bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive analysis of insertion sequences within rRNA genes of CPR bacteria and biochemical characterization of a homing endonuclease encoded by these sequences
Authors: Tsurumaki Megumi , Sato Asako , Saito Motofumi , Kanai Akio 
Published: March 2024

ABSTRACTThe Candidate Phyla Radiation (CPR) represents an extensive bacterial clade comprising primarily uncultured lineages and is distinguished from other bacteria by a significant prevalence of insertion sequences (ISs) within their rRNA genes. However, our understanding of the taxonomic distribution and characteristics of these ISs remains limited. In this study, we used a comprehensive approach to systematically determine the nature of the rRNA ISs in CPR bacteria. The analysis of hundreds of rRNA gene sequences across 65 CPR phyla revealed that ISs are present in 48% of 16S rRNA genes and 82% of 23S rRNA genes, indicating a broad distribution across the CPR clade, with exceptions in the 16S and 23S rRNA genes of Saccharibacteria and the 16S rRNA genes of Peregrinibacteria. Over half the ISs display a group-I-intron-like structure, whereas specific 16S rRNA gene ISs display features reminiscent of group II introns. The ISs frequently encode proteins with homing endonuclease (HE) domains, centered around the LAGLIDADG motif. The LAGLIDADG HE (LHE) proteins encoded by the rRNA ISs of CPR bacteria predominantly have a single-domain structure, deviating from the usual single- or double-domain configuration observed in typical prokaryotic LHEs. Experimental analysis of one LHE protein, I-ShaI fromCa. Shapirobacteria, confirmed that its endonuclease activity targets the DNA sequence of its insertion site, and chemical cross-linking experiments demonstrated its capacity to form homodimers. These results provide robust evidence supporting the hypothesis that the explosive proliferation of rRNA ISs in CPR bacteria was facilitated by mechanisms involving LHEs.IMPORTANCEInsertion sequences (ISs) in rRNA genes are relatively limited and infrequent in standard bacteria. With a comprehensive bioinformatic analysis, we show that in CPR bacteria, which are characterized by a high frequency of ISs, these ISs occur in 48% of 16S rRNA genes and 82% of 23S rRNA genes. We also report the systematic and biochemical characterization of the LAGLIDADG homing endonucleases (LHEs) encoded by these ISs in the first such analysis of the CPR bacteria. This study significantly extends our understanding of the phylogenetic positions of rRNA ISs within CPR bacteria and the biochemical features of their LHEs.
An overview of GabRat edge disruption and its new extensions for unbiased quantification of disruptive camouflaging patterns using randomization technique
Authors: Tanahashi Masahiko , Lin Min-Chen , Lin Chung-Ping 
Published: March 2024

AbstractDisruptive colorations are camouflaging patterns that use contrasting colorations to interrupt the continuously of object’s edge and disturb the observer’s visual recognition. The GabRat method has been introduced and widely used to quantify the strength of edge disruption. The original GabRat method requires a composite image where a target object is placed on a particular background. It computes the intensities of ’frequency components’ parallel and perpendicular to the edge direction at each edge point using Gabor filters, and summarize the ratios of these two intensities around the perimeter of the shape. However, we found that the original GabRat method has an issue which produces false signals and biases to overestimating the GabRat value depending on the edge angle. Here, we introduce GabRat-R, which can diminish that angle dependency using Gabor filters with randomized base angles. Additionally, we developed GabRat-RR, which iteratively places a target object on a background with random positions and rotation angles to average the effects of the heterogeneity and anisotropy of background. Compared with the original GabRat, our GabRat-R and GabRat-RR programs run more efficiently using multithreading techniques. GabRat-R and GabRat-RR were freely available inNatsumushi2.0 software of the authors’ website.
Generative Haplotype Prediction Outperforms Statistical Methods for Small Variant Detection in NGS Data
Authors: O’Fallon Brendan , Bolia Ashini , Durtschi Jacob , Yang Luobin , Fredrickson Eric , Best Hunter 
Published: March 2024

