bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yeast DNA Polymerase δ Proofreading Nuclease Suppresses Translesion Synthesis and Facilitates Recombination in DNA Lesion Bypass
Authors: Che Jun , Wang Quan , He Jiapeng , Zhang Zhao , Chung Jee Min , Gallagher Danielle N. , Hong Xin , Rao Hai , Shim Eun , Haber James E. , Niu Hengyao , Lee Sang Eun 
Published: January 2025

AbstractTranslesion synthesis (TLS) employs specialized polymerases to incorporate nucleotides opposite DNA lesions, allowing replication to continue temporarily without repairing the lesions, while sacrificing replication fidelity (1). TLS depends on a ubiquitin molecule attached to the clamp PCNA at residue Lys164(2, 3); the precise biochemical and molecular basis how PCNA modification stimulates TLS is still elusive (4-10). In this study, we discovered that DNA polymerase δ (Pol δ) 3’ to 5’ “proofreading” exonuclease degrades nascent TLS synthesis opposite pyrimidine dimers and inhibits TLS on both leading and lagging strands. Rad18 E3 ligase and PCNA ubiquitylation become dispensable for TLS when Pol δ exonuclease is inactive. Biochemical reconstitution showed that the major UV lesion bypass polymerase Rad30 is intrinsically inefficient at bypassing thymidine dimers and requires multiple turnovers. Pol δ exonuclease impedes Rad30 activity both catalytically and non-catalytically during and post-lesion bypass. Importantly, PCNA and PCNA ubiquitylation enhance processivity of Rad30 after thymidine dimer bypass, a critical step for further DNA synthesis extension and overcoming Pol δ inhibition. Our study reveals a new paradigm how PCNA ubiquitylation facilitates TLS and the new role of Pol δ nuclease in lesion bypass pathway choice and replication fidelity at fork-blocking DNA lesions.
Exploring the Pathogen Profiles of Ancient Feces
Authors: Capone Drew , Holcomb David , Lai Amanda , Reinhard Karl , Brown Joe 
Published: January 2025

AbstractAnalysis of ancient desiccated feces – termed paleofeces or coprolites – can unlock insights into the lives of ancient people. We collected desiccated feces from caves in the Rio Zape Valley in Mexico (725-920 CE). First, we extracted DNA with methods previously optimized for paleofeces. Then, we applied highly sensitive modern molecular tools (i.e., PCR pre-amplification followed by multi-parallel qPCR) to assess the presence of 30 enteric pathogens. We detected ≥1 pathogen associated gene in each of the ten samples and a mean of 3.9 pathogens per sample. The targets detected includedBlastocystisspp. (n=7), atypical enteropathogenicE. coli(n=7),Enterobius vermicularis(n=6),Entamoebaspp. (n=5), enterotoxigenicE. coli(n=5),Shigellaspp./enteroinvasiveE. coli(n=3),Giardiaspp. (n=2), andE. coliO157:H7 (n=1). The protozoan pathogens we detected (i.e.,Giardiaspp. andEntamoebaspp.) have been previously detected in paleofeces via enzyme-linked immunoassay (ELISA), but have not via PCR. This work represents the first detection ofBlastocystisspp. atypical enteropathogenicE. coli, enterotoxigenicE. coli, Shigellaspp./enteroinvasiveE. coli, andE. coliO157:H7 in paleofeces. These results suggest that sensitive modern molecular tools, such as PCR, can be used to evaluate ancient materials for genes of interest.
Deciphering the Host-Pathogen Interface in COVID-19: The precision molecular insight into epitranscriptomic modifications of high-impact transcripts
Authors: Maździarz Mateusz , Krawczyk Katarzyna , Lepiarczyk Ewa , Paukszto Łukasz , Makowczenko Karol G. , Moczulska Beata , Iwanowicz Piotr , Kocbach Piotr , Sawicki Jakub , Gromadziński Leszek , Majewska Marta 
Published: January 2025

