bluuebunny/crossref_metadata_2025_split huggingface dataset:
The IL-33/ST2 signaling axis drives pathogenesis in acute SARS-CoV-2 infection
Authors: Fleming Claire , McSorley Henry J , Allen Judith E , Petri William A 
Published: November 2024

ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), remains a significant threat to global public health. Immunopathological damage plays a role in driving pneumonia, acute respiratory distress syndrome (ARDS), and multiorgan failure in severe COVID-19. Therefore, dissecting the pulmonary immune response to SARS-CoV-2 infection is critical to understand disease pathogenesis and identify immune pathways targetable by therapeutic intervention. Considering that the type 2 cytokine IL-13 enhances COVID-19 disease severity, therapeutic targeting of upstream signals that drive type 2 immunity may confer further protection. In this study, we investigate the role of the IL-33/ST2 signaling axis, a potent inducer of type 2 immunity in the lung, in a mouse model of COVID-19. Upon infection with mouse-adapted SARS-CoV-2 MA10, ST2-/-mice had significantly improved weight loss and survival (69.2% vs 13.3% survival; P = 0.0005), as compared to wild-type mice. In a complementary pharmacologic approach, IL-33/ST2 signaling was inhibited using HpBARI_Hom2, a helminth derived protein that binds to mouse ST2 and blocks IL-33 signaling. In SARS-CoV-2 MA10 infection, HpBARI_Hom2-treated mice had significantly improved weight loss and survival (60% vs 10% survival; P = 0.0035), as compared to inert control-treated mice. These data demonstrate that loss of IL-33/ST2 signaling confers protection during acute SARS-CoV-2 MA10 infection, implicating the IL-33/ST2 signaling axis as an enhancer of COVID-19 disease severity. The protection conferred by pharmacologic blockade of IL-33/ST2 signaling was independent of viral control, as HpBARI_Hom2-treated mice had no reduction in viral titers. This finding suggests an immunopathogenic role for IL-33/ST2 signaling. One potential mechanism through which IL-33/ST2 signaling may drive severe disease is through enhancement of type 2 immune pathways including IL-5 production, as pulmonary IL-5 concentrations were found to depend on IL-33/ST2 signaling in acute SARS-CoV-2 MA10 infection.
Structural and functional role of residues undergoing hereditary spastic paraplegias-linked mutations: insights from a simulation of the spiral to ring transition in katanin
Authors: Kelly Maria S. , Capelli Riccardo , Dima Ruxandra I. , Carloni Paolo 
Published: November 2024

Several dozen mutations in the large human spastin enzyme assembly have been associated with mobility impairment in hereditary spastic paraplegias. Some of them impact the structural determinants of two functional conformations of the protein, spiral and ring. Here we investigate the possible effect of the mutations on the transition between the two conformations, which is essential for the enzymatic function. By performing a variety of molecular simulations (including metadynamics) on the closely related protein katanin, we suggest that about one fourth of the known disease-associated mutations affect the transition and/or the stability of a previously unrecognized intermediate. The protocol used here can be applied to the study of conformational changes in other large biomolecular complexes.Significance StatementBy combining molecular dynamics and enhanced sampling simulations with custom-designed collective variables, we explore transient intermediate states in a large protein assembly, the severing enzyme katanin. This enzyme plays a critical role in neuronal microtubule remodeling. By targeting the transition between the spiral and ring conformations of the protein, we reveal mechanisms associated with neurodegenerative mutations that impair the function of spastin, a structurally and functionally similar enzyme. These findings provide insights that may inform future therapeutic strategies. They also expand our ability to simulate molecular processes relevant to health and disease, as our approach can be readily applied to study structural changes in other complex biological systems.
Motor protein-assisted glycan translocation and sequencing using nanopores
Authors: Ke Wenjun , Wu Pengcheng , Ma Shengzhou , Yang Yuting , Zhang Yiwei , Zhang Qingqing , Lu Xiaojie , Xia Bingqing , Wen Liuqing , Bai Jingwei , Gao Zhaobing 
Published: November 2024

