bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetically and Functionally Distinct Immunoglobulin Heavy Chain Locus Duplication in Bats
Authors: Pursell Taylor , Reers Ashley , Mikelov Artem , Kotagiri Prasanti , Ellison James A. , Hutson Christina L. , Boyd Scott D. , Frank Hannah K. 
Published: August 2024

AbstractThe genetic locus encoding immunoglobulin heavy chains (IgH) is critical for vertebrate humoral immune responses and diverse antibody repertoires. Immunoglobulin and T cell receptor loci of most bat species have not been annotated, despite the recurrent role of bats as viral reservoirs and sources of zoonotic pathogens. We investigated the genetic structure and function of IgH loci across the largest bat family, Vespertilionidae, focusing on big brown bats(Eptesicus fuscus). We discovered thatE. fuscusand ten other species within Vespertilionidae have two complete, functional, and distinct immunoglobulin heavy chain loci on separate chromosomes. This locus organization is previously unknown in mammals, but is reminiscent of more limited duplicated loci in teleost fish. Single cell transcriptomic data validate functional rearrangement and expression of immunoglobulin heavy chains of both loci in the expressed repertoire ofEptesicus fuscus, with maintenance of allelic exclusion, bias of usage toward the smaller and more compact IgH locus, and evidence of differential selection of antigen-experienced B cells and plasma cells varying by IgH locus use. This represents a unique mechanism for mammalian humoral immunity and may contribute to bat resistance to viral pathogenesis.
Evidence for S331-G-S-L within the amyloid core of myocilin olfactomedin domain fibrils based on low-resolution 3D solid-state NMR spectra
Authors: Saccuzzo Emily G. , Robang Alicia S. , Gao Yuan , Chen Bo , Lieberman Raquel L. , Paravastu Anant K. 
Published: August 2024

ABSTRACTMyocilin-associated glaucoma is a protein-conformational disorder associated with formation of a toxic amyloid-like aggregate. Numerous destabilizing single point variants, distributed across the myocilin olfactomedin β-propeller (OLF, myocilin residues 245-504, 30 kDa) are associated with accelerated disease progression.In vitro, wild type (WT) OLF can be promoted to form thioflavin T (ThT)-positive fibrils under mildly destabilizing (37°C, pH 7.2) conditions. Consistent with the notion that only a small number of residues within a protein are responsible for amyloid formation, 3D13C-13C solid-state NMR spectra show that OLF fibrils are likely to be composed of only about one third of the overall sequence. Here, we probe the residue composition of fibrils formedde novofrom purified full-length OLF. We were able to make sequential assignments consistent with the sequence S331-G-S-L334. This sequence appears once within a previously identified amyloid-prone region (P1, G326AVVYSGSLYFQ) internal to OLF. Since nearly half of the pairs of adjacent residues (di-peptides) in OLF occur only once in the primary structure and almost all the 3-residue sequences (tri-peptides) are unique, remarkably few sequential assignments are necessary to uniquely identify specific regions of the amyloid core. This assignment approach could be applied to other systems to expand our molecular comprehension of how folded proteins undergo fibrillization.TOC GRAPHIC
The SH Protein of Mumps Virus is a Druggable Pentameric Viroporin
Authors: Devantier Kira , Toft-Bertelsen Trine L. , Prestel Andreas , Kjær Viktoria M. S. , Sahin Cagla , Giulini Marco , Louka Stavroula , Spiess Katja , Manandhar Asmita , Qvortup Katrine , Ulven Trond , Bentzen Bo H. , Bonvin Alexandre MJJ , MacAulay Nanna , Kragelund Birthe B. , Rosenkilde Mette M. 
Published: August 2024

AbstractViral infections are on the rise and drugs targeting viral proteins are needed. Viroporins constitute a growing group of virus-encoded transmembrane oligomeric proteins that allow passage of small molecules across the membrane. Despite sparsity in viroporin structures, recent work has revealed diversity in both the number of transmembrane helices and oligomeric states. Here we provide evidence that the small hydrophobic protein (SH) from mumps virus is a pentameric viroporin. From extensive biophysical data, a HADDOCK model of full-length SH shows its intracellular C-terminal region to form an extended structure crucial to stabilization of the pentamer. Heterologous expression of wild type SH and variants inXenopus laevisoocytes reveals the viroporin as a chloride channel, facilitated by conserved hydroxyl-carrying residues lining the pore. The channel function of SH is inhibited by the small-molecule BIT225, highlighting the potential for antiviral targeting through SH.
The Rad52 superfamily as seen by AlphaFold
Authors: Al-Fatlawi Ali , Hossen Md. Ballal , de Paula Lopes Stella , Stewart A. Francis , Schroeder Michael 
Published: August 2024