AbstractDetection of germline variants in next-generation sequencing data is an essential component of modern genomics analysis. Variant detection tools typically rely on statistical algorithms such as de Bruijn graphs or Hidden Markov Models, and are often coupled with heuristic techniques and thresholds to maximize accuracy. Here, we introduce a new approach that replaces these handcrafted statistical techniques with a single deep generative model. The model’s input is the set of reads aligning to a single genomic region, and the model produces two sets of output tokens, each representing the nucleotide sequence of a germline haplotype. Using a standard transformer-based encoder and double-decoder architecture, our model learns to construct germline haplotypes in a generative fashion identical to modern Large Language Models (LLMs). We train our model on 37 Whole Genome Sequences (WGS) from Genome-in-a-Bottle samples, and demonstrate that our method learns to produce accurate haplotypes with correct phase and genotype for all classes of small variants. We compare our method, called Jenever, to FreeBayes, GATK HaplotypeCaller, Clair3 and DeepVariant, and demonstrate that our method has superior overall accuracy compared to other methods. AtF1-maximizing quality thresholds, our model delivers the highest sensitivity, precision, and the fewest genotyping errors for insertion and deletion variants. For single nucleotide variants our model demonstrates the highest sensitivity but at somewhat lower precision, and achieves the highest overallF1 score among all callers we tested.
Enterohemorrhagic Escherichia coli (EHEC) Disrupts Intestinal Barrier Integrity in Translational Canine Stem Cell-Derived Monolayers
Authors: Nagao Itsuma , Kawasaki Minae , Goyama Takashi , Kim Hyun Jung , Call Douglas R. , Ambrosini Yoko M. 
Published: March 2024

AbstractThis study addresses the gap in translatablein vitromodels for investigating EnterohemorrhagicE. coli(EHEC) infections, particularly relevant to both canine and human health. EHEC is known to induce acute colitis in dogs, leading to symptoms like hemorrhagic diarrhea and hemolytic uremic syndrome, similar to those observed in humans. However, understanding the pathophysiology and developing treatment strategies have been challenging due to the lack of effective models that replicate the clinical disease caused by EHEC in both species. Our approach involved the development of colonoid-derived monolayers using intestinal tissues from healthy, client-owned dogs. These monolayers were exposed to EHEC and the impact of EHEC was assessed through several techniques, including trans-epithelial electrical resistance (TEER) measurement, immunofluorescence staining for junction proteins and mucus, and scanning electron microscopy for morphological analysis. Modified culture with saline, which was intended to prevent bacterial overgrowth, maintained barrier integrity and cell differentiation. EHEC infection led to significant decreases in TEER and ZO-1 expression, but not in E- cadherin levels or mucus production. Additionally, EHEC elicited a notable increase in TNF-α production, highlighting its distinct impact on canine intestinal epithelial cells compared to non-pathogenicE. coli. These findings closely replicatein vivoobservations in dogs and humans with EHEC enteropathy, validating the canine colonoid-derived monolayer system as a translational model to study host- pathogen interactions in EHEC and potentially other clinically significant enteric pathogens.
Distinct roles of the major binding residues in the cation-binding pocket of MelB
Authors: Hariharan Parameswaran , Bakhtiiari Amirhossein , Liang Ruibin , Guan Lan 
Published: March 2024

AbstractSalmonella entericaserovar Typhimurium melibiose permease (MelBSt) is a prototype of the major facilitator superfamily (MFS) transporters, which play important roles in human health and diseases. MelBStcatalyzed the symport of galactosides with either H+, Li+, or Na+, but prefers the coupling with Na+. Previously, we determined the structures of the inward- and outward-facing conformation of MelBSt, as well as the molecular recognition for galactoside and Na+. However, the molecular mechanisms for H+- and Na+-coupled symport still remain poorly understood. We have solved two x-ray crystal structures of MelBStcation-binding site mutants D59C at an unliganded apo-state and D55C at a ligand-bound state, and both structures display the outward-facing conformations virtually identical as published previously. We determined the energetic contributions of three major Na+-binding residues in cation selectivity for Na+and H+by the free energy simulations. The D55C mutant converted MelBStto a solely H+-coupled symporter, and together with the free-energy perturbation calculation, Asp59 is affirmed to be the sole protonation site of MelBSt. Unexpectedly, the H+-coupled melibiose transport with poor activities at higher ΔpH and better activities at reversal ΔpH was observed, supporting that the membrane potential is the primary driving force for the H+-coupled symport mediated by MelBSt. This integrated study of crystal structure, bioenergetics, and free energy simulations, demonstrated the distinct roles of the major binding residues in the cation-binding pocket.
tRNA modifications tune decoding of codon pairs to prevent cellular quality control responses
Authors: Wu Jie , Eggers Cristian , Sin Olga , Koziej Łukasz , Mancilla Hector , Mollet Fabienne , Schöler Hans R. , Drexler Hannes C.A. , Ranff Tristan , Fufezan Christian , Kraft Claudine , Glatt Sebastian , Bruder Jan M. , Leidel Sebastian A. 
Published: March 2024