ABSTRACTThe COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had a profound global impact since its emergence in late 2019. Characterized by a wide spectrum of clinical manifestations, ranging from asymptomatic infection to severe respiratory distress and death, COVID-19 has necessitated extensive research into the host-pathogen interactions that drive disease progression. Understanding the molecular mechanisms underlying the host response to SARS-CoV-2 infection is crucial for the development of effective therapeutic interventions and preventative strategies. This study employed a multi-omic approach that combined direct RNA sequencing (DRS) and Illumina cDNA sequencing to investigate whole blood transcriptomic profiles in COVID-19 patients. By leveraging the unique capabilities of Nanopore DRS, which provides long-read sequencing data, we were able to capture not only gene expression levels but also crucial RNA modifications, including poly(A) tail length, non-adenine residue (non-A), pseudouridylation (psU), and 5-methylcytosine (m5C) methylation. This comprehensive analysis allowed us to identify differentially expressed genes (DEGs) and explore the impact of these RNA modifications on gene expression and function within the context of COVID-19. Our findings reveal significant alterations in gene expression patterns, poly(A) tail lengths, non-A and the prevalence of psU and m5C modifications in COVID-19 patients compared to healthy controls. These results provide valuable insights into the complex interplay between viral infection, host immune response, and RNA processing, contributing to a deeper understanding of COVID-19 pathogenesis.
Deciphering landscape-scale plant cover and biodiversity from soil eDNA
Authors: Goodall Tim , Griffiths Robert I. , Gweon Hyun S. , Norton Lisa , Busi Susheel Bhanu , Read Daniel S. 
Published: January 2025

AbstractBiodiversity surveys are critical for detecting environmental change; however, undertaking them at scale and capturing all available diversity through observation is challenging and costly. This study evaluated the potential of soil-extracted eDNA to describe plant communities and compared these findings to traditional, observation-based, field surveys. We analysed 789 soil samples using high-throughput amplicon sequencing and compared DNA-based diversity metrics, indicator taxa, predicted vegetation class, and plant cover in a comparison with co-located field survey data. The results indicated that taxonomically aggregated (genus) eDNA-derived data, while showing slightly reduced Shannon’s diversity scores, yielded remarkably similar overall richness and composition estimates. However, the DNA indicator taxa and predictive power for vegetation community classification were also lower overall than those recorded by the field survey. However, in many cases plant cover could be inferred from amplicon abundance data with some accuracy despite widely differing scales of sampling – 0.25 g crumb of soil versus a 1 m2quadrat. Overall, results from eDNA demonstrated lower sensitivity but were broadly in accordance with traditional surveys, with our findings revealing comparable taxonomic resolution at the genus level. We demonstrate the potential and limitations of a simple molecular method to inform landscape-scale plant biodiversity surveys, a vital tool in the monitoring of land use and environmental change.
Convergent molecular evolution associated with repeated transitions to gregarious larval behaviour in Heliconiini
Authors: Cicconardi Francesco , McLellan Callum F. , Seguret Alice , McMillan W. Owen , Montgomery Stephen H. 
Published: January 2025

AbstractCollective behaviour forms the basis for many anti-predator strategies. Within Lepidoptera, larval gregariousness has evolved convergently across many phylogenetically disparate lineages. While the selection pressures shaping variation in larval social behaviours are well investigated, much less is known about the mechanisms that control social attraction and behavioural coordination. Similarly, little is known about how secondary selection pressures associated with social living shape genome evolution. Here, using genomic data for over 60 species from an adaptive radiation of Neotropical butterflies, the Heliconiini, in which gregarious behaviour has evolved repeatedly, we explore the molecular basis of repeated convergent shifts towards gregarious larvae. We focus on three main areas of genomic evolution: differential selection on homologous genes, accelerated rates of evolution on non-coding regions of key genes, and differential gene expression in the brains of solitary and gregarious larvae. We identify strong signatures of convergent molecular evolution, on both coding and non-coding loci, in Heliconiini lineages which evolved gregarious behaviour. Molecular convergence is also detected at the transcriptomic level in larval brains, suggesting convergent shifts in gene regulation in neural tissue. Among loci showing strong signals of convergent evolution in gregarious lineages, we identify several strong candidates linked to neural activity, feeding behaviour, and immune pathways. Our results suggest sociality profoundly changes the selection pressures acting on multiple physiological, immunological and behavioural traits.
A Simple, Low-Cost, and Efficient Protocol for Rapid Isolation of Pathogenic Bacteria from Human Blood
Authors: Coskun Fatma S. , Quick Joshua , Toprak Erdal 
Published: January 2025

