuesta Rosa Maria , D’Ascanio Rocco , Delaria Erin , Doughty Cheryl , Fatoyinbo Temilola , Gewirtzman Jonathan , Hanisco Thomas F. , Hull Moshema , Kawa S. Randy , Hannun Reem , Lagomasino David , Lait Leslie , Malone Sparkle , Newman Paul , Raymond Peter , Rosentreter Judith , Thomas Nathan , Wolfe Glenn M. , Xiong Lin , Ying Qing , Zhang Zhen 
Published: September 2022

AbstractThe BlueFlux field campaign is supported by NASA’s Carbon Monitoring System (CMS) and will develop prototype blue carbon products to inform coastal carbon management. Blue carbon is included in carbon-dioxide removal actions proposed to reduce atmospheric CO2concentrations to mitigate climate change. Due to their high productivity and carbon storage, combined with historic losses and a wide-range of beneficial ecosystem services, the restoration and conservation of mangrove ecosystems features prominently in blue-carbon planning. The goal of BlueFlux is to carry out multi-scale measurements of CO2and CH4fluxes using chambers, flux towers, and aircraft and scale these to gridded products using space-based observations of forest structure and surface reflectance. The measurements cover gradients in disturbance, mainly from the history of hurricanes in the region that drive the dieback of mangroves and the formation of ‘ghost forests’. The fluxes of CH4emissions will be contrasted with CO2uptake to provide a more complete budget of radiative forcing and to understand the net climate benefits of blue carbon. BlueFlux demonstrates that quantifying the removals of CO2and emissions of CH4using a multi-scale approach can provide increased confidence in regional greenhouse-gas accounting, contribute to process-understanding, and help inform restoration and conservation efforts in the context of climate mitigation.
Base Editor-Mediated Large-Scale Screening of Functional Mutations in Bacteria for Industrial Phenotypes
Authors: Yuan Yaomeng , Liao Xihao , Li Shuang , Xing Xin-hui , Zhang Chong 
Published: September 2022

AbstractBase editing, the targeted introduction of point mutations into cellular DNA, holds promise for improving genome-scale functional genome screening to single-nucleotide resolution. Current efforts in prokaryotes, however, remain confined to loss-of-function screens using the premature stop codons-mediated gene inactivation library, which falls far short of fully releasing the potential of base editors. Here, we developed a base editor-mediated functional single nucleotide variant screening pipeline inE. coli. We constructed a library with 31,123 sgRNAs targeting 462 stress response-related genes inE. coli, and screened for adaptive mutations under isobutanol and furfural selective conditions. Guided by the screening results, we successfully identified several known and novel functional mutations. Our pipeline might be expanded to the optimization of other phenotypes or the strain engineering in other microorganisms.
Research on the laws of transition zone of non-deformation area for 90° V-bending forming process
Authors: Miah Md. Helal , Zhang Jianhua , Malhi Gurmail Singh 
Published: September 2022

Purpose
“V-bending” is the most commonly used bending process in which the sheet metal is pressed into a “V-shaped” die using a “V-shaped” punch to form a required angular bend. When the punch is removed after the operation, because of elastic recovery, the bent angle varies. This shape discrepancy is known as spring back which causes problems in the assembly of the component in the modern aerospace industry. Regarding the optimization of spring-back accuracy, this research will illustrate the laws of the transition area (TA) of the nondeformation area (NDA) during the 90° “V-shape” bending process.

Design/methodology/approach
According to the traditional “V-bending” process to optimize the spring-back accuracy, the bent sheets are divided into deformation area (DA) and NDA. For this reason, the traditional “V-bending” process may prolong error to optimize the spring-back accuracy because NDA has a certain amount of deformation, which the researcher always avoids. Firstly, bent sheets are divided into three parts in this research: DA, TA and NDA to avoid the distortion error in TA that are not considered in the NDA in traditional theory. Then, the stress and strain in the DA and TA were discussed during theoretical derivation and some hypotheses were proposed. In this research, the interval, position and distortion degree of the TA of the bending sheet are used by finite element analysis. Finally, V-shape bending tests for aluminum alloy at room temperature are used and labeled all the work pieces' TAs to realize the deformation amount in the TA.

Findings
The bending radius does not affect the range of the TA, it only changes the position of TA in the bending sheet. It is evident that the laws of TA were explored in the width direction and gradually changed from the inner layer to the outer layer based on the ratio of width and thickness of the bending plate/sheet.

Originality/value
In the modern aerospace industry, aircraft manufacturing technology must maintain high accuracy. This research has practical value in the 90° “V-shape” bending of metal sheets and the development of its spring-back accuracy.