bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improvement in the enzymatic efficiency of a zinc metalloprotease through random mutagenesis approach: Studies on the enzymatic and structural properties of the mutant
Authors: Srivastava Nitin , Khare Sunil Kumar 
Published: January 2025

ABSTRACTMicrobial proteases are significant enzymes acquiring 60% of the enzyme market. The heterologous expression provides higher enzymatic yield, yet such proteases possess less stability and low catalytic efficiency. A directed evolution strategy could improve protease’s properties to meet industrial demands. This study attempted the directed evolution of a recombinant metalloprotease (rsep) gene by a single round of error-prone PCR, wherein four hundred PCR were performed for random mutant gene library preparation. Eighteen amplicons (1230 bp) originated from modified PCR conditions were selected, cloned into pET22b+ plasmid, and overexpressed inEscherichia coliBL21(DE3). The recombinants showing soluble expression were screened, and one of the mutants (rsepA1) showed an 8.04-fold enhancement in the relative protease activity. It was purified to homogeneity with 92kDa molecular size. Its enzymatic properties like pH, temperature optima, and stability were comparable torsep(WT). Furthermore, it exhibited improved enzymatic efficiency (∼ 4.2-fold towards casein) and better substrate affinity. The structural elucidation studies through bioinformatic tools, sequencing data, and comparative biophysical studies (Fluorescence-CD spectra-DSC) of the wild and mutantrsepshowed increased histidine in the mutant. This probably resulted in enhanced substrate affinity and catalytic efficiency ofrsepA1, which were well correlated with the ICP-MS analysis.Graphical Abstract
Dynamic interactions of retroviral Gag condensates with nascent viral RNA at transcriptional burst sites: implications for genomic RNA packaging
Authors: Kaddis Maldonado Rebecca J. , Parent Leslie J. 
Published: January 2025

AbstractRetroviruses are responsible for significant pathology in humans and animals, including the acquired immunodeficiency syndrome and a wide range of malignancies. A crucial yet poorly understood step in the replication cycle is the recognition and selection of unspliced viral RNA (USvRNA) by the retroviral Gag protein, which binds to the psi (Ψ) packaging sequence in the 5’ leader, to package it as genomic RNA (gRNA) into nascent virions. It was previously thought that Gag initially bound gRNA in the cytoplasm. However, previous studies demonstrated that the Rous sarcoma virus (RSV) Gag protein traffics transiently through the nucleus, which is necessary for efficient gRNA packaging. These data formed a strong premise for the hypothesis that Gag selects nascent gRNA at transcription sites in the nucleus, the location of the highest concentration of USvRNA molecules in the cell. In support of this model, previous studies using fixed cells infected with RSV revealed that Gag co-localizes with large USvRNA nuclear foci representing viral transcriptional burst sites. To test this idea, we used single molecule labeling and imaging techniques to visualize fluorescently-tagged, actively transcribing viral genomes, and Gag proteins in living cells. Gag condensates were observed in the nucleus, transiently co-localized with USvRNA at transcriptional burst sites, forming co- localized viral ribonucleoprotein complexes (vRNPs). These results support a novel paradigm for retroviral assembly in which Gag traffics to transcriptional burst sites and interacts through a dynamic kissing interaction to capture nascent gRNA for incorporation into virions.
Sparse modeling of interactions enables fast detection of genome-wide epistasis in biobank-scale studies
Authors: Stamp Julian , Smith Samuel Pattillo , Weinreich Daniel , Crawford Lorin 
Published: January 2025

AbstractThe lack of computational methods capable of detecting epistasis in biobanks has led to uncertainty about the role of non-additive genetic effects on complex trait variation. The marginal epistasis framework is a powerful approach because it estimates the likelihood of a SNP being involved in any interaction, thereby reducing the multiple testing burden. Current implementations of this approach have failed to scale to large human studies. To address this, we present the sparse marginal epistasis (SME) test, which concentrates the scans for epistasis to regions of the genome that have known functional enrichment for a trait of interest. By leveraging the sparse nature of this modeling setup, we develop a novel statistical algorithm that allows SME to run 10 to 90 times faster than state-of-the-art epistatic mapping methods. In a study of blood traits measured in 349,411 individuals from the UK Biobank, we show that reducing searches of epistasis to variants in accessible chromatin regions facilitates the identification of genetic interactions associated with regulatory genomic elements.
A temporal coordination between Nodal and Wnt signalling governs the emergence of the mammalian body plan
Authors: Dias André , Pascual-Mas Pau , Torregrosa-Cortés Gabriel , McNamara Harold M. , Wehmeyer Alexandra E. , Arnold Sebastian J. , Martinez Arias Alfonso 
Published: January 2025