AbstractThe glycan sequencing remains a significant bottleneck in glycoscience. While nanopore platforms have achieved substantial progress in single-molecule nucleic acid sequencing, their application to glycan sequencing has faced considerable challenges, with limited advancements to date. In this study, we propose a novel strategy for controlling glycan translocation through the MspA nanopore as an initial step toward glycan sequencing. By conjugating the target glycan with a helicase-controlled single-stranded DNA, we successfully achieved sequencing reads of up to eleven glycans. For the first time, we isolated glycan-associated electrical signals, enabling the translocation, stretching, and controlled speed of neutral glycans through the nanopore. This method provides a platform for obtaining glycan read lengths and identifying different glycan modifications, demonstrating the capability to resolve monosaccharide composition and glycosidic linkages. To further improve resolution, we propose engineered M2-MspA to reduce the pore constriction size and enhance precision by minimizing the random thermal motion of the translocating glycan. These modifications are expected to increase the sequencing accuracy and reliability. This work represents the first proof-of-concept demonstration of glycan chain nanopore sequencing and lays a promising foundation for the development of single-molecule glycan fingerprinting and sequencing technologies. We anticipate that this approach will significantly advance the development and commercialization of nanopore-based glycan sequencing techniques.
Genome Organization with CUT and Tag (GO-CaT) identifies substructure and maturation of lamina-associated domains in neurons of the developing human brain
Authors: Zhang Chujing , Gil Eugene , Ahanger Sajad Hamid , Li Lynn Mingcong , Wang Li , Li Jingjing , Kriegstein Arnold R. , Lim Daniel A. 
Published: November 2024

AbstractApproximately 30-40% of the human genome is anchored to the nuclear lamina through variably sized (10 kb–10 Mb) lamina-associated domains (LADs). Previous work in cultured murine and human cell lines indicate that LADs are not homogenous but can be classified into two subtypes (T1 and T2) based on levels of lamina-association. Due in part to technical limitations, the LAD substructure of neurons maturingin vivois poorly understood. Here, we developed Genome Organization with CUT and Tag (GO-CaT) to map LAD substructure in neurons isolated from the midgestational human cortex and adult human brain. GO-CaT with LaminB1 antibodies mapped LADs with high efficiency as compared to other methods, and in prenatal neurons, we distinguished T1- and T2-LADs based on levels of LaminB1 enrichment. While T1-LADs had the transcriptional and epigenomic characteristics of cell type-invariant LADs including strong transcriptional repression, T2-LADs had a distinct epigenomic state that included enrichment of promoter-enhancer DNA interactions and intermediate levels of gene expression. In prenatal neurons, T2-LADs defined genomic regions that play key roles in neuronal development and were enriched for neurological GWAS phenotypes including those of human cognitive disorders. In a population of adult brain neurons, most prenatal T2-LADs were repositioned to either inter-LAD regions or further sequestered into T1-LADs, perhaps representing the completed, life-long spatial genome architecture of human neurons. These studies highlight the utility of GO-CaT for LAD subdomain mapping in cells isolated from human tissues and illustrate how the substructure of LADs may contribute to neural development, neuronal maturation, and human brain disease.
Postprandial glycaemic response in different ethnic groups in East London and its association with vitamin D status: study protocol for an acute randomised crossover trial
Authors: Dong Honglin , Reynolds Christian , Islam AFM Saiful , Sarkar Swrajit , Turner Sophie 
Published: November 2024

