bluuebunny/crossref_metadata_2025_split huggingface dataset:
The structure and diversity of the bacterial community in the overlying water of the Yangzong Lake in Yunnan
Authors: Huang Kai , Li Likun , Li Jin , Chen Han , Ma Zhiqiang , Ye Wenlong , Kong Deping , Zhang Jun 
Published: March 2024

AbstractBacteria are critical components of lake ecosystems, and understanding the characteristics of bacterial community structure and diversity indices is of significant importance for the analysis and management of lake ecology. In this study, overlying water samples were collected from Yangzong Lake in May, June, and July 2021. High-throughput sequencing and statistical analysis were employed to investigate the relationships between physicochemical factors, bacterial community structure, and diversity in the overlying water of Yangzong Lake. The results showed significant differences in oxidation-reduction potential among the sampling points. The order of oxidation-reduction potential was as follows: Yangzong DAHE > Yangzong Lake South > Yangzong Lake Middle > Yangzong Lake North, while other physicochemical factors exhibited minor differences. The number of OTUs and bacterial alpha diversity index in the overlying water of Yangzong Lake Middle were higher than those in Yangzong Lake North, Yangzong Lake South, and Yangzong DAHE. The dominant bacterial phyla in the overlying water were Actinobacteriota, Bacteroidota, and Proteobacteria. Actinobacteriota had the highest relative abundance of 34.63% in Yangzong Lake North, while Bacteroidota had the highest relative abundance of 33.79% in Yangzong Lake South, and Proteobacteria had the highest relative abundance of 27.29% in Yangzong Lake Middle. The dominant genera were hgcI_clade, CL500-29_marine_group, and Flavobacterium. Among them, hgcI_clade had the highest relative abundance of 37.56% in Yangzong Lake North, CL500-29_marine_group had the highest relative abundance of 35.22% in Yangzong Lake South, and Flavobacterium had the highest relative abundance of 42.02% in Yangzong Lake Middle. Correlation analysis revealed significant correlations between Campilobacterota at the phylum level and dissolved oxygen (DO) and total phosphorus (TP). At the genus level, Flavobacterium, Limnohabitans, and Pseudarcicella showed significant correlations with DO and TP.
WITHDRAWN: Effects of ethyl acetate fraction ofPsychotria vogelianaleaf on liver function, kidney function, and cytokines level of induced rheumatoid arthritis in albino rats
Authors: Ezean Nkiru N. , Ogbu Celestine O. , Aja Patrick M. , Uti Daniel E. , Uche Orji Obasi , Agu Peter C. , Zakari Suleiman , Zakari Hajara , Offor Christian E. , Awoke Joshua N. 
Published: March 2024

WITHDRAWAL STATEMENTThe authors have withdrawn their manuscript owing to [some fundamental errors discovered in the methods and result of this study which was discovered during the review process which can obviously change our major findings and conclusion]. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Alpha-synuclein distribution and seeding activity in rectal biopsies in Parkinson’s disease
Authors: Kluge Annika , Kintrup Carmen , Kulcsarova Kristina , Schröder Katja , Welzel Julius , Heinzel Sebastian , Wedel Thilo , Böttner Martina , Lucius Ralph , Bonkat Sarah Kim , Pendziwiat Manuela , Schoch Stephan , Ellrichmann Mark , Berg Daniela , Schaeffer Eva , Cossais François 
Published: March 2024