AbstracttRNA modifications tune translation rates and codon optimality, thereby optimizing co-translational protein folding, but how codon optimality defects trigger cellular phenotypes remains unclear. Here, we show that ribosomes stall at specific modification-dependent codon pairs, triggering ribosome collisions and inducing a coordinated and hierarchical response of cellular quality control pathways. Ribosome profiling reveals an unexpected functional diversity for wobble-uridine (U34) modifications during decoding. The same modification can have different effects at the A and P sites. Furthermore, modification-dependent stalling codon pairs induce ribosome collisions, triggering ribosome-associated quality control (RQC) to prevent protein aggregation by degrading aberrant nascent peptides and mRNAs. RQC inactivation stimulates the expression of molecular chaperones to remove protein aggregates. Our results show that loss of tRNA modifications primarily disrupts translation rates of suboptimal codon pairs and reveal the coordinated regulation and adaptability of cellular surveillance systems to ensure efficient and accurate protein synthesis and maintain protein homeostasis.
Designing a hybrid in silico/in-cell controller robust to process–model mismatch associated with dynamically regulated enzyme overexpression
Authors: Ohkubo Tomoki , Sakumura Yuichi , Zhang Fuzhong , Kunida Katsuyuki 
Published: March 2024

AbstractDiscrepancy between model predictions and actual processes, known as process–model mismatch (PMM), remains a serious challenge in bioprocess optimization. Previously, we proposed the hybrid in silico/in-cell controller (HISICC) concept combining model-based optimization with cell-based feedback to address the PMM problem. Herein, this approach was advanced to regulate intracellular concentrations of rate-limiting enzymes. Advanced HISICC was demonstrated using an engineeredEscherichia colistrain for fatty acid production (FA3). This strain harbors an in-cell feedback controller, which decelerates acetyl-CoA carboxylase (ACC) overexpression in response to sensing the concentration of malonyl-CoA formed by this enzyme. A mathematical model for FA3 was constructed and validated using experimental data. Simulations assuming various PMM revealed that the HISICC using FA3 effectively mitigates toxicity from excessive ACC by robustly adapting braking its overexpression, minimizing yield loss. This study confirmed HISICC as a viable strategy for enhancing bioprocess efficiency, especially in balancing the bottleneck enzyme levels.
‘You are too much in this modern world, that’s why you are like this’: Understanding perceptions of mental health among Somali people in London
Authors: Gonzalez Caitlin , Humberstone Elizabeth , Willott Chris 
Published: March 2024

AbstractThis is a qualitative study exploring the perceptions of mental health among Somali people living in London. Participants, over the age of 18 and identifying as Somali, were recruited from a community centre in West London. Seven participants were recruited, and semi-structured interviews were conducted to better understand perceptions of mental health, care-seeking, treatment and different understandings of these issues within their community. Interview transcripts were imported into NVIVO version 14 to be coded, and description-focussed thematic analysis was used to interpret key themes.Concerns around judgement, shame and stigma are key issues affecting attitudes towards mental health in this group. Other important issues affecting conceptualisations and attitudes towards mental health were intergenerational differences, isolation from the community, stigma and secrecy. Participants also reported the importance of protective factors, particularly faith and family in their lives. This research adds to existing literature in exploring perceptions of mental health in Somali communities in the UK, and such research is helpful in identifying cultural barriers to recognition and treatment of mental health within this community.
Anticoagulation-related complications and their outcomes in hemodialysis patients with acute kidney injury at selected hospitals in Ethiopia
Authors: Kedir Hanan Muzeyin , Yabeyu Abdella Birhan , Ejigu Addisu Melkie , Tadesse Tamrat Assefa , Sisay Eskinder Ayalew 
Published: March 2024

