bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sociodemographic Determinants of Multidrug-Resistant Tuberculosis in Lesotho: A Case-Control Study
Authors: Yahaya Jerry Yakubu 
Published: December 2024

AbstractThe emergence of multidrug-resistant tuberculosis (MDR-TB) poses a significant challenge to tuberculosis control efforts in Lesotho. To better understand the occurrence of MDR-TB, it is crucial to identify the sociodemographic risk factors associated with the disease. Despite the critical importance of this issue, there is a gap in the literature regarding how sociodemographic variables influence MDR-TB outcomes in Lesotho. This case-control study aimed to assess the association between age, employment, income, sex, education, and place of residence and the risk of MDR-TB. Additionally, the relationship between HIV status and MDR-TB was examined. Drawing on the health belief model and social cognitive theory, the study employed a retrospective case-control design and a proportionate stratified random sample of 306 participants from 12 TB clinics across Lesotho, collected between March 2021 and February 2022. Participants included confirmed TB patients aged 18 and above. Data analysis involved Chi-square tests and multivariate logistic regression to identify significant sociodemographic factors associated with MDR-TB. Results showed that increased age beyond 18–26 years and higher income levels (above $1,026.00) were significantly associated with reduced odds of MDR-TB (OR = 0.8, 95% CI [0.673, 0.991], p = 0.040; OR = 0.5, 95% CI [0.222, 0.943], p = 0.034). Conversely, the absence of a caregiver increased the odds of MDR-TB by 80% (OR = 1.8, 95% CI [1.039, 3.110], p = 0.036). These findings underscore the need for targeted public health interventions and education campaigns to address the role of caregivers in preventing MDR-TB transmission and to improve knowledge about infection control, particularly among younger patients. Furthermore, improving the socioeconomic conditions of TB patients, particularly those who are poor and vulnerable, is essential for reducing the risk of MDR-TB. Addressing these sociodemographic determinants can significantly enhance the effectiveness of MDR-TB control strategies in Lesotho.
Evolutionary Flexibility of Ribosome Biogenesis in Bacteria
Authors: Amikura Kazuaki , Ishii Shun’ichi , Shimizu Yoshihiro , Suzuki Shino 
Published: December 2024

AbstractRibosomes are essential for protein synthesis and require ribosome biogenesis factors (RBFs) for assembly. To uncover the evolutionary diversity of ribosome biogenesis, we analyzed over 30,000 bacterial genomes and revealed that Candidate Phyla Radiation (CPR), also known as the phylum Patescibacteria, characterized by reduced genomes and smaller ribosomes, has about half the average number of RBFs compared with non-CPR bacteria. Notably, key RBFs such as der, obgE, and rbfA, considered indispensable, are conserved in only around 20%–70% of CPR genomes. Since such repertoires were not observed in reduced genomes of other phyla, CPR presumably diverged early in bacterial evolution. We further confirmed that ribosomal structural changes correlate with reduced RBFs, evidencing co-evolution between RBFs and the ribosome. These findings suggest that ribosomal biogenesis is more flexible than recognized, and the small cell and genome sizes of CPR bacteria and their early divergence may influence the unusual repertoires of RBFs.TeaserRibosome biogenesis in CPR bacteria was unexpectedly flexible, challenging traditional views of this essential process in evolution.
Influenza A virus-induced PI4P production at the endoplasmic reticulum involves ATG16L1 and promotes the egress of viral ribonucleoproteins
Authors: Alemany Carla , Graça Juliane Da , Giai-Gianetto Quentin , Paisant Sylvain , Dupont Maud , Douché Thibaut , Isel Catherine , Delevoye Cédric , Danglot Lydia , Matondo Mariette , Morel Etienne , Brault Jean-Baptiste , Naffakh Nadia 
Published: December 2024