AbstractBackgroundParkinson’s disease (PD) is characterized by the accumulation of alpha-synuclein (aSyn) pathology, not only in the brain but also in the gastrointestinal (GI) tract. This study investigates the use of unique aSyn antibodies and an aSyn seed amplification assay (SAA) for detecting pathological aSyn in rectal biopsy samples from PD patients and healthy individuals. These samples were preserved using formalin-fixed paraffin-embedded (FFPE) methods.Materials and MethodsThe study analyzed the seeding capacity of FFPE submucosal rectal biopsies from 24 PD patients and 20 healthy controls using an aSyn-SAA. The distribution of aSyn was examined using immunohistochemistry with antibodies targeting specific conformations and phosphorylated forms of aSyn at S129 and Y39.ResultsPathological forms of aSyn were found in all FFPE biopsies from PD patients, as confirmed by SAA, and these were linked to the severity of motor symptoms (MDS-UPDRS-III). However, the immunoreactive patterns of conformation-specific or phosphorylated aSyn in rectal biopsies did not show notable differences between PD patients and healthy subjects.ConclusionPathological aSyn strains are detectable in FFPE rectal biopsies from PD patients with high accuracy using aSyn-SAA. However, the utility of immunohistochemical detection with current antibodies for identifying pathological aSyn forms appears limited. The findings advocate the use of aSyn-SAA as a diagnostic tool for PD, contributing to a deeper understanding of the gut-brain connection in the disease.
Lingo: an automated, web-based deep phenotyping platform for language ability
Authors: Casten Lucas G. , Koomar Tanner , Elsadany Muhammad , McKone Caleb , Tysseling Ben , Sasidharan Mahesh , Tomblin J. Bruce , Michaelson Jacob J. 
Published: March 2024

AbstractBackgroundLanguage and the ability to communicate effectively are key factors in mental health and well-being. Despite this critical importance, research on language is limited by the lack of a scalable phenotyping toolkit.MethodsHere, we describe and showcase Lingo – a flexible online battery of language and nonverbal reasoning skills based on seven widely used tasks (COWAT, picture narration, vocal rhythm entrainment, rapid automatized naming, following directions, sentence repetition, and nonverbal reasoning). The current version of Lingo takes approximately 30 minutes to complete, is entirely open source, and allows for a wide variety of performance metrics to be extracted. We asked > 1,300 individuals from multiple samples to complete Lingo, then investigated the validity and utility of the resulting data.ResultsWe conducted an exploratory factor analysis across 14 features derived from the seven assessments, identifying five factors. Four of the five factors showed acceptable test-retest reliability (Pearson’s R > 0.7). Factor 2 showed the highest reliability (Pearson’s R = 0.95) and loaded primarily on sentence repetition task performance. We validated Lingo with objective measures of language ability by comparing performance to gold-standard assessments: CELF-5 and the VABS-3. Factor 2 was significantly associated with the CELF-5 “core language ability” scale (Pearson’s R = 0.77, p-value < 0.05) and the VABS-3 “communication” scale (Pearson’s R = 0.74, p-value < 0.05). Factor 2 was positively associated with phenotypic and genetic measures of socieconomic status. Interestingly, we found the parents of children with language impairments had lower Factor 2 scores (p-value < 0.01). Finally, we found Lingo factor scores were significantly predictive of numerous psychiatric and neurodevelopmental conditions.ConclusionsTogether, these analyses support Lingo as a powerful platform for scalable deep phenotyping of language and other cognitive abilities. Additionally, exploratory analyses provide supporting evidence for the heritability of language ability and the complex relationship between mental health and language.
Structural factors of RGS14 regulating hormone-dependent phosphate transport mediated by NPT2A
Authors: Sneddon W. Bruce , Ramineni Suneela , Van Doorn G. Emme , Hepler John R. , Friedman Peter A. 
Published: March 2024