1AbstractRad52, a highly conserved eukaryotic protein, plays a crucial role in DNA repair, especially in double-strand break repair. Recent findings reveal that its distinct structural features, including a characteristicβ-sheet andβ-hairpin motif, are shared with the lambda phage single-strand annealing proteins, Redβ, indicating a common superfamily. Our analysis of over 10,000 single-strand annealing proteins (SSAPs) across all kingdoms of life supports this hypothesis, confirming their possession of the characteristic motif despite variations in size and composition. We found that archaea, representing only 1% of the studied proteins, exhibit most of these variations. Through the examination of four representative archaeal SSAPs, we elucidate the structural relationship between eukaryotic and bacterial SSAPs, highlighting differences inβ-sheet size andβ-hairpin complexity. Furthermore, we identify an archaeal SSAP with a structure nearly identical to the human variant and screen over 100 million unannotated proteins for potential SSAP candidates. Our computational analysis complements existing sequence with structural evidence supporting the suggested orthology among five SSAP families across all kingdoms: Rad52, Redβ, RecT, Erf, and Sak3.
A survey of duckweed species in Southern Italy provided first distribution records of the hybridLemna×mediterraneain nature
Authors: Romano Leone Ermes , Braglia Luca , Iannelli Maria Adelaide , Lee Yuri , Gianì Silvia , Gavazzi Floriana , Morello Laura 
Published: August 2024

AbstractInterspecific hybridisation and polyploidization are two main driving forces in plant evolution, shaping genomes and favouring evolutionary novelty and ecological adaptation. Recent studies have demonstrated hybridisation within the genusLemna(Lemnaceae Martinov) as well as triploid.L. ×mediterranea, a recently described hybrids betweenLemna minorandLemna gibbawas identified among only long lasting germplasm collections ofin vitropropagated plants, originally collected at different times in the Mediterranean area.We report the first distribution record ofL. × mediterraneain the nature, in the Campania region of Southern Italy, the same area whereLemna symmeterwas described as a new species about 50 years ago, confirming their synonymy. Eight specimens isolated from five different sampling sites over an area of about 4200 Km2showed identical genetic profiles by Tubulin-Based Polymorphism (TBP) analysis, suggesting their common origin from the same hybridisation event, followed by clonal dispersal. TheL. × mediterraneapopulation of Campania is genetically different from any of the previously analysed clones, suggesting that recurrent hybridisation between the parental species may occur. The natural hybrid clone is triploid, withL.gibbaas the plastid donor, and remarkably similar to it by morphology, although the typical gibbosity of this species becomes evident only uponin vitroflower induction. Flowers are protogynous and self-sterile. Ecological factors including competition with parental and invasive species, niche and climate change adaptation, stability in time and space likely played a role in the successful establishment ofL. × mediterranea.HighlightsInterspecific hybridisation within the genus Lemna documented in natureβ-tubulin intron length polymorphism for tracking duckweed species distributionFlower induction in Lemna × mediterranea
Prediction of symptomatic and asymptomatic bacteriuria in spinal cord injury patients using machine learning
Authors: Hoque M. Mozammel , Noorian Parisa , Espinoza-Vergara Gustavo , To Joyce , Leo Dominic , Chari Priyadarshini , Weber Gerard , Pryor Julie , Duggin Iain G. , Lee Bonsan B. , Rice Scott A. , McDougald Diane 
Published: August 2024