AbstractThe genomic RNAs of influenza A viruses (IAVs) are replicated in the nucleus of infected cells in the form of viral ribonucleoproteins (vRNP) before being exported to the cytoplasm. The small GTPase RAB11A is involved in the transport of vRNPs to the sites of viral assembly at the plasma membrane, but the molecular mechanisms involved remain largely unknown. Here we show that IAV infection remodels the architecture of the endoplasmic reticulum (ER) sheets, where vRNPs tend to accumulate in the absence of RAB11A. To decipher the interplay between RAB11A, vRNPs and the ER, we investigated viral-induced perturbations of RAB11A proximity interactome. To this end, we generated cells stably expressing a TurboID-RAB11A fusion protein and performed biotin-based proximity labeling upon viral infection. We found that cellular regulators of phophatidylinositol-4-phosphate (PI4P) homeostasis, including the autophagic and stress response protein ATG16L1, are significantly enriched at the vicinity of RAB11A in infected cells. Infection induces an increase in cellular PI4P levels in an ATG16L1-dependent manner, while ATG16L1 relocalizes to ER membranes upon infection. Depletion of ATG16L1 decreases the co-distribution of vRNPs with PI4P punctae on ER membranes, and reduces the accumulation of vRNPs at the plasma membrane as well as the production of IAV infectious particles. Our data extend to IAVs the notion that viruses can modulate the metabolism and localization of phosphoinositides to control host membrane dynamics and point to the ER as an essential platform for vRNP transport. They provide evidence for a pivotal role of ATG16L1 in regulating the identity of endomembranes and coordinating RAB11A and PI4P-enriched membranes to ensure delivery of vRNPs to the plasma membrane.
The RBR E3 ubiquitin ligase HOIL-1 can ubiquitinate diverse non-protein substratesin vitro
Authors: Wang Xiangyi S. , Jiou Jenny , Cerra Anthony , Cobbold Simon A. , Jochem Marco , Mak Ka Hin Toby , Corcilius Leo , Payne Richard J. , Goddard-Borger Ethan D. , Komander David , Lechtenberg Bernhard C. 
Published: December 2024

ABSTRACTHOIL-1 is a RING-between-RING (RBR)-family E3 ubiquitin ligase and component of the linear ubiquitin chain assembly complex (LUBAC). While most E3 ubiquitin ligases conjugate ubiquitin to protein lysine sidechains, HOIL-1 has been reported to ubiquitinate hydroxyl groups in protein serine and threonine sidechains and glucosaccharides, such as glycogen and its building block maltose,in vitro. However, HOIL-1 substrate specificity is currently poorly defined. Here we show that HOIL-1 is unable to ubiquitinate lysine but can efficiently ubiquitinate serine as well as a variety of model and physiologically relevant di- and monosaccharidesin vitro. We identify a critical catalytic histidine residue, His510, in the flexible catalytic site of HOIL-1 that enables this O-linked ubiquitination and prohibits ubiquitin discharge onto lysine sidechains. Finally, we utilise HOIL-1’sin vitronon-proteinaceous ubiquitination activity and an engineered, constitutively active HOIL-1 variant to produce preparative amounts of different ubiquitinated saccharides that can be used as tool compounds and standards in the rapidly emerging field of non-proteinaceous ubiquitination.
Role of a FAD-dependent monooxygenase in diazo group functionalisation of kinamycin inStreptomyces ambofaciens
Authors: Vicente Cláudia M , Boutilliat Alexis , Hôtel Laurence , Paris Cédric , Aigle Bertrand 
Published: December 2024

AbstractKinamycin biosynthesis is a complex process which has been extensively studied over the years, yet specific enzymatic steps continue to be unveiled. A diazo group present in the molecule is responsible for the promising antitumoral activity of kinamycins but its specific installation inStreptomyces ambofaciensis not fully understood. In this study, we explore the diazo functionalization of kinamycin in this strain. A new FAD-dependent monooxygenase is identified which is essential for kinamcyin biosynthesis. In its absence, stealthin C accumulates instead likely as a pathway shunt-product. Furthermore, as a result of the position of the gene encoding this monooxygenase, namedalp2F, we also propose new boundaries of the kinamycin biosynthetic gene cluster resulting in a large cluster spanning over 72kb. This work paves the way for the continued understanding of the biosynthetic steps that are characteristic of diazo-containing natural products, and provides new biocatalysts for molecular engineering and accelerate bioactive compounds production.
Direct Feature Identification from Raman Spectra and Precise Data-driven Classification of Phytopathogens at Single Conidium-Species Level
Authors: Xu Xinze , Cheng Zhang , Liu Wenbo , Lin Chunhua , Miao Weiguo , Yuan Heyang 
Published: December 2024