SummaryNodal and Wnt signalling play an important role in the emergence of the mammalian body plan, primarily by orchestrating gastrulation and primitive streak formation. While the literature suggests that these pathways cooperate to build the primitive streak, their individual contributions remain poorly understood, largely due to pleiotropic effects observed when key pathway components are knocked out in mouse embryos. In this study, we used gastruloids - a non-integrated stem cell model of mammalian gastrulation - to dissect the roles of Wnt and Nodal signalling. We found that Wnt/β-catenin signalling drives a genetic program characteristic of the late primitive streak, promoting the development of posterior body structures in a time and dose-dependent manner. Conversely, Nodal signalling activates a distinct developmental module resembling the early primitive streak. By engineering gastruloids with elevated Nodal signalling, we demonstrate that the decreasing temporal gradient of Nodal activity in the mouse primitive streak likely plays a pivotal role in establishing the anterior body plan, with higher Nodal levels producing more anterior structures in a concentration-dependent manner. Our findings suggest that rather than cooperating, Nodal and Wnt signalling act antagonistically, initiating distinct developmental modules within the primitive streak. This antagonism is likely the core mechanism driving the early body plan in mammals. Additionally, our results also lead to the suggestion that the gastruloid system models the primitive streak and reveals its self-organizing potential.
Epigenetic phase variation in the gut microbiome enhances bacterial adaptation
Authors: Ni Mi , Fan Yu , Liu Yujie , Li Yangmei , Qiao Wanjin , Davey Lauren E. , Zhang Xue-Song , Ksiezarek Magdalena , Mead Edward , Touracheau Alan , Jiang Wenyan , Blaser Martin J. , Valdivia Raphael H. , Fang Gang 
Published: January 2025

AbstractThe human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase variation (ePV) mediated by bacterial DNA methylation, which can regulate gene expression, enhance clonal heterogeneity, and enable a single bacterial strain to exhibit variable phenotypic states. Genome-wide and site-specific ePV have been well characterized in human pathogens’ antigenic variation and virulence factor production. However, the role of ePV in facilitating adaptation within the human microbiome remains poorly understood. Here, we comprehensively cataloged genome-wide and site-specific ePV in human infant and adult gut microbiomes. First, using long-read metagenomic sequencing, we detected genome-wide ePV mediated by complex structural variations of DNA methyltransferases, highlighting the ones associated with antibiotics or fecal microbiota transplantation. Second, we analyzed an extensive collection of public short-read metagenomic sequencing datasets, uncovering a greater prevalence of genome-wide ePV in the human gut microbiome. Third, we quantitatively detected site-specific ePVs using single-molecule methylation analysis to identify dynamic variations associated with antibiotic treatment or probiotic engraftment. Finally, we performed an in-depth assessment of anAkkermansia muciniphilaisolate from an infant, highlighting that ePV can regulate gene expression and enhance the bacterial adaptive capacity by employing a bet-hedging strategy to increase tolerance to differing antibiotics. Our findings indicate that epigenetic modifications are a common and broad strategy used by bacteria in the human gut to adapt to their environment.
Digital Health Technologies for Accessing Contraceptive Services among Young People in Sub-Saharan Africa: A Scoping Review Protocol
Authors: Kyamulabi Agnes , Oberle Eva , Olisaeloka Lotenna , Kamya Innocent , Nyesigire Ingrid , Abdulai Abdul-Fatawu , Norman Wendy 
Published: January 2025