AbstractIntroductionDuring hemodialysis (HD), the presence of clots in the dialyzer can diminish the effective surface area of the device. In severe cases, clot formation in the circuit can halt treatment and lead to blood loss in the system. Thus, ensuring proper anticoagulation during HD is crucial to prevent clotting in the circuit while safeguarding the patient from bleeding risks. This study aimed to evaluate anticoagulation outcomes and related factors in HD patients with acute kidney injury (AKI) at selected hospitals in Ethiopia.MethodA prospective, multicenter observational study was carried out between October 1, 2021, and March 31, 2022. The study encompassed all AKI patients undergoing HD at least once during the study period. Descriptive statistics were utilized to summarize the data, and multinomial logistic regression analysis was employed to identify factors associated to clotting and bleeding.ResultsData were gathered from 1010 HD procedures conducted on 175 patients. Extracorporeal circuit clotting was detected in 34 patients during 39 (3.9%) dialysis sessions, while bleeding incidents occurred in 27 patients across 29 (2.9%) sessions. A statistically significant association was found between both the total number of HD treatments and blood flow rate with incidents of clotting. Factors such as length of hospitalization, serum creatinine levels at admission, signs and symptoms associated with uremia, along with utilization of anticoagulants or antiplatelet medications demonstrated an association with bleeding events.ConclusionClotting affected 19.4% of participants, while bleeding occurred in 15.4%, underscoring the importance of close monitoring. The frequency of HD sessions and blood flow rate are correlated with clotting, while hospitalization duration, serum creatinine levels, uremic symptoms, and anticoagulant use are associated with bleeding events.
Comparison of monomeric variants of StayGold
Authors: Shimozono Satoshi , Ando Ryoko , Sugiyama Mayu , Hirano Masahiko , Niino Yusuke , Miyawaki Atsushi 
Published: March 2024

AbstractStayGold is a bright and highly photostable fluorescent protein (FP) that forms an obligate dimer, thereby limiting its application as a soluble marker. On the basis of the structural information of this FP, we disrupted the dimerization to generate a monomeric variant, mStayGold, which inherits both the extremely high photostability and the high practical brightness of StayGold, for molecular fusion and membrane-targeting applications. Meanwhile, two other research groups have independently monomerized StayGold using different strategies. As a result, multiple StayGold monomers are currently available, creating confusion in the research community. In the present study, we investigated the three basic properties—photostability, brightness, and dispersibility—of these monomers by performing detailed side-by-side comparisons. This study highlights the difficulties of StayGold monomerization with emphasis on the tradeoff between photostability and brightness in FP technology.
mulea - an R package for enrichment analysis using multiple ontologies and empirical FDR correction
Authors: Turek Cezary , Ölbei Márton , Stirling Tamás , Fekete Gergely , Tasnádi Ervin , Gul Leila , Bohár Balázs , Papp Balázs , Jurkowski Wiktor , Ari Eszter 
Published: March 2024

AbstractTraditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrectedp-values. To address these challenges, we introducemulea, an R package offering comprehensive overrepresentation and functional enrichment analysis.muleaemploys an innovativeempirical false discovery rate (eFDR) correction method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies.muleaexpands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis,muleaprovides gene sets (in standardised GMT format) for 27 model organisms, covering 16 databases and various identifiers resulting in almost 900 files. Additionally, themuleaDataExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally,mulea’s architecture allows for easy integration of user-defined ontologies, expanding its applicability across diverse research areas.Availability and ImplementationSoftware for the tools demonstrated in this article is available as anRpackage on GitHub:https://github.com/ELTEbioinformatics/mulea.
Heat Shock alters the distribution andin vivointeraction of major nuclear structural proteins – Lamin B with DNA Topoisomerase II, and with nucleic acids
Authors: Rowińska Marta , Tomczak Aleksandra , Jabłońska Jadwiga , Piekarowicz Katarzyna , Machowska Magdalena , Rzepecki Ryszard 
Published: March 2024

