bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reprogramming the metabolism of an acetogenic bacterium to homoformatogenesis
Authors: Moon Jimyung , Schubert Anja , Waschinger Lara M , Müller Volker 
Published: April 2023

Abstract
Methyl groups are abundant in anoxic environments and their utilization as carbon and energy sources by microorganisms involves oxidation of the methyl groups to CO2, followed by transfer of the electrons to an acceptor. In acetogenic bacteria, the electron acceptor is CO2 that is reduced to enzyme bound carbon monoxide, the precursor of the carboxyl group in acetate. Here, we describe the generation of a mutant of the acetogen Acetobacterium woodii in which the last step in methyl group oxidation, formate oxidation to CO2 catalyzed by the HDCR enzyme, has been genetically deleted. The mutant grew on glycine betaine as methyl group donor, and in contrast to the wild type, formed formate alongside acetate, in a 1:2 ratio, demonstrating that methyl group oxidation stopped at the level of formate and reduced electron carriers were reoxidized by CO2 reduction to acetate. In the presence of the alternative electron acceptor caffeate, CO2 was no longer reduced to acetate, formate was the only product and all the carbon went to formate. Apparently, acetogenesis was not required to sustain formatogenic growth. This is the first demonstration of a genetic reprogramming of an acetogen into a formatogen that grows by homoformatogenesis from methyl groups. Formate production from methyl groups is not only of biotechnological interest but also for the mechanism of electron transfer in syntrophic interactions in anoxic environments.
A bibliometric analysis of ferroptosis, necroptosis, pyroptosis, and cuproptosis in cancer from 2012 to 2022
Authors: Miao Yan-Dong , Quan Wuxia , Dong Xin , Gan Jian , Ji Cui-Feng , Wang Jiang-Tao , Zhang Fang 
Published: April 2023

AbstractThis study aims to visualize research hotspots and trends of “ferroptosis in cancer”, “necroptosis in cancer”, “pyroptosis in cancer”, and “cuproptosis in cancer” through a bibliometric analysis to facilitate understanding of future developments in basic and clinical research and to provide a new perspective on cancer treatment. From January 1, 2012 to October 31, 2022, in the field of “ferroptosis in cancer”, a total of 2467 organizations from 79 different countries published 3302 articles. 2274 organizations from 72 different countries published 2233 articles in the field of “ necroptosis in cancer”. 1366 institutions from 58 different countries contributed 1445 publications in the field of “pyroptosis in cancer”. In the field of “ cuproptosis in cancer”, the number of articles published in the last 10 years is relatively low, with a total of 109 articles published by 116 institutions from four different countries. In the field of “ferroptosis in cancer”, Tang Daolin had published 66 documents, ranked the first, while Dixon SJ is the most cited author, cited 3148 times; In the fields of “necroptosis in cancer”, Vandenabeele peter had published 35 papers and Degterev had been cited 995 times, ranked the first, respectively; Kanneganti thirumala-devi had published 24 papers, is the highest number of publications in the fields of “pyroptosis in cancer”, while Shi JJ was the most cited author with being cited 508 times. Both Huang Yan and Wang Tao published three papers and tied for first place and Tsvetkov p ranks first with being cited 107 times in “cuproptosis in cancer”. “Cell”, “Cell”, “Nature”, and “Science” was the most frequently co-cited journal on “ferroptosis in cancer”, “necroptosis in cancer”, “pyroptosis in cancer”, and “cuproptosis in cancer”, respectively. Further exploration of inhibitors of different Programmed cell death (PCD) and their targeted therapies are potential treatment options for cancer, but more direct clinical evidence as well as higher level clinical trials remain to be explored. Further clarification of the mechanisms of crosstalk between these PCDs may provide effective cancer treatments. And the role of different types of PCDs, especially the novel ones discovered, in cancer can be expected to remain a hot topic of research in the cancer field for quite some time to come.
Ferroptosis landscape in prostate cancer from molecular and metabolic perspective
Authors: Liang Jiaming , Liao Yihao , Wang Pu , Yang Kun , Wang Youzhi , Wang Keke , Zhong Boqiang , Zhou Diansheng , Cao Qian , Li Junbo , Zhao Yang , Jiang Ning 
Published: April 2023