AbstractIn the UK, black African-Caribbeans (ACs) and South Asians (SAs) have 3–6 times greater risks of developing diabetes than white Caucasians do. East London is among the areas with the highest prevalence of type 2 diabetes and the highest proportion of minority groups. This ethnic health inequality is ascribed to socioeconomic standing, dietary habits, culture, and attitudes, while biological diversity has rarely been investigated. The evidence shows that the postprandial glucose peak values in SAs are 2–3 times greater than those in white Caucasians after the same carbohydrate loads; however, the mechanism is poorly understood. In the UK, 50% of SAs and 33% of ACs have vitamin D (vitD) deficiency, whereas 18% of white Caucasians have vitamin D deficiency. There is evidence that vitD status is inversely associated with insulin resistance in healthy adults and diabetic patients and that vitD supplementation may help improve glycaemic control and insulin resistance in type 2 diabetes patients. However, little evidence is available on minority groups or East London. This study will investigate the postprandial glycaemic response (PGR) in three ethnic groups (white Caucasians, SAs and ACs) in East London and link PGR to plasma 25(OH)D (an indicator of vitD status). Ninety-six healthy adults (n=32 per group) will be recruited. Two test drinks will be provided to the participants (300 ml of glucose drink containing 75 g glucose, and 300 ml of pure orange juice) on different occasions. PGR is monitored before and after drinking every 30 min for up to 2 hours via finger prick. A fasting blood sample obtained via phlebotomy will be used for 25(OH)D and relevant tests. A knowledge/perception questionnaire about vitD and a 4-day food diary (analysing vitD dietary intake) will also be collected. The findings of the study will be shared with participants, published in journals, disseminated via social media, and used to inform a randomized controlled trial of the effects of vitD supplementation on PGR in minority groups.The study complies with the Helsinki Declaration II and was approved by the Senate Research Ethics Committee at City, University of London (ETH2223-2000). The study findings will be published in open access peer-reviewed journals and disseminated at national and international conferences.ClinicalTrials.govIdentifier:NCT06241976
Prevalence and etiology of strabismus in Down syndrome: A systematic review and meta-analysis with a focus on ethnic differences in the esotropia/exotropia ratio
Authors: von Bartheld Christopher S. , Chand Avishay , Wang Lingchen 
Published: November 2024

AbstractPurposeWe sought to determine the prevalence of strabismus and the esotropia/exotropia ratio in Down syndrome. Wide ranges of an increased strabismus prevalence have been reported and it is unclear by how much esotropia exceeds exotropia in people with Down syndrome.MethodsWe compiled in a systematic review and meta-analysis the results of over 100 studies that report the strabismus prevalence and ratio of esotropia/exotropia in cohorts of Down syndrome. We calculated the pooled global prevalence and established the geographical distribution of the strabismus prevalence and the esotropia/exotropia ratio.ResultsThe ethnically-adjusted global prevalence of strabismus in Down syndrome is 30.2%. In subjects 15 years and older, the global prevalence is 53.2%, and the lifetime prevalence is 51.0%. In populations which normally have more esotropia than exotropia (e.g., Caucasians), Down syndrome subjects have a further increased bias towards esotropia. In populations which normally have more exotropia (e.g., West Africans, Asians and Hispanics), Down syndrome subjects have a significantly lower esotropia/exotropia ratio (3.21) than reported in Caucasians with Down syndrome (9.98).ConclusionWorldwide, about 1.81 million people with Down syndrome have strabismus: 1.42 million of them have esotropia, and 0.37 million have exotropia. Differences in the esotropia/exotropia ratio between ethnicities point to the orbital anatomy as a major contributing factor to the etiology of strabismus in Down syndrome. The narrow-set eyes (reduced orbital width) in Down syndrome favor esotropia over exotropia, especially in Caucasians, thus explaining why Down syndrome patients from different ethnicities have different prevalences of esotropia and exotropia.
Optogenetic manipulation of nuclear Dorsal reveals temporal requirements and consequences for transcription
Authors: Pimmett Virginia L , McGehee James , Trullo Antonio , Douaihy Maria , Radulescu Ovidiu , Stathopoulos Angelike , Lagha Mounia 
Published: November 2024

ABSTRACTMorphogen gradients convey essential spatial information during tissue patterning. While both concentration and timing of morphogen exposure are crucial, how cells interpret these graded inputs remains challenging to address. We employed an optogenetic system to acutely and reversibly modulate the nuclear concentration of the morphogen Dorsal (DL), homologue of NF-κB, which orchestrates dorso-ventral patterning in theDrosophilaembryo. By controlling DL nuclear concentration while simultaneously recording target gene outputs in real time, we identified a critical window for DL action that is required to instruct patterning, and characterized the resulting effect on spatio-temporal transcription of target genes in terms of timing, coordination, and bursting. We found that a transient decrease in nuclear DL levels at nuclear cycle 13 leads to reduced expression of the mesoderm-associated genesnail (sna)and partial derepression of the neurogenic ectoderm-associated targetshort gastrulation(sog)in ventral regions. Surprisingly, the mispatterning elicited by this transient change in DL is detectable at the level of single cell transcriptional bursting kinetics, specifically affecting long inter-burst durations. Our approach of using temporally-resolved and reversible modulation of a morphogenin vivo, combined with mathematical modeling, establishes a framework for understanding the stimulus-response relationships that govern embryonic patterning.
Modeling and measuring how codon usage modulates the relationship between burden and yield during protein overexpression in bacteria
Authors: Roots Cameron T. , Hill Alexis M. , Wilke Claus O. , Barrick Jeffrey E. 
Published: November 2024