AbstractThe NPT2A sodium phosphate cotransporter-2a mediates basal and parathyroid hormone (PTH)- and fibroblast growth factor-23 (FGF23)-regulated phosphate transport in kidney proximal tubule cells. Both basal and hormone-sensitive transport require sodium hydrogen exchanger regulatory factor-1 (NHERF1), a scaffold protein with 2 PDZ domains. NPT2A binds to PDZ1. RGS14 persistently represses hormone action by binding to PDZ2. RGS14 contains an RGS domain, two Ras/Rap-binding domains (RBD1, RBD2), a G protein regulatory (GPR) motif, and a carboxy-terminal PDZ ligand. The intrinsic RGS14 domains cannot explain its regulatory effects on hormone-sensitive phosphate transport because these actions are mediated not only by the PTH receptor, a G protein-coupled receptor (GPCR) but also by fibroblast growth factor receptor-1 (FGFR1), a receptor tyrosine kinase that is not governed by G protein activity. Here, we sought to identify the RGS14 structural elements mutually controlling PTH and FGF23 action. RGS14 truncation constructs lacking upstream sequence and the RGS domain were fully functional. Removing the linker sequence between RGS and RBD1 domains was sufficient to abrogate RGS14 action. Examination of the alpha-helical linker region suggested candidate serine residues that might facilitate regulatory activities. Ser266and Ser269replacement by Ala abolished RGS14 regulatory actions on hormone-sensitive phosphate transport and binding to NHERF1. The results establish that RGS14 actions require targeted phosphorylation within the linker and an intact PDZ ligand.
Striated fibre assemblins localise in the feeding groove of the ‘typical excavate’Paratrimastix pyriformis
Authors: Heiss Aaron A. , Fang Yi-Kai , Priscila Peña-Diaz C. , Zítek Justyna , Novák Ji•í , Šmída Adam , Zelená Marie , Švagr Ezra , Hampl Vladimír 
Published: March 2024

ABSTRACTSpatial arrangement of the cytoskeleton in the cells of protists has been used for decades for taxonomy and phylogenetic inference at various levels. In contrast, the protein composition of non-microtubular structures is mostly unknown. Exceptions are system I fibres in algae, which are built of striated fiber assemblins (SFA). Interestingly, SFAs are also components of a range of other, dissimilar structures, playing a role in the cortex of ciliates, cells division in apicomplexans, and adhesion of the parasite Giardia to the intestine. In a broad bioinformatic survey, we show the presence of three ancestral eukaryotic paralogues of SFA, and note that they are present in all ‗typical excavates‘ – simple flagellates bearing a ventral feeding groove. In one representative, Paratrimastix pyriformis, we localised one of the SFA paralogues using specific antibodies and expansion microscopy. We show that it co-localises specifically with structures attached to the basal body of the posterior flagellum, namely the right microtubular root, composite fibre, and B-fibre. As the morphology of the ‗typical excavates‘ may be ancestral to eukaryotes, we speculate that the role in the development or function of this feeding apparatus may be ancestral to the protein.
Effect of shipping on the microbiome of donor mice used to reconstitute germ-free recipients
Authors: McAdams Zachary L. , Yates Jared , Turner Giedre , Dorfmeyer Rebecca A. , Wight-Carter Mary , Amos-Landgraf James , Franklin Craig L. , Ericsson Aaron C. 
Published: March 2024

AbstractThe gut microbiota (GM) influences multiple processes during host development and maintenance. To study these events, fecal microbiota transfer (FMT) to germ-free (GF) recipients is often performed. Mouse models of disease are also susceptible to GM-dependent effects, and cryo-repositories often store feces from donated mouse strains. Shipping live mice may affect the GM and result in an inaccurate representation of the baseline GM. We hypothesize that the use of such fecal samples for FMT would transfer shipping-induced changes in the donor GM to GF recipients. To test this, donor mice originating from two suppliers were shipped to the University of Missouri. Fecal samples collected pre- and post-shipping were used to inoculate GF mice. Pre- and post-shipping fecal samples from donors, and fecal and/or cecal contents were collected from recipients at one and two weeks post-FMT. 16S rRNA sequencing revealed supplier-dependent effects of shipping on the donor microbiome. FMT efficiency was independent of shipping timepoint or supplier, resulting in transmission of shipping-induced changes to recipient mice, however the effect of supplier-origin microbiome remained evident. While shipping may cause subtle changes in fecal samples collected for FMT, such effects are inconsistent among supplier-origin GMs and minor in comparison to other biological variables.
A mechanism that transduces lysosomal damage signals to stress granule formation for cell survival
Authors: Duran Jacob , Poolsup Suttinee , Allers Lee , Lemus Monica Rosas , Cheng Qiuying , Pu Jing , Salemi Michelle , Phinney Brett , Jia Jingyue 
Published: March 2024