AbstractProstate cancer is a major disease that threatens men’s health. Its rapid progression, easy metastasis, and late castration resistance have brought obstacles to treatment. It is necessary to find new effective anticancer methods. Ferroptosis is a novel iron-dependent programmed cell death that plays a role in various cancers. Understanding how ferroptosis is regulated in prostate cancer will help us to use it as a new way to kill cancer cells. In this review, we summarize the regulation and role of ferroptosis in prostate cancer and the relationship with AR from the perspective of metabolism and molecular pathways. We also discuss the feasibility of ferroptosis in prostate cancer treatment and describe current limitations and prospects, providing a reference for future research and clinical application of ferroptosis.
Trim-Away ubiquitinates and degrades lysine-less and N-terminally acetylated substrates
Authors: Kiss Leo , Rhinesmith Tyler , Luptak Jakub , Dickson Claire F. , Weidenhausen Jonas , Smyly Shannon , Yang Ji-Chun , Maslen Sarah L. , Sinning Irmgard , Neuhaus David , Clift Dean , James Leo C. 
Published: April 2023

AbstractTRIM proteins are the largest family of E3 ligases in mammals. They include the intracellular antibody receptor TRIM21, which is responsible for mediating targeted protein degradation during Trim-Away. Despite their importance, the ubiquitination mechanism of TRIM ligases has remained elusive. Here we show that while Trim-Away activation results in ubiquitination of both ligase and substrate, ligase ubiquitination is not required for substrate degradation. N-terminal TRIM21 RING ubiquitination by the E2 Ube2W can be inhibited by N-terminal acetylation, but this doesn’t prevent substrate ubiquitination nor degradation. Instead, uncoupling ligase and substrate degradation prevents ligase recycling and extends functional persistence in cells. Further, Trim-Away degrades substrates irrespective of whether they contain lysines or are N-terminally acetylated, which may explain the ability of TRIM21 to counteract fast-evolving pathogens and degrade diverse substrates.
Piezo2 regulates colonic mechanical sensitivity in a sex specific manner in mice
Authors: Madar Jonathan , Tiwari Namrata , Smith Cristina , Sharma Divya , Shen Shanwei , Elmahdi Alsiddig , Qiao Liya Y. 
Published: April 2023

AbstractThe mechanosensitive ion channel Piezo2 in mucosa and primary afferents transduces colonic mechanical sensation. Here we show that chemogenetic activation or nociceptor-targeted deletion of Piezo2 is sufficient to regulate colonic mechanical sensitivity in a sex dependent manner. Clozapine N-oxide-induced activation of Piezo2;hM3Dq-expressing sensory neurons evokes colonic hypersensitivity in male mice, and causes dyspnea in female mice likely due to effects on lung sensory neurons. Activation of Piezo2-expressing colonic afferent neurons also induces colonic hypersensitivity in male but not female mice. Piezo2 levels in nociceptive neurons are higher in female than in male mice. We also show that Piezo2 conditional deletion from nociceptive neurons increases body weight growth, slows colonic transits, and reduces colonic mechanosensing in female but not male mice. Piezo2 deletion blocks colonic hypersensitivity in male but not female mice. These results suggest that Piezo2 in nociceptive neurons mediates innocuous colonic mechanosensing in female mice and painful sensation in male mice, suggesting a sexual dimorphism of Piezo2 function in the colonic sensory system.
Controlling protein stability with SULI, a highly sensitive tag for stabilization upon light induction
Authors: Mao Miaowei , Qian Yajie , Zhang Wenyao , Zhou Siyu , Wang Zefeng , Chen Xianjun , Yang Yi 
Published: April 2023