AbstractBacteremia is a serious clinical condition in which pathogenic bacteria enter the bloodstream, putting patients at risk of septic shock and necessitating antibiotic treatment. Choosing the most effective antibiotic is crucial not only for resolving the infection but also for minimizing side effects, such as dysbiosis in the healthy microbiome and reducing the selection pressure for antibiotic resistance. This requires prompt identification of the pathogen and antibiotic susceptibility testing, yet these processes are inherently slow in standard clinical microbiology labs due to reliance on growth-based assays. Although alternative methods exist, they are rarely adopted in clinical settings because they involve complex protocols and high costs for training and infrastructure. Here, we present an optimized, simple protocol for rapidly and efficiently isolating bacterial pathogens from blood without altering typical laboratory workflows. Our method is cost-effective and compatible with commonly available laboratory instruments, offering the advantage of isolating bacterial cells directly, which bypasses the delays associated with traditional blood culture methods and enables faster diagnostic results. The protocol achieved over 70% efficiency within 30 minutes, remained effective at low bacterial concentrations (1–10 bacteria/0.3 mL blood), and preserved bacterial viability with no notable change in growth lag times. We validated the protocol on several clinically relevant bacterial strains, includingEscherichia coli, Klebsiella pneumoniae, andStaphylococcus aureus. These findings highlight our protocol’s potential utility in clinical and research settings, facilitating timely cultures and minimizing diagnostic delays.
Resetting public adherence: iterative strategies to counteract pandemic fatigue
Authors: Rikani Albano , Di Domenico Laura , Sabbatini Chiara E. , Navarro Victor , Ferres Leo , Raude Jocelyn , Colizza Vittoria 
Published: January 2025

AbstractNon-pharmaceutical interventions (NPIs) are essential for controlling infectious diseases during pre-vaccine periods, yet their success hinges on sustained public adherence. This study investigates adherence dynamics to tiered restriction systems implemented during COVID-19 in six geographical regions across Europe, North America, Africa, and South America. Using daily mobility data and linear-mixed models, we assessed three types of fatigue: overall fatigue (linked to cumulative time under restrictions), tier fatigue (linked to time spent under a specific tier), and iteration fatigue (linked to repeated implementation of the same tier). Tier fatigue caused the most rapid adherence loss, producing effects within days that overall fatigue required months of restrictions to achieve. Iterative application of shorter NPIs, interspersed with temporary relaxation, helped reset adherence, mitigating fatigue and sometimes even improving compliance. Psychological relief and a sense of regained autonomy during relaxation periods may renew public willingness to comply when restrictions are reintroduced. These findings emphasize the dual benefits of short, strategic NPIs for epidemic control and public resilience, offering actionable insights for designing more sustainable pandemic interventions.
The effects of antibiotic prescribing for respiratory tract infection on future consultations in primary care: a systematic review and meta-analysis
Authors: Adamu Ibrahim , Lambert Amanda , Bello Safiyya , Abdulmalik Fatima Aminu , Marshall Tom 
Published: January 2025