SUMMARYLysosomal damage poses a significant threat to cell survival. Our previous work has reported that lysosomal damage induces stress granule (SG) formation. However, the importance of SG formation in determining cell fate and the precise mechanisms through which lysosomal damage triggers SG formation remains unclear. Here, we show that SG formation is initiated via a novel calcium-dependent pathway and plays a protective role in promoting cell survival in response to lysosomal damage. Mechanistically, we demonstrate that during lysosomal damage, ALIX, a calcium-activated protein, transduces lysosomal damage signals by sensing calcium leakage to induce SG formation by controlling the phosphorylation of eIF2α. ALIX modulates eIF2α phosphorylation by regulating the association between PKR and its activator PACT, with galectin-3 exerting a negative effect on this process. We also found this regulatory event of SG formation occur on damaged lysosomes. Collectively, these investigations reveal novel insights into the precise regulation of SG formation triggered by lysosomal damage, and shed light on the interaction between damaged lysosomes and SGs. Importantly, SG formation is significant for promoting cell survival in the physiological context of lysosomal damage inflicted by SARS-CoV-2 ORF3a, adenovirus infection, Malaria hemozoin, proteopathic tau as well as environmental hazard silica.
Towards prospective in-silico trials in atrial fibrillation: the case of polypharmacological SK and K2P channel block
Authors: Dasí Albert , Berg Lucas M , Martinez-Navarro Hector , Bueno-Orovio Alfonso , Rodriguez Blanca 
Published: March 2024

AbstractBackgroundVirtual evaluation of medical therapy through human-based modelling and simulation can accelerate and augment clinical investigations. Treatment of the most common cardiac arrhythmia, atrial fibrillation (AF), requires novel approaches.ObjectivesTo prospectively evaluate and mechanistically explain novel pharmacological therapies for atrial fibrillation through in-silico trials, considering single and combined SK and K2P channel block.MethodsA large cohort of 1000 virtual patients was developed for simulations of AF and pharmacological action. Extensive calibration and validation with experimental and clinical data support their credibility.ResultsSustained AF was observed in 654 (65%) virtual patients. In this cohort, cardioversion efficacy increased to 82% (534 of 654) through combined SK+K2P channel block, from 33% (213 of 654) and 43% (278 of 654) for single SK and K2P blocks, respectively. Drug-induced prolongation of tissue refractoriness, dependent on the virtual patient’s ionic current profile, explained cardioversion efficacy (atrial refractory period increase: 133.0±48.4 ms for combined vs. 45.2±43.0 and 71.0±55.3 for single SK and K2P block, respectively). Virtual patients cardioverted by SK channel block presented lower K2P densities, while lower SK densities favoured the success of K2P channel inhibition. Both ionic currents had a crucial role on atrial repolarization, and thus, a synergism resulted from the polypharmacological approach. All three strategies, including the multi-channel block, preserved atrial electrophysiological function (i.e., conduction velocity and calcium transient dynamics) and thus, its contractile properties (safety).ConclusionIn-silico trials identify key factors determining efficacy of single vs combined SK+K2P channel block as effective and safe strategies for AF management.
Cryo-electron tomography reveals the nanoscale architecture of the actin cortex in cellular blebs
Authors: Cassani Davide A.D. , Martins Bruno , Smith Matthew B. , Medalia Ohad , Paluch Ewa K. 
Published: March 2024