AbstractOptogenetics tools for precise temporal and spatial control of protein abundance are valuable in studying diverse complex biological processes. In the present study, we engineer a monomeric tag of stabilization upon light induction (SULI) for yeast and zebrafish based on a single light-oxygen-voltage domain from Neurospora crassa. Proteins of interest fused with SULI are stable upon light illumination but are readily degraded after transfer to dark conditions. SULI shows a high dynamic range and a high tolerance to fusion at different positions of the target protein. Further studies reveal that SULI-mediated degradation occurs through a lysine ubiquitination-independent proteasome pathway. We demonstrate the usefulness of SULI in controlling the cell cycle in yeast and regulating protein stability in zebrafish, respectively. Overall, our data indicate that SULI is a simple and robust tool to quantitatively and spatiotemporally modulate protein levels for biotechnological or biomedical applications.
Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19
Authors: Yu Meng , Charles Afandi , Cagigi Alberto , Christ Wanda , Österberg Björn , Falck-Jones Sara , Azizmohammadi Lida , Åhlberg Eric , Falck-Jones Ryan , Svensson Julia , Nie Mu , Warnqvist Anna , Hellgren Fredrika , Lenart Klara , Arcoverde Cerveira Rodrigo , Ols Sebastian , Lindgren Gustaf , Lin Ang , Maecker Holden , Bell Max , Johansson Niclas , Albert Jan , Sundling Christopher , Czarnewski Paulo , Klingström Jonas , Färnert Anna , Loré Karin , Smed-Sörensen Anna 
Published: April 2023

AbstractEffective humoral immune responses require well-orchestrated B and T follicular helper (Tfh) cell interactions. Whether these interactions are impaired and associated with COVID-19 disease severity is unclear. Here, longitudinal blood samples across COVID-19 disease severity are analysed. We find that during acute infection SARS-CoV-2-specific circulating Tfh (cTfh) cells expand with disease severity. SARS-CoV-2-specific cTfh cell frequencies correlate with plasmablast frequencies and SARS-CoV-2 antibody titers, avidity and neutralization. Furthermore, cTfh cells but not other memory CD4 T cells, from severe patients better induce plasmablast differentiation and antibody production compared to cTfh cells from mild patients. However, virus-specific cTfh cell development is delayed in patients that display or later develop severe disease compared to those with mild disease, which correlates with delayed induction of high-avidity neutralizing antibodies. Our study suggests that impaired generation of functional virus-specific cTfh cells delays high-quality antibody production at an early stage, potentially enabling progression to severe disease.
Global scale analysis on the extent of river channel belts
Authors: Nyberg Björn , Henstra Gijs , Gawthorpe Rob L. , Ravnås Rodmar , Ahokas Juha 
Published: April 2023

AbstractRivers form channel belts that encompass the area of the river channel and its associated levees, bars, splays and overbank landforms. The channel belt is critical for understanding the physical river evolution through time, predicting river behavior and management of freshwater resources. To date, there is no global-scale, quantitative study of the extent of river channel belts. Here we show, based on a pattern recognition algorithm, the global surface area of channel belts at an approximate 1 km resolution is 30.5 × 105 km2, seven times larger than the extent of river channels. We find 52% of river channels associated with the channel belts have a multi-threaded planform with the remaining 48% being single-threaded by surface area. The global channel belt (GCB) datasets provide new methods for high-resolution global scale landform classifications and for incorporating the channel belt into flood mitigation, freshwater budgets, ecosystem accounting and biogeochemical analyses.
Evaluation of the methane paradox in four adjacent pre-alpine lakes across a trophic gradient
Authors: Ordóñez César , DelSontro Tonya , Langenegger Timon , Donis Daphne , Suarez Ena L. , McGinnis Daniel F. 
Published: April 2023

AbstractContrasting the paradigm that methane is only produced in anoxic conditions, recent discoveries show that oxic methane production (OMP, aka the methane paradox) occurs in oxygenated surface waters worldwide. OMP drivers and their contribution to global methane emissions, however, are not well constrained. In four adjacent pre-alpine lakes, we determine the net methane production rates in oxic surface waters using two mass balance approaches, accounting for methane sources and sinks. We find that OMP occurs in three out of four studied lakes, often as the dominant source of diffusive methane emissions. Correlations of net methane production versus chlorophyll-a, Secchi and surface mixed layer depths suggest a link with photosynthesis and provides an empirical upscaling approach. As OMP is a methane source in direct contact with the atmosphere, a better understanding of its extent and drivers is necessary to constrain the atmospheric methane contribution by inland waters.
Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins
Authors: Kubo Shintaroh , Black Corbin S. , Joachimiak Ewa , Yang Shun Kai , Legal Thibault , Peri Katya , Khalifa Ahmad Abdelzaher Zaki , Ghanaeian Avrin , McCafferty Caitlyn L. , Valente-Paterno Melissa , De Bellis Chelsea , Huynh Phuong M. , Fan Zhe , Marcotte Edward M. , Wloga Dorota , Bui Khanh Huy 
Published: April 2023

AbstractCilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of two central singlets and nine outer doublet microtubules. Cryo-electron microscopy-based studies have revealed a complex network inside the lumen of both tubules composed of microtubule-inner proteins (MIPs). However, the functions of most MIPs remain unknown. Here, we present single-particle cryo-EM-based analyses of the Tetrahymena thermophila native doublet microtubule and identify 42 MIPs. These data shed light on the evolutionarily conserved and diversified roles of MIPs. In addition, we identified MIPs potentially responsible for the assembly and stability of the doublet outer junction. Knockout of the evolutionarily conserved outer junction component CFAP77 moderately diminishes Tetrahymena swimming speed and beat frequency, indicating the important role of CFAP77 and outer junction stability in cilia beating generation and/or regulation.
Next-generation large-scale binary protein interaction network for Drosophila melanogaster
Authors: Tang Hong-Wen , Spirohn Kerstin , Hu Yanhui , Hao Tong , Kovács István A. , Gao Yue , Binari Richard , Yang-Zhou Donghui , Wan Kenneth H. , Bader Joel S. , Balcha Dawit , Bian Wenting , Booth Benjamin W. , Coté Atina G. , de Rouck Steffi , Desbuleux Alice , Goh Kah Yong , Kim Dae-Kyum , Knapp Jennifer J. , Lee Wen Xing , Lemmens Irma , Li Cathleen , Li Mian , Li Roujia , Lim Hyobin Julianne , Liu Yifang , Luck Katja , Markey Dylan , Pollis Carl , Rangarajan Sudharshan , Rodiger Jonathan , Schlabach Sadie , Shen Yun , Sheykhkarimli Dayag , TeeKing Bridget , Roth Frederick P. , Tavernier Jan , Calderwood Michael A. , Hill David E. , Celniker Susan E. , Vidal Marc , Perrimon Norbert , Mohr Stephanie E. 
Published: April 2023

AbstractGenerating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) forDrosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000Drosophilaproteins result in the ‘FlyBi’ dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binaryDrosophilareference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. Thedeformed wings(dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.
Long-chain anionic surfactants enabling stable perovskite/silicon tandems with greatly suppressed stress corrosion
Authors: Wang Xinlong , Ying Zhiqin , Zheng Jingming , Li Xin , Zhang Zhipeng , Xiao Chuanxiao , Chen Ying , Wu Ming , Yang Zhenhai , Sun Jingsong , Xu Jia-Ru , Sheng Jiang , Zeng Yuheng , Yang Xi , Xing Guichuan , Ye Jichun 
Published: April 2023

AbstractDespite the remarkable rise in the efficiency of perovskite-based solar cells, the stress-induced intrinsic instability of perovskite active layers is widely identified as a critical hurdle for upcoming commercialization. Herein, a long-alkyl-chain anionic surfactant additive is introduced to chemically ameliorate the perovskite crystallization kinetics via surface segregation and micellization, and physically construct a glue-like scaffold to eliminate the residual stresses. As a result, benefiting from the reduced defects, suppressed ion migration and improved energy level alignment, the corresponding unencapsulated perovskite single-junction and perovskite/silicon tandem devices exhibit impressive operational stability with 85.7% and 93.6% of their performance after 3000 h and 450 h at maximum power point tracking under continuous light illumination, providing one of the best stabilities to date under similar test conditions, respectively.
Dynamic machine vision with retinomorphic photomemristor-reservoir computing
Authors: Tan Hongwei , van Dijken Sebastiaan 
Published: April 2023