AbstractObjectiveThis scoping review aims to examine and synthesize existing literature on the use of digital health technologies, with a focus on the extent and types of technologies used to access contraceptive services among young people in Sub-Saharan Africa (SSA).IntroductionGlobally, digital health technologies have emerged as pivotal tools in addressing contraceptive needs among young people. In SSA, where traditional healthcare systems often face numerous challenges, these technologies offer innovative solutions to improve access to contraceptive services. Despite growing interest in digital health technologies, comprehensive reviews on contraceptive access among young people in SSA are still lacking. Most existing studies focus broadly on sexual and reproductive health (SRH) or adult populations, leaving a gap in understanding the unique needs and experiences of young people using digital technologies for contraception services. It is unclear how much research has been conducted to examine how these technologies can facilitate contraceptive use, which technologies are used and why, where this evidence is concentrated within SSA, and the prevailing gaps. Therefore, we propose to undertake a scoping review.Inclusion criteriaThis scoping review will include studies focusing on young people aged 10-24 years in SSA, addressing access challenges to contraceptive services within this age group. The review will consider client-facing digital health technologies. All methodological approaches and designs will be included. Reviews, protocols, conference papers, policy briefs and studies conducted outside SSA will be excluded.MethodsThe review will apply the comprehensive search strategy recommended by JBI. The initial limited search of MEDLINE (Ovid) and CINAHL Complete (EBSCOhost) was conducted with guidance from the University Librarian. This informed the selection of keywords, along with index terms, to develop a full search strategy for MEDLINE (Ovid), CINAHL Complete (EBSCOhost), Scopus, Compendix Engineering Village, and IEEE Xplore. The scoping review shall also use supplementary resources such as google scholar, and African Journal online (AJOL). We will also review the reference lists of articles that meet the inclusion criteria to ascertain articles that were not returned by the search criteria. Data will be presented using tables and charts, accompanied by a narrative summary. This scoping review was registered in Open Science Framework:https://doi.org/10.17605/OSF.IO/5QJ6P
Identification of critical factors of the replication stress response in human cells
Authors: Janssen Louise M.E. , Baltasar Perez Empar , Vaarting Chantal , Mazouzi Abdelghani , Raaben Matthijs , Brummelkamp Thijn R. , Medema René H. , Raaijmakers Jonne A. 
Published: January 2025

AbstractHigh fidelity of replication is important to preserve genomic integrity and ensure healthy progeny. Perturbations of replication, also known as replication stress, is frequently observed in cancer cells and is considered a cancer cell-specific trait. Although replication stress drives genomic instability and tumor progression, it also generates a targetable cancer-specific vulnerability. In order to identify potential therapeutic targets in cancer cells that experience replication stress, we performed a genome wide genetic screen in human HAP1 cells challenged with low doses of replication stress-inducing drugs. We identified a large set of genes that specifically hamper cell survival in the context of replication stress. In addition to well-known players in the replication stress response and DNA repair, such as RNASEH1, BRIP1, and MDC1, we identified several genes with no prior described role in DNA replication, damage tolerance or repair. We validated that the loss of GIGYF2, HNRNPA2B1, and SUMO2 renders cells more vulnerable to replication stress. For GIGYF2 and SUMO2, we could implicate a role in homologous recombination. Taken together, our replication stress screen identified several known as well as some novel factors that protect against the toxic implications of replication stress. These factors could entail potential therapeutic targets for cancer cells experiencing replication stress.
Gut microbiota-derived lithocholic acid leads to intestinal barrier dysfunction via LPCAT1 in irritable bowel syndrome
Authors: Zhai Lixiang , Li Baohua , Xu Shujun , Peng Jiao , Zhang Yingdi , He Jiayu , Bao Gengyu , Li Yunlyu , Deng Huan , Zhao Ling , Ning Ziwan , Lyu Junfang , Lin Chengyuan , Xavier Wong Hoi Leong , Bian Zhaoxiang , Xiao Haitao 
Published: January 2025