AbstractObjectivesPrescribing antibiotics may reinforce patients’ beliefs antibiotics are needed and increase future consultations for similar symptoms. This review determines the effect of antibiotic prescribing for respiratory infections in primary care on future reattendance.Design, setting and participantsA systematic review and meta-analysis of randomised controlled trials and cohort studies, following Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines.Participants were adults or children presenting with respiratory infection in primary care.InterventionsPrescription of antibiotics.Primary outcome measureReattendance at least 28 days after initial consultation.MethodEligible studies included open-label randomised controlled trials (RCT) or cohort studies of antibiotics compared to no antibiotics in adults or children with respiratory infections. MEDLINE (Ovid), PubMed, Embase, the Cochrane Central Register of Controlled Trials, clinical trial registries and grey literature sources were searched from inception until 6thFebruary 2024. Two reviewers independently screened, selected, assessed quality and extracted data. Separate meta-analyses were presented for RCT and cohort studies.ResultsWe identified 2128 records and reviewed 48 full texts, of which five met inclusion criteria. These reported three RCTs (1207 randomised to antibiotics, 672 controls) and three cohort studies (209,138 exposed to antibiotics, 46,469 controls). In the meta-analysis of randomised trials, relative risk (RR) of reattendance with antibiotics was 1.10 (95%CI: 0.99 to 1.23) and in the cohort studies RR was 1.21 (95%CI: 0.94 to 1.49). An important limitation is that most studies were in UK primary care.ConclusionEvidence suggests prescribing antibiotics for acute respiratory tract infections in primary care probably modestly increases future reattendance for similar conditions. Reducing antibiotic prescribing may help reduce demand for primary care.PROSPERO registration numberCRD42023470731Article summaryThis systematic review of antibiotic prescribing for uncomplicated upper respiratory tract infections finds that antibiotics probably increase future consultations.Strengths and limitationsThis is the first systematic review of the effects of antibiotic prescribing for upper respiratory tract infections.The finding that antibiotic prescribing increases future consultations for upper respiratory tract infections is consistent with other evidence.The effect just fails to meet statistical significance.Almost all the studies were undertaken in the UK, which may limit the generalisability.
DNA-encoded Library Screening Uncovers Potent DNMT2 Inhibitors Targeting a Cryptic Allosteric Binding Site
Authors: Frey Ariane F. , Schwan Merlin , Weldert Annabelle C. , Kadenbach Valerie , Kopp Jürgen , Nidoieva Zarina , Zimmermann Robert A. , Gleue Lukas , Zimmer Collin , Jörg Marko , Friedland Kristina , Helm Mark , Sinning Irmgard , Barthels Fabian 
Published: January 2025

ABSTRACTThe human RNA methyltransferase DNMT2 is thought to be involved in various pathophysiological processes, yet, a major challenge in drug targeting DNMT2 is given by the fact that current SAH-derived inhibitors have poor target selectivity and limited cellular permeability. In this study, we have performed a DNA-encoded library (DEL) screening on DNMT2 yielding five non-SAH-like hit structures, three of which feature a peptidomimetic scaffold. All DEL hits could be validated by orthogonal biophysical and biochemical assays for DNMT2 binding. At the same time, the lead structure did not interact with related methyltransferases from the DNMT and NSUN families highlighting an unmatched DNMT2-targeting selectivity profile. Subsequent crystallographic studies revealed the unique ligand binding mode including an active site loop rearrangement and the formation of a cryptic allosteric binding pocket able to modulate the enzymatic activity by non-covalent DNMT2 dimerization. Based on the crystallographic results, we performed a structure-activity relationship study around the inhibitor lead structure resulting in an optimized DNMT2 inhibitor (KD=3.04 µM), which was able to reduce m5C levels in MOLM-13 tRNA.GRAPHICAL ABSTRACT
Identifying memory gene expression from single sample scRNA-seq data using power law signatures
Authors: Ghosh Suvranil , Chakrabarti Shaon , Raju Archishman 
Published: January 2025

1AbstractGenes with expression levels that fluctuate on time scales longer than cell division times are associated with cancer drug tolerance. However, current methods for identifying such ‘memory’ genes rely on variants of the Luria-Delbrück experiment and require either multiple replicates or lineage information, limiting their use to model systems orin-vitrosettings. We develop a new conceptual approach using recent results in Random Matrix Theory to demonstrate that the existence of memory genes results in a power-law signature in the cell covariance matrix eigenspectrum. Utilizing this theoretical framework, we develop Power-Seek, an algorithm to discover memory genes from a single time point scRNA-seq dataset. Without using prior information on lineages or cell-cycle times, Power-Seek correctly identifies memory genes in a melanoma cell line. Our results open up the possibility of identifying expression states driving drug tolerance in real-world scenarios, as we demonstrate using data from a human breast cancer tissue sample.
The histone modification regulator, SIN3, plays a role in the cellular response to changes in glycolytic flux
Authors: Soukar Imad , Mitra Anindita , Vo Linh , Rofoo Melanie , Greenberg Miriam L. , Pile Lori A. 
Published: January 2025