AbstractExcess utilization of translational resources is a critical source of burden on cells engineered to over-express exogenous proteins. To improve protein yields and genetic stability, researchers often use codon optimization strategies that improve translational efficiency by matching an exogenous gene’s codon usage with that of the host organism’s highly expressed genes. Despite empirical data that shows the benefits of codon optimization, little is known quantitatively about the relationship between codon usage bias and the burden imposed by protein overexpression. Here, we develop and experimentally evaluate a stochastic gene expression model that considers the impact of codon usage bias on the availability of ribosomes and different tRNAs in a cell. In agreement with other studies, our model shows that increasing exogenous protein expression decreases production of native cellular proteins in a linear fashion. We also find that the slope of this relationship is modulated by how well the codon usage bias of the exogenous gene and the host’s genes match. Strikingly, we predict that an overoptimization domain exists where further increasing usage of optimal codons worsens yield and burden. We test our model by expressing sfGFP and mCherry2 from constructs that have a wide range of codon optimization levels inEscherichia coli. The results agree with our model, including for an mCherry2 gene sequence that appears to lose expression and genetic stability from codon overoptimization. Our findings can be leveraged by researchers to predict and design more optimal cellular systems through the use of more nuanced codon optimization strategies.
Deciphering Structural Complexity of Brain, Joint, and Muscle Tissues Using Fourier Ptychographic Scattered Light Microscopy
Authors: van Staalduine Simon E. , Bianco Vittorio , Ferraro Pietro , Menzel Miriam 
Published: November 2024

AbstractFourier Ptychographic Microscopy (FPM) provides high-resolution imaging and morphological information over large fields of view, while Computational Scattered Light Imaging (ComSLI) excels at mapping interwoven fiber organization in unstained tissue sections. This study introduces Fourier Ptychographic Scattered Light Microscopy (FP-SLM), a new multi-modal approach that combines FPM and ComSLI analyses to create both high-resolution phase-contrast images and fiber orientation maps from a single measurement. The method is demonstrated on brain sections (frog, monkey) and sections from thigh muscle and knee (mouse). FP-SLM delivers high-resolution images while revealing fiber organization in nerve, muscle, tendon, cartilage, and bone tissues. The approach is validated by comparing the computed fiber orientations with those derived from structure tensor analysis of the high-resolution images. The comparison shows that FPM and ComSLI are compatible with each other and yield fully consistent results. Remarkably, this combination surpasses the sum of its parts, so that applying ComSLI analysis to FPM recordings and vice-versa outperforms both methods alone. This cross-analysis approach can be retrospectively applied to analyze any existing FPM or ComSLI dataset (acquired with LED array and low numerical aperture), significantly expanding the application range of both techniques and enhancing the study of complex tissue architectures in biomedical research.
Evolution of drug-binding residues in eukaryotic ribosomes
Authors: Chan Lewis I. , Ekemezie Chinenye L. , Helena-Bueno Karla , Brown Charlotte R. , Williams Tom A. , Melnikov Sergey V. 
Published: November 2024

ABSTRACTDrugs that target eukaryotic ribosomes are becoming increasingly important as research tools and potential therapies against cancer and pathogenic eukaryotes. However, in the absence of comparative studies, we currently do not know how many eukaryotes possess ribosomal drug-binding sites identical to those in humans, and how many significantly differ from humans. To address this, we traced the evolutionary history of individual ribosomal drug-binding residues from the emergence of eukaryotes to the present day. We found that ribosomal drug-binding sites are divergent across eukaryotic clades, with some of the clades exhibiting more substitutions in their ribosomal drug-binding sites compared to humans than humans do compared to bacteria. Overall, our work provides a resource for understanding the evolutionary divergence of drug-binding sites in eukaryotic ribosomes, which may inform the use of ribosome inhibitors as research tools and lineage-specific drugs against eukaryotic parasites.
Cross-tissue isoform switches by human transcription factors suggest a widespread regulatory mechanism
Authors: Sidorov Sviatoslav , Pal Koustav , Lenhard Boris , Luscombe Nicholas M. 
Published: November 2024