AbstractIntestinal barrier dysfunction is widely observed in patients with irritable bowel syndrome (IBS) and significantly contributes to the persistence of IBS symptoms. The association between gut dysbiosis and the pathogenesis of IBS, as well as its connection to intestinal barrier dysfunction, has been established. However, the precise roles of gut bacteria in inducing intestinal barrier dysfunction and the underlying mechanisms of IBS remain unclear. In the present study, we showed that microbiota-derived lithocholic acid (LCA) is positively associated with intestinal barrier dysfunction biomarkers in patients with IBS-D. We found excessive LCA disrupts intestinal barrier function in normal mice and aggravates colonic inflammation in a mouse model of experimental colitis. Mechanistically, LCA modulates phospholipid metabolism and compromises the intestinal barrier by directly activating lysophosphatidylcholine acyltransferase 1 (LPCAT1). Our results demonstrated that LCA significantly upregulates LPCAT1 expression, and its overexpression leads to intestinal barrier dysfunction and promotes colonic inflammation via the activation of matrix metalloproteinase-1 (MMP1). Furthermore, we found inhibition of LPCAT1 ameliorates intestinal barrier dysfunction, diarrhea symptoms and colonic inflammation in LCA-treated mice and those with experimental colitis, highlighting LPCAT1 as a potential therapeutic target for gastrointestinal diseases characterized by intestinal barrier dysfunction and colonic inflammation. Additionally, our findings showed a positive correlation between LPCAT1 and biomarkers of intestinal barrier dysfunction and colonic inflammation in patients with ulcerative colitis. Collectively, these findings reveal the essential role of gut microbiota-derived LCA in the development of intestinal barrier dysfunction by activating LPCAT1, which worsens diarrhea symptoms in IBS and colonic inflammation in IBD. Inhibiting LPCAT1, therefore, presents a promising therapeutic strategy for both IBS-D and ulcerative colitis. This study provides insights into the molecular mechanisms involving LCA and an associated gut dysbiosis pattern in the pathogenesis of IBS-D, while also identifying new therapeutic targets aimed at maintaining intestinal homeostasis in gastrointestinal diseases, particularly in reducing IBD risks among the IBS-D population.
Comparing Clinicopathologic Features and Outcomes Between Young Children, Adolescents, and Adults with Rhabdomyosarcoma at a Single Institution
Authors: Boyd Karla , Leelatian Nalin , Morotti Raffaella , Deshpande Hari , Christison-Lagay Emily , McCollum Sarah , Shabanova Veronika , Pashankar Farzana , Vasquez Juan C. 
Published: January 2025

AbstractBackgroundThere are limited data comparing clinical and pathologic features and outcomes of rhabdomyosarcoma (RMS) between young children, adolescent/young adults (AYAs), and adults.Design/MethodsWe performed a retrospective chart review of patients with RMS treated at our institution between 2000 and 2017. We compared clinical and pathologic features, treatment modalities, and outcomes among three different age groups (young children: <15 years of age, AYA: 15-39 years of age, and older adults: >39 years of age).ResultsAmong 65 patients, 33 (50.8%) were young children, 14 (21.5%) were AYAs, and 18 (27.7%) were older adults. Head and neck was the most common tumor site among young children, AYAs tumor sites were variable, while extremities were the most frequent location for adults. AYAs were more likely to have stage 4 disease at presentation (64.3% vs. 21.2% in children, p=0.01, and vs. 27.8% in adults, p=0.08). Similarly, clinical group and risk classifications were higher among AYAs as compared to the other two age groups. Tumors in children were alveolar and embryonal histology, while AYAs primarily developed alveolar RMS. Older adults had tumors with diverse histologies, including pleiomorphic and spindle cell. Children and AYAs received multimodal therapy, but a subset of adults did not. Five-year overall survival (OS) varied by age at diagnosis (p=0.001), with highest OS among young children (81.8%) following by adults (50.0%), with the lowest OS among AYAs (14.29%).ConclusionThis study highlights the need for ongoing collaboration between pediatric and adult multidisciplinary teams to improve outcomes for patients with RMS across the age spectrum.
INSIGHTFUL: Insight Generation through Clinical Annotation, Analysis, and Modeling of Suicide-Related Factors towards Understanding and Lifesaving
Authors: Li Zehan , Vieira Rodrigo M , Fu Sunyang , Hu Yan , Wang Wanjing , Wen Andrew , Lane Scott , Selek Salih , Shahani Lokesh , Xu Hua , Soares Jair C , Liu Hongfang , Huang Ming 
Published: January 2025