AbstractIn animal cells, cellular deformations driving cytokinesis, migration, and epithelial constriction are driven by contractile tension in the actomyosin cortex, a thin network of actin and myosin underlying the plasma membrane. Cortical tension results from myosin-generated forces and as such, cortical myosin organization and dynamics have received significant attention. However, recent studies highlight that alongside myosin motor activity, the organization of the cortical actin network is a key regulator of tension. Yet, very little is known about the structural arrangement of cortical actin filaments. This is mostly due to the small thickness and high density of the cortex, which makes the visualization of cortical actin filaments challenging. Here, we use cryo-electron tomography (cryo-ET) to unveil the structural organization of cortical actin. As a model, we use isolated cellular blebs, which assemble an actin cortex comparable to the cortex of entire cells, but are small enough to be amenable to cryo-ET. We find that the bleb actin cortex is mostly composed of short and straight actin filaments. We then characterize cortex structural parameters, including the density of potential cross-linking and membrane attachment points. Our study unveils the nanoscale three-dimensional organization of the cortical actin network in cellular blebs. As such, it provides a quantitative framework for models of cortical tension generation, and will help understanding the nanoscale basis of cell surface contractions.
Genomic and transcriptomic analyses of the elite rice variety Huizhan provide insight into disease resistance and heat tolerance
Authors: Yang Wei , Yang Zhou , Yang Lei , Li Zheng , Zhang Zhaowu , Wei Tong , Huang Renliang , Li Guotian 
Published: March 2024

AbstractRice is an important crop and serves as a model for crop genomics and breeding studies. Here, we used Oxford Nanopore ultra-long sequencing and next-generation sequencing technologies to generate a chromosome-scale genome assembly of Huizhan, a disease-resistant and heat-tolerantindicarice variety. The final genome assembly was 395.20 Mb with a scaffold N50 of 31.87 Mb. We identified expanded gene families in Huizhan that are potentially associated with both organ growth and development, as well as stress responses. We observed that three functional rice blast resistance genes, includingPi2,PiaandPtr, and bacterial blight resistance geneXa27, likely contribute to disease resistance of Huizhan. In addition, integrated genomics and transcriptomics analyses show thatOsHIRP1,OsbZIP60, the SOD gene family, and various transcription factors are likely involved in heat tolerance of Huizhan. Results presented in this study will serve as a valuable resource for rice functional genomics studies and breeding.
Cyclocarya paliuruspolysaccharides improve high fat diet-fed mice lipid dysmetabolism through gut microbiota
Authors: Huang Chengyan , Jia Yanmei , Chai Ping , He Huizhen , Liu Wei , Cheng Lirong 
Published: March 2024

AbstractObesity is associated with low-grade chronic inflammation and intestinal dysbiosis.Cyclocarya paliurus(C.paliurus) has been shown to improve lipid metabolism and gut microbiota communities in animals and humans; however, it remains to know whetherCyclocarya paliuruspolysaccharides (CCPP) prevents obesity through gut microbiota. Here, we found that high fat diet promoted the lipid accumulation and intestinal microbiota dysbiosis in mice, while drinkCyclocarya paliuruspolysaccharides reduces body weight, inflammation, alleviated the lipid accumulation, and reversed gut microbiota dysbiosis, including the diversity of intestinal microbiota, relative abundances ofLachnospiraceae. By transplanting faeces from CP-treated mice to HFD-fed mice, the effects of anti-obesity and microbiome regulation can be transferred through gut microbiota. Our results indicate thatCyclocarya paliuruspolysaccharides can prevent gut dysbiosis and obesity-related metabolic disorders in obese individuals, the mechanism is related to the remodeling of intestinal flora.
Enhanced metabolic entanglement emerges during the evolution of an interkingdom microbial community
Authors: Scarinci Giovanni , Ariens Jan-Luca , Angelidou Georgia , Schmidt Sebastian , Glatter Timo , Paczia Nicole , Sourjik Victor 
Published: March 2024

AbstractMetabolic interactions are common in microbial communities and are believed to be a key factor in the emergence of complex life forms. However, while different stages of mutualism can be observed in nature, the dynamics and mechanisms underlying the gradual erosion of independence of the initially autonomous organisms are not yet fully understood. In this study, we conducted the laboratory evolution of an engineered microbial community and were able to reproduce and molecularly track its stepwise progression towards enhanced partner entanglement. The evolution of the community both strengthened the existing metabolic interactions and led to the emergence ofde novointerdependence between partners for nitrogen metabolism, which is a common feature of natural symbiotic interactions. Selection for enhanced metabolic entanglement repeatedly occurred indirectly, via pleiotropies and trade-offs within cellular regulatory networks. This indicates that indirect selection may be a common but overlooked mechanism that drives the evolution of mutualistic communities.