AbstractBackgroundIndividuals with spinal cord injuries (SCI) frequently rely on urinary catheters to drain urine from the bladder, making them susceptible to asymptomatic and symptomatic catheter-associated bacteriuria and urinary tract infections (UTI). Proper identification of these conditions lacks precision, leading to inappropriate antibiotic use which promotes selection for drug-resistant bacteria. Since infection often leads to dysbiosis in the microbiome and correlates with health status, this study aimed to develop a machine learning-based diagnostic framework to predict potential UTI by monitoring urine and/or catheter microbiome data, thereby minimising unnecessary antibiotic use and improving patient health.ResultsMicrobial communities in 609 samples (309 catheter and 300 urine) with asymptomatic and symptomatic bacteriuria status were analysed using 16S rRNA gene sequencing from 27 participants over 18 months. Microbial community compositions were significantly different between asymptomatic and symptomatic bacteriuria, suggesting microbial community signatures have potential application as a diagnostic tool. A significant decrease in local (alpha) diversity was noted in symptomatic bacteriuria compared to the asymptomatic bacteriuria (P< 0.01). Beta diversity measured in weighted unifrac also showed a significant difference (P< 0.05) between groups. Supervised machine learning models trained on amplicon sequence variant (ASVs) counts and bacterial taxonomic abundances (Taxa) to classify symptomatic and asymptomatic bacteriuria with a 10-fold cross-validation approach. Combining urine and catheter microbiome data improved the model performance during cross-validation, yielding a mean area under the receiver operating characteristic curve (AUROC) of 0.91-0.98 (Interquartile range, IQR 0.93-0.96) and 0.78-0.91 (IQR 0.86-0.88) for ASVs and taxonomic features, respectively. ASVs and taxa features achieve a mean AUROC of 0.85-1 (IQR 0.93-0.98) and 0.69-0.99 (IQR 0.78-0.88) in the independent held-out test set, respectively, signifying their potential in differentiating symptomatic and asymptomatic bacteriuria states.ConclusionsOur findings demonstrate that signatures within catheter and urine microbiota could serve as tools to monitor the health status of SCI patients. Establishing an early warning system based on these microbial signatures could equip physicians with alternative management strategies, potentially reducing UTI episodes and associated hospital costs, thus significantly improving patient quality of life while mitigating the impact of drug-resistant UTI.
Optimized LC-MS/MS method for Doxorubicin quantification: validating drug uptake and tumor reduction in zebrafish xenograft model of breast cancer
Authors: Rahman Ghazala , Pramanik Atanu , Das Susmita , Roy Anindya , Bhargava Anamika 
Published: August 2024

AbstractDoxorubicin, a potent chemotherapeutic drug, is widely used against various cancers, notably breast cancer. While its efficacy is well-documented, precise dosage determination in experimental models remains challenging. Zebrafish xenografts of various cancers confirm doxorubicin’s anti-cancerous effect; however, since doxorubicin treatment of zebrafish larva is done by adding doxorubicin to fish water, the precise chemotherapeutic dosage for zebrafish larva remains unknown. In this study, we provide a liquid chromatography tandem mass-spectrometry (LC-MS/MS) method for quantifying doxorubicin uptake in zebrafish larvae and thus provide a direct estimate of doses required for the therapeutic effect. Alongside quantification, we measured the therapeutic effect of doxorubicin in zebrafish larvae xenografted with triple negative breast cancer cell line, MDA-MB-231. LD50value of doxorubicin was first determined by incubating 3-days post fertilization (dpf) larvae with different doses of doxorubicin for 72 h. Doxorubicin was quantified both from zebrafish larval homogenate and treatment solution. Analysis was performed by selected-reaction monitoring (SRM) scans in positive ionization mode. LD50value for 72 h calculated to be 35.95 mg/L. As expected, doxorubicin-treated xenografts exhibited a significant reduction in tumor growth. The range of limit of detection (LOD) and limit of quantification (LOQ) for doxorubicin were 2 and 5 μg/L respectively. Intra- and inter-day accuracy was within the range of 82-114%. Overall, in this study we describe a reliable method for quantifying doxorubicin in zebrafish larvae. Our study facilitates precise dosage estimation, enhancing the relevance of zebrafish xenograft model in cancer research and potentially improving translational applications of chemotherapeutic treatments.
Outcome of H5N1 clade 2.3.4.4b virus infection in calves and lactating cows
Authors: Halwe Nico Joel , Cool Konner , Breithaupt Angele , Schön Jacob , Trujillo Jessie D. , Nooruzzaman Mohammed , Kwon Taeyong , Ahrens Ann Kathrin , Britzke Tobias , McDowell Chester D. , Piesche Ronja , Singh Gagandeep , dos Reis Vinicius Pinho , Kafle Sujan , Pohlmann Anne , Gaudreault Natasha N. , Corleis Björn , Ferreyra Franco Matias , Carossino Mariano , Balasuriya Udeni B.R. , Hensley Lisa , Morozov Igor , Covaleda Lina M. , Diel Diego , Ulrich Lorenz , Hoffmann Donata , Beer Martin , Richt Juergen A. 
Published: August 2024

SummaryIn March 2024, highly pathogenic avian influenza virus (HPAIV) clade 2.3.4.4b H5N1 infections in dairy cows were first reported from