ABSTRACTLamins and topoisomerases have been studied as major karyoskeletal proteins since early 80-ties. Today, lamins are thought to be responsible not only for maintenance and structural support of cell nuclei but also involved, directly or indirectly, in regulation of chromatin structure, chromatin distribution, gene expression, splicing, transcription and transport. Topoisomerases are involved in maintenance of chromosomal scaffold and structural functions in cell nuclei and topology of chromatin and DNA, and play an important role in regulation of transcription. They are also necessary in mitosis. For studying lamins and topoisomerase II,Drosophila melanogastermodel has been used for many years since flies genome contains only single gene coding for B-type lamins (lamin Dm) and single gene coding for A-type lamins (lamin C). Flies have only single gene coding for topoisomerase II (Top2).We previously reported that lamin Dm (Lam Dm) and topoisomerase II (Top2) bindin vivoboth DNA and RNA and the properties of both proteins have been modulated by specific phosphorylation on particular sites. Here we report the first part of results of the project focused on the demonstration of the role of lamins and Top2 in the regulation of gene expression and chromatin organization upon heat shock (HS) induction and recovery (R). We demonstrated that heat shock significantly induced specific phosphorylation of lamin Dm at least on S25, which affects lamin properties and distribution. Lam Dm and Top2 were relocated and changed properties including solubility. Both proteins interact with each other directly and indirectly and binding was significantly increased under HS. The relocation of Lam Dm and Top2 was associated with the relocation of chromatin as detected in polyploid third instar larvae nuclei.In vivophotocrosslinking and IP (immunoprecipitation) studies indicated a significant increase in binding to chromatin and nucleic acids upon HS induction. The highest binding affinity showed a soluble fraction of lamin Dm and topoisomerase II while the lowest was the insoluble fraction (“nuclear matrix” fraction). All the detected changes in properties and location of proteins returned to “normal” after recovery from heat shock. Based on thi s data and our preliminary interactome data for lamin Dm and Top2 we believe that both proteins play essential roles in the proper response of fly cells to HS by participation in the rearrangement of protein complexes, also associated with DNA and RNA, chromatin remodelling and proper gene expression regulation.
Defining the most potent osteoinductive culture conditions for MC3T3-E1 cells reveals no implication of oxidative stress or energy metabolism
Authors: Semicheva Alexandra , Ersoy Ufuk , Vasilaki Aphrodite , Myrtziou Ioanna , Kanakis Ioannis 
Published: March 2024

AbstractMC3T3-E1 preosteoblastic cell line is widely utilised as a reliablein vitrosystem to assess bone formation. However, the experimental growth conditions for these cells hugely diverge and, particularly, the osteogenic medium (OSM) composition varies in research studies. Therefore, we aimed to define the ideal culture conditions for MC3T3-E1 subclone 4 cells with regards to mineralization capacity and explore if oxidative stress or cellular metabolism processes are implicated. Cells were treated with 9 different combinations of long-lasting ascorbate (Asc) and β-glycerophosphate (βGP) and osteogenesis/calcification were evaluated at 3 different time-points by qPCR, Western blotting and bone nodule staining. Key molecules of oxidative and metabolic pathways were also assessed. It was found that sufficient mineral deposition was achieved only in 150μg.mL-1/2mM Asc/βGP combination at 21d in OSM and this was supported byRunx2, Alpl, BglapandCol1a1expression levels increase. NOX2 and SOD2 as well as PGC1α and Tfam were also monitored as indicators of redox and metabolic processes, respectively, where no differences were observed. Elevation in OCN protein levels and ALP activity showed that mineralisation comes as a result of these differences. This work defines the most appropriate culture conditions for MC3T3-E1 cells and could be used by other research laboratories in this field.