ABSTRACTConidia can cause outbreaks of fungal plant diseases, resulting in significant losses in crop yield and economy. Traditional diagnosis of phytopathogenic conidia based on morphology and molecular biology is time-consuming, labor-intensive, and often fails to differentiate fungal conidia. To overcome these challenges, a new classification approach was developed in this study by integrating Raman spectroscopy with data-driven modeling. Eight fungal species were selected and characterized using Raman spectra. Three characteristic Raman wavenumbers at 1003 to 1005 cm-1, 1153 to 1157 cm-1, and 1515 to 1522 cm-1shared a consistent pattern across species and could be attributed to carotenoids. Clustering of the Raman spectra using principal component analysis (PCA) showed substantial overlap, indicating inaccurate classification of conidia. Three data-driven models, support vector machines (SVMs), decision trees (DTs), and eXtreme Gradient Boosting Forest (XGBoost) were trained with three categories of features (number of peaks, maximum peak, and curve roughness) identified within eight characteristic wavenumber ranges, The optimal SVM, DT, and XGBoost determined by hyperparameter tuning achieved prediction precision of 0.88, 0.88, and 0.96, respectively. PCA-XGBoost trained by feeding principal components of PCA to XGBoost achieved prediction precision of 0.94, suggesting that features extracted from the raw datasets outperformed those extracted with PCA in terms of data-driven classification. This study has demonstrated the great potential of Raman spectroscopy combined with data-driven modeling for classification of phytopathogenic conidia.
Dysregulated RNA splicing induces regeneration failure in alcohol-associated liver disease
Authors: Chembazhi Ullas V. , Bangru Sushant , Dutta Rajesh , Das Diptatanu , Peiffer Brandon , Natua Subhashis , Toohill Katelyn , Leona Aurelia , Purwar Ishita , Bhowmik Anuprova , Goyal Yogesh , Sun Zhaoli , Diehl Anna Mae , Kalsotra Auinash 
Published: December 2024

ABSTRACTIndividuals with progressive liver failure are at a high risk of mortality without liver transplantation. However, our understanding of derailed regenerative responses in failing livers is limited. Here, we performed comprehensive multi-omic profiling of healthy and diseased human livers using bulk and single-nucleus RNA-plus ATAC-seq. We report that hepatic immune milieu alterations in alcohol-associated liver disease (ALD) prevent hepatocytes from transitioning to a proliferative progenitor-like state, trapping them into an unproductive intermediate state. We discovered striking changes in RNA binding protein (RBP) expression, particularly ESRP, PTBP, and SR families, that cause misregulation of developmentally controlled RNA splicing in ALD. Our data pinpoint ESRP2 as a pivotal disease-sensitive RBP and support a causal role of its deficiency in ALD pathogenesis. Notably, splicing defects in ESRP2-targetsTcf4andSlk, amongst others, directly alter their nuclear localization and activities, disrupting WNT and Hippo signaling pathways, which are critical for normal liver regeneration. We demonstrate that changes in stromal cell populations enrich failing ALD livers with TGF-β, which suppresses ESRP2-driven epithelial splicing program and replaces functional parenchyma with quasi-progenitor-like cells lacking liver-specific functions. This unprecedented account of transcriptional and post-transcriptional dysregulation in ALD suggests that targeting misspliced RNAs could improve recovery and serve as biomarkers for poor ALD outcomes.
Ultra-Efficient Integration of Gene Libraries onto Yeast Cytosolic Plasmids
Authors: Pisera Alexander (Olek) , Yu Yutong , Williams Rory L. , Liu Chang C. 
Published: December 2024