AbstractDynamic machine vision requires recognizing the past and predicting the future of a moving object based on present vision. Current machine vision systems accomplish this by processing numerous image frames or using complex algorithms. Here, we report motion recognition and prediction in recurrent photomemristor networks. In our system, a retinomorphic photomemristor array, working as dynamic vision reservoir, embeds past motion frames as hidden states into the present frame through inherent dynamic memory. The informative present frame facilitates accurate recognition of past and prediction of future motions with machine learning algorithms. This in-sensor motion processing capability eliminates redundant data flows and promotes real-time perception of moving objects for dynamic machine vision.
Global patterns and edaphic-climatic controls of soil carbon decomposition kinetics predicted from incubation experiments
Authors: Xiang Daifeng , Wang Gangsheng , Tian Jing , Li Wanyu 
Published: April 2023

AbstractKnowledge about global patterns of the decomposition kinetics of distinct soil organic matter (SOM) pools is crucial to robust estimates of land-atmosphere carbon fluxes under climate change. However, the current Earth system models often adopt globally-consistent reference SOM decomposition rates (kref), ignoring effects from edaphic-climate heterogeneity. Here, we compile a comprehensive set of edaphic-climatic and SOM decomposition data from published incubation experiments and employ machine-learning techniques to develop models capable of predicting the expected sizes and kref of multiple SOM pools (fast, slow, and passive). We show that soil texture dominates the turnover of the fast pools, whereas pH predominantly regulates passive SOM decomposition. This suggests that pH-sensitive bacterial decomposers might have larger effects on stable SOM decomposition than previously believed. Using these predictive models, we provide a 1-km resolution global-scale dataset of the sizes and kref of these SOM pools, which may improve global biogeochemical model parameterization and predictions.
Transcriptomics of Hirschsprung disease patient-derived enteric neural crest cells reveals a role for oxidative phosphorylation
Authors: Li Zhixin , Lui Kathy Nga-Chu , Lau Sin-Ting , Lai Frank Pui-Ling , Li Peng , Chung Patrick Ho-Yu , Wong Kenneth Kak-Yuen , Tam Paul Kwong-Hing , Garica-Barcelo Maria-Mercedes , Hui Chi-Chung , Sham Pak Chung , Ngan Elly Sau-Wai 
Published: April 2023

AbstractHirschsprung disease is characterized by the absence of enteric neurons caused by the defects of enteric neural crest cells, leading to intestinal obstruction. Here, using induced pluripotent stem cell-based models of Hirschsprung and single-cell transcriptomic analysis, we identify a gene set of 118 genes commonly dysregulated in all patient enteric neural crest cells, and suggest HDAC1 may be a key regulator of these genes. Furthermore, upregulation of RNA splicing mediators and enhanced alternative splicing events are associated with severe form of Hirschsprung. In particular, the higher inclusion rate of exon 9 in PTBP1 and the perturbed expression of a PTBP1-target, PKM, are significantly enriched in these patient cells, and associated with the defective oxidative phosphorylation and impaired neurogenesis. Hedgehog-induced oxidative phosphorylation significantly enhances the survival and differentiation capacity of patient cells. In sum, we define various factors associated with Hirschsprung pathogenesis and demonstrate the implications of oxidative phosphorylation in enteric neural crest development and HSCR pathogenesis.
Pyro-layered heterostructured nanosheet membrane for hydrogen separation
Authors: Wang Ruoxin , Qian Jianhao , Chen Xiaofang , Low Ze-Xian , Chen Yu , Ma Hongyu , Wu Heng-An , Doherty Cara M. , Acharya Durga , Xie Zongli , Hill Matthew R. , Shen Wei , Wang Fengchao , Wang Huanting 
Published: April 2023

AbstractEngineering different two-dimensional materials into heterostructured membranes with unique physiochemical properties and molecular sieving channels offers an effective way to design membranes for fast and selective gas molecule transport. Here we develop a simple and versatile pyro-layering approach to fabricate heterostructured membranes from boron nitride nanosheets as the main scaffold and graphene nanosheets derived from a chitosan precursor as the filler. The rearrangement of the graphene nanosheets adjoining the boron nitride nanosheets during the pyro-layering treatment forms precise in-plane slit-like nanochannels and a plane-to-plane spacing of ~3.0 Å, thereby endowing specific gas transport pathways for selective hydrogen transport. The heterostructured membrane shows a high H2permeability of 849 Barrer, with a H2/CO2selectivity of 290. This facile and scalable technique holds great promise for the fabrication of heterostructures as next-generation membranes for enhancing the efficiency of gas separation and purification processes.