AbstractMany human genes, including transcription factor (TF) genes, produce alternative coding isoforms. Although some alternative coding TF isoforms have been experimentally studied, a genome-wide characterisation of all such isoforms in normal human physiology is still lacking. Here, we integrate RNA sequencing and protein domain data to reveal the expression levels, tissue specificity and putative functional classes of alternative coding isoforms of human TF genes. We found that isoforms lacking a DNA-binding domain (DBD) are annotated for almost a third of known TF genes, comprise 17% of all annotated TF isoforms and likely reverse the regulatory effects of DBD-containing isoforms. Considering all coding TF isoforms, we uncovered 536 switches between the highest-expressed alternative isoforms produced by 360 TF genes across 43 adult tissues. We predicted functional consequences of these switches using a functional annotation of structural domains present in switching isoforms. Furthermore, we found 45 isoform switches between the brain and non-brain tissues and interpreted six of these switches in detail. Finally, we assembled a literature-based compendium of human TF genes with experimentally studied alternative isoforms. In total, our results suggest that the switches of alternative coding TF isoforms between adult tissues represent a widespread, yet understudied, functional mechanism.
Mountain roads across the globe significantly alter local soil microclimates
Authors: Lejeune Renée , Fuentes-Lillo Eduardo , Haesen Stef , Pirée Amber , Wiegmans Dymphna , Hostens Lore , Lenoir Jonathan , Pergl Jan , Vítková Michaela , Seipel Tim , Kutlvašr Josef , Nuñez Martin A. , Dimarco Romina D. , Alexander Jake , Backes Amanda Ratier , Haider Sylvia , Pauchard Aníbal , Nijs Ivan , Lembrechts Jonas J. 
Published: November 2024

AbstractMountain roads have repeatedly shown to host significantly different plant species communities compared to the adjacent natural vegetation. Besides the effect of propagule pressure, altered disturbance regime and soil processes, one of the reasons given for the strong influence of mountain roads on species distributions is a significantly altered microclimate in the roadside compared to the adjacent vegetation, a direct consequence of the altered disturbance regime. However, the microclimatic differences between roadside and natural vegetation have rarely been quantified, particularly lacking global analyses, hampering a better understanding of their importance for mountain biodiversity. In this study, we analysed in-situ measured soil temperatures along mountain roads in seven mountain regions across the globe, in order to assess the impact of mountain roads on a range of bioclimatic variables across the elevational gradient. Our results undeniably show the importance of roadsides as unique microhabitats, even in heterogeneous mountain environments. In most regions, roadside soils had warmer maxima (3.95 ± 2.35°C warmer) and colder minima (0.85 ± 1.11 °C colder) than the soil in the adjacent vegetation, with higher frost risks in winter. Therefore, we recommend future research to incorporate the notion that the local microclimates created by mountain roads could play a critical role in species redistributions in space and time.
Efficient Ribosomal Rna Depletion fromDrosophilaTotal Rna for Next-Generation Sequencing Applications
Authors: Koppaka Omkar , Tandon Shweta , Chodankar Ankita , Pandit Awadhesh , Bakthavachalu Baskar 
Published: November 2024

AbstractWe developed a cost-effective enzyme-based rRNA-depletion method tailored forDrosophila melanogaster, addressing the limitations of existing commercial kits and the lack of peer-reviewed alternatives. Our method employs single-stranded DNA probes complementary toDrosophilarRNA, forming DNA-RNA hybrids. These hybrids are then degraded using the RNase H enzyme, effectively removing rRNA and enriching all non-ribosomal RNAs, including mRNA, lncRNA and small RNA. When compared to a commercial rRNA removal kit, our approach demonstrated superior rRNA removal efficiency and mapping percentage, confirming its effectiveness. Additionally, our method successfully enriched the non-coding transcriptome, making it a valuable tool for studying ncRNA inDrosophila. The probe sequences and rRNA-depletion protocol are made freely available, offering a reliable alternative for rRNA-depletion experiments.