AbstractObjectiveSuicide is a critical medical and public health challenge, particularly among individuals with mental illnesses in safety-net hospitals. To uncover insights about suicidality embedded in unstructured clinical notes, we propose to annotate, analyze, and model a corpus for suicidality understanding and lifesaving.MethodsA multidisciplinary panel developed an annotation guideline to capture four key suicide-related factors: Suicidal Ideation (SI), Suicide Attempt (SA), Exposure to Suicide (ES), and Non-Suicidal Self-Injury (NSSI). We created an annotated corpus of 500 notes through a clinically validated annotation process and performed cohort analysis to characterize demographic and suicidal distributions. A large language model was deployed for automatic classification.ResultsThe annotated corpus was created with a Cohen’s Kappa of 0.95 and further de-identified for data sharing. Most notes (79.4%) contained one (34.4%) or more (45%) suicide-related labels, with SI and SA co-occurrence as the most frequent combination (35.6%), which demonstrates significant overlap. The cohort was characterized with a mean age of 33.4, 51.7% male, and 75.8% singles. Prevalent stressors included unemployment (24.2%), homelessness (12.0%), limited healthcare access (5.4%), and legal challenges (5.0%). We identified four key insights to improve documenting suicidality, including implicitness, confliction, ambiguity, and definition coverage incompleteness. The baseline model achieved a micro-averaged F1 score of 0.70, demonstrating satisfying performance in multi-label classification.ConclusionThe near-perfect inter-annotator agreement underscores the proposed annotation process and data quality. Cohort analysis highlights the distribution and documentation insights of suicidality. Data modeling demonstrates the potential of insight generation via AI-powered methods for mining large-scale clinical notes.
Evaluation of the Prognostic Value of Four ECM-Associated Genes in Recurrence and Metastasis of Colorectal Cancer
Authors: Avcıoğlu Seçil Durel , Charyeva Sulgun , Erdoğan Beyza Doğanay , Kaymaz Özlem , Durhan Abdullah , Aksel Bülent , Yazıcı Ozan , Savaş Berna , Ensari Arzu , Kıvrak Hale , Engin Evren Doruk , Belder Nevin , Özdağ Hilal 
Published: January 2025

ABSTRACTColorectal cancer is a significant public health issue due to its high incidence and high mortality rate, especially when diagnosed late. Identifying new biomarkers that can predict the diagnosis and prognosis of CRC is critical to reducing the mortality rate of the disease. This study tested the relationship of four extracellular matrix genes (COL1A1, COL5A1, THBS2 and FN1) with CRC prognosis at the mRNA and protein levels. Our previous studies identified these genes as candidate prognostic biomarkers for CRC. They were analysed in two cohorts: retrospective (130 CRC tumours and 70 healthy colon tissues) and prospective (160 paired tumours and normal tissues with 180 CRC serum samples).Accordingly, in the retrospective cohort, COL1A1 (p>0.0001), COL5A1 (p>0.0001), THBS2 (0.0001) and FN1 (0.001) were expressed at higher levels in tumours compared to controls by qRT-PCR and in metastatic cases compared to non-metastatic cases. In the same cohort, immunohistochemistry analysis showed that increasing protein levels of COL1A1 and FN1 correlated with mRNA levels. In addition, high COL1A1 mRNA levels were associated with OS (p>0.011), RFS (p>0.0001), and DMFS (p>0.0001), high COL5A1 mRNA levels were associated with OS (0.042), RFS (0.013), DMFS (p>0.003) and high FN1 levels were associated with DMFS (p>0.039). In the prospective cohort, COL1A1, COL5A1 and THBS2 were found to be higher in tumour tissue compared to matched normal tissue and in metastatic tumours compared to primary tumours by qRT-PCR in 160 tumours and matched normal tissues. In this cohort, FN1 levels were unexpectedly higher in normal tissues than in tumour tissues. In the prospective cohort, where 180 CRC serum samples were also tested by ELISA, COL1A1 (p>0.0001), COL5A1 (p>0.05), and THBS2 (p>0.05) levels were higher in metastatic cases than in the sera of non-metastatic cases. As a result, this study associated COL1A1, COL5A1 and THBS2 genes, which have different data on their prognostic effects in the literature, with poor prognosis of CRC at both mRNA and protein levels.
Genetic variants within silencer elements contribute to human blood cell traits
Authors: Tan Minkang , van Weerd Jan , Yavas Alper , Pang Baoxu 
Published: January 2025

AbstractGenome-wide association studies (GWAS) have identified numerous non-coding loci associated with human complex traits and diseases. However, assigning the functional impacts to the underlying variants remains challenging. In this study, we performed high-throughput ReSE screening to characterize the effects of 14,720 fine-mapped causal non-coding SNPs associated with 15 diverse blood traits on the potential silencer activity. By prioritizing non-coding variants that confer allelic imbalances in silencer activity, we identified epigenomic signatures of silencer-related variants and assessed their heritability contributions to specific blood traits. We conducted mechanistic studies on individual silencer variants and characterized the transcriptional factors (TF) that may recognize the silencer elements harboring the blood traits-related GWAS variants. We showed the silencer activity of GWAS variantsrs4808806which is related to red blood cell distribution width (RDW) andrs10758656which is associate with mean corpuscular hemoglobin (MCH) and mean corpuscular volume (MCV) traits. Our study underscores the importance of investigating the silencer-activity-related variants in post-GWAS functional studies.