AbstractEpigenetic regulation and metabolism are connected. Epigenetic regulators, like the SIN3 complex, affect the expression of a wide range of genes, including those encoding metabolic enzymes essential for central carbon metabolism. The idea that epigenetic modifiers can sense and respond to metabolic flux by regulating gene expression has long been proposed. In support of this cross-talk, we provide data linking SIN3 regulatory action on a subset of metabolic genes with the cellular response to changes in metabolic flux. Furthermore, we show that loss of SIN3 is linked to decreases in mitochondrial respiration and the cellular response to mitochondrial and glycolytic stress. Data presented here provide evidence that SIN3 is important for the cellular response to metabolic flux change.
Dynamics of Bacterial and Viral Transmission in Experimental Microbiota Transplantation
Authors: Weagley James , Makimaa Heyde , Cárdenas Luis Alberto Chica , Romani Ana , Sullender Meagan , Aggarwal Somya , Hogarty Michael , Rodgers Rachel , Kennedy Elizabeth , Foster Lynne , Schriefer Lawrence A. , Baldridge Megan T. 
Published: January 2025

AbstractMouse models are vital tools for discerning the relative contributions of host and microbial genetics to disease, often requiring the transplantation of microbiota between different mouse strains. Transfer methods include antibiotic treatment of recipients and colonization using either co-housing with donors or the transplantation of fecal or cecal donor material. However, the efficiency and dynamics of these methods in reconstituting recipients with donor microbes is not well understood. We thus directly compared co-housing, fecal transplantation, and cecal transplantation methods. Donor mice from Taconic Biosciences, possessing distinct microbial communities, served as the microbial source for recipient mice from Jackson Laboratories, which were treated with antibiotics to disrupt their native microbiota. We monitored microbial populations longitudinally over the course of antibiotics treatment and reconstitution using 16S rRNA gene sequencing, quantitative PCR, and shotgun sequencing of viral-like particles. As expected, antibiotic treatment rapidly depleted microbial biomass and diversity, with slow and incomplete natural recovery of the microbiota in non-transplanted control mice. While all transfer methods reconstituted recipient mice with donor microbiota, co-housing achieved this more rapidly for both bacterial and viral communities. This study provides valuable insights into microbial transfer methods, enhancing reproducibility and informing best practices for microbiota transplantation in mouse models.
ER-associated degradation relying on protein O-mannosylation
Authors: Lemus Leticia , Meyer Hadar , Rodriguez Ana , Schuldiner Maya , Goder Veit 
Published: January 2025

SummaryProtein quality control in the secretory pathway, whose dysfunction is linked to various human diseases, begins in the endoplasmic reticulum (ER) and involves ER-associated degradation (ERAD) of terminally misfolded species. We have addressed the roles of protein O-mannosylation in ERAD using complementary genome-wide screens in yeast. Our findings reveal that protein O-mannosylation by the conserved ER-resident O-mannosyltransferase complex Pbn1-Gpi14 generates ERAD cues. This mechanism participates in regulating ERAD of substrates that contain serine-rich regions and provides a fail-safe mechanism for the degradation of non-N-glycosylated misfolded proteins. Our data suggest that thede novosynthesis of ERAD cues through protein O-mannosylation is an essential component of ER quality control.
Defining the networks that connect RNase III and RNase J-mediated regulation of primary and specialized metabolism inStreptomyces venezuelae
Authors: Pepler Meghan A.D. , Mulholland Emma L. , Montague Freddie R. , Elliot Marie A. 
Published: January 2025

ABSTRACTRNA metabolism involves coordinating RNA synthesis with RNA processing and degradation. Ribonucleases play fundamental roles within the cell, contributing to the cleavage, modification, and degradation of RNA molecules, with these actions ensuring appropriate gene regulation and cellular homeostasis. Here, we employed RNA-sequencing to explore the impact of RNase III and RNase J on the transcriptome ofStreptomyces venezuelae. Differential expression analysis comparing wild type and RNase mutant strains at distinct developmental stages revealed significant changes in transcript abundance, particularly in pathways related to multicellular development, nutrient acquisition, and specialized metabolism. Both RNase mutants exhibited dysregulation of the BldD regulon, including altered expression of many cyclic-di-GMP-associated enzymes. We also observed precocious chloramphenicol production in these RNase mutants and found that in the RNase III mutant, this was associated with PhoP-mediated regulation. We further found that RNase III directly targeted members of the PhoP regulon, suggesting a link between RNA metabolism and a regulator that bridges primary and specialized metabolism. We connected RNase J function with translation through the observation that RNase J directly targets multiple ribosomal protein transcripts for degradation. These findings establish distinct, but complementary roles for RNase III and RNase J in coordinating the gene expression dynamics critical forS. venezuelaedevelopment and specialized metabolism.