AbstractEfficient methods for diversifying genes of interest (GOIs) are essential in protein engineering. For example, OrthoRep, a yeast-based orthogonal DNA replication system that achieves the rapidin vivodiversification of GOIs encoded on a cytosolic plasmid (p1), has been successfully used to drive numerous protein engineering campaigns. However, OrthoRep-based GOI evolution has almost always started from single GOI sequences, limiting the number of locations on a fitness landscape from where evolutionary search begins. Here, we present a simple approach for the high-efficiency integration of GOI libraries onto OrthoRep. By leveraging integrases, we demonstrate recombination of donor DNA onto the cytosolic p1 plasmid at exceptionally high transformation efficiencies, even surpassing the transformation efficiency of standard circular plasmids into yeast. We demonstrate our method’s utility through the straightforward construction of mock nanobody libraries encoded on OrthoRep, from which rare binders were reliably enriched. Overall, integrase-assisted manipulation of yeast cytosolic plasmids should enhance the versatility of OrthoRep in continuous evolution experiments and support the routine construction of large GOI libraries in yeast in general.
Intact messenger RNA exists in human blood plasma and urine, and their purified macromolecular compartments
Authors: Verwilt Jasper , Verniers Kimberly , De Geyter Sofie , Roelandt Sofie , Pinheiro Cláudio , Hendrix An , Mestdagh Pieter , Vandesompele Jo 
Published: December 2024

AbstractIt is generally assumed that extracellular long RNA molecules in biofluids are fragmented. Few studies have indirectly hinted at the existence of possibly functional, intact long RNA transcripts. In search for such RNA molecules, we developed a long-read full transcript sequencing workflow for low-input and low-quality samples. We applied our method to human blood plasma, urine, and their isolated macromolecular compartments, in parallel with total RNA sequencing. This approach enabled us to find intact messenger RNA molecules in human biofluids and macromolecular compartments. We showed that the full-length transcriptome of human urine and blood plasma differs, but we also reveal intact messenger RNA molecules shared between biofluids. In addition, we show that these intact molecules are differentially distributed over fractionated macromolecular compartments. This study provides a foundation for future extracellular RNA studies to elucidate the human biofluid full-length transcriptome.
Bridgingin vitroandin vivoinsights: A PKPD model for effective phage therapy against multidrug-resistantPseudomonas aeruginosa
Authors: Cha Jun Seok , Kim Kyungnam , You Hwa Jeong , Kim Dasom , Park Hyun Hee , Heo SuJin , Kim Choon Ok , Jin Byung Hak , Yong Dongeun , Chae Dongwoo 
Published: December 2024

SUMMARYBacteriophage therapy provides a promising solution for multidrug-resistantPseudomonas aeruginosa. However, optimizing phage combinations and dosages remains challenging. Here, we developed and validated a pharmacokinetic-pharmacodynamic (PKPD) model integratingin vitroandin vivoefficacy data using three phage strains (MP-A, PP-A, and PP-B), administered both alone and in combination.In vitrophage resistance was substantially delayed by combining phages that exhibit collateral sensitivity. However, multiple phage resistance eventually emerged.In vivo,growth of phage-resistant mutants was minimal. Our model suggests that this outcome was due to an initial phage-induced reduction in bacterial load, followed by immune clearance of the phage-resistant bacteria. Simulations indicated that higher phage exposure at the site of infection caused a faster decline in bacterial levels below the immune clearance threshold and prevented excessive immune activation. Overall, this study offers crucial guidance for treatment strategies and highlights the importance of mathematical modeling in advancing phage therapy.
Internal states emerge early during learning of a perceptual decision-making task
Authors: Cuturela Lenca I. ,   The International Brain Laboratory, Pillow Jonathan W. 
Published: December 2024

SummaryRecent work has shown that during perceptual decision-making tasks, animals frequently alternate between different internal states or strategies. However, the question of how or when these emerge during learning remains an important open problem. Does an animal alternate between multiple strategies from the very start of training, or only after extensive exposure to a task? Here we address this question by developing a dynamic latent state model, which we applied to training data from mice learning to perform a visual decision-making task. Remarkably, we found that mice exhibited distinct “engaged” and “biased” states even during early training, with multiple states apparent from the second training session onward. Moreover, our model revealed that the gradual improvement in task performance over the course of training arose from a combination of two factors: (1) increased sensitivity to stimuli across all states; and (2) increased proportion of time spent in a higher-accuracy “engaged” state relative to biased or disengaged states. These findings highlight the power of our approach for characterizing the temporal evolution of multiple strategies across learning.
Robust characterization of selectivity of individual neurons to distinct task-relevant behavioral states using calcium imaging
Authors: Huang Huixin , Shah Garima , Adwanikar Hita , Mysore Shreesh P. 
Published: December 2024

ABSTRACTInvestigations into the neural basis of behavior have recently employed fluorescence imaging of calcium dynamics in a variety of brain areas to measure neural responses. However, across studies, diverse and seemingly subjective methodological choices have been made in assessing the selectivity of individual neurons to task-relevant behavioral states. Here, we examine systematically the effect of different choices in the values of key parameters from data acquisition through statistical testing on the inference of the selectivity of individual neurons for task states. We do so by using as an experimental testbed, neuronal calcium dynamics imaged in the medial prefrontal cortex of freely behaving mice engaged in a classic exploration-avoidance task involving spontaneous (animal-controlled) state transitions - navigation in the elevated zero maze (EZM). We report that a number of key variables in this pipeline substantially impact the selectivity label assigned to neurons, and do so in distinct ways. By quantitatively comparing newly defined accuracy and robustness metrics for all the 128 possible combinations of levels of the key parameters, we discover in a data-driven manner, two optimal combinations that reliably characterize neuronal selectivity – one using discrete calcium events and another using continuous calcium traces. This work establishes objective and standardized parameter settings for reliable, calcium imaging-based investigations into the neural encoding of task-states.
Anorectic and anxiogenic actions of cocaine– and amphetamine-regulated transcript in the lateral septum
Authors: Shankhatheertha Anjali , Payant Mikayla A , Phy-Lim Jenny , Chee Melissa J 
Published: December 2024

AbstractCocaine-and amphetamine-regulated transcript (CART) is produced in several brain regions including the hypothalamus where it is made in cells that also produce melanin-concentrating hormone (MCH). MCH+CART cells densely innervate the lateral septum (LS), which integrates food– and mood-related behaviours. However, while MCH typically promotes feeding and anxiolysis, CART suppresses feeding and promotes anxiogenesis. The LS is a target site of the orexigenic actions of MCH, but it is not known if the actions of CART converge or oppose that of MCH in the LS. We implanted a bilateral cannula over the lateral or central LS of male and female wildtype mice and infused vehicle, CART55–102, or co-infused CART and MCH. CART did not alter chow intake but suppressed the intake of a palatable high sugar diet in male and female mice, especially when delivered in the medial LS. Furthermore, CART also prevented the orexigenic effect of MCH on palatable feeding intake when infused in the medial LS. We then assessed if CART regulated anxiety-like behaviour via the LS and found that intra-LS CART infusion reduced time spent in the center of an open field in male but not female mice. Our findings indicated that CART elicited anorectic and anxiogenic actions and may function in opposition to or independently of MCH in the LS. These outcomes suggested that putative CART and MCH co-release from MCH neurons may provide biphasic regulation of feeding and anxiety via the LS.
Differential Expression of Edar and Xedar During Mouse and Rat Tail Appendage Development
Authors: Wisniewski Slawomir A. 
Published: December 2024

AbstractSkin appendages, such as hair follicles and scales, represent evolutionary adaptations that vary among different species. Mouse and rat tails exhibit distinct appendage types, with mice developing hair follicles and rats developing scales. The study investigated whether the differential expression of Edar and Xedar, critical regulators of ectodermal development, could explain these distinct developmental outcomes by measuring Edar and Xedar expression in mouse and rat tail tissues during embryonic development using quantitative real-time PCR. Expression levels were normalized to actin and analyzed using mathematical modeling and statistical approaches. It was found that distinct temporal patterns of gene expression between species. Mouse tissues showed a dramatic peak in Xedar expression during days 3-4, coinciding with hair follicle initiation, while rat tissues maintained relatively stable Xedar expression. Edar expression showed opposing trends between species, with a gradual increase in mice and a decrease in rats. These findings provide the first quantitative evidence for species-specific regulation of Edar and Xedar during appendage development, suggesting a molecular basis for determining hair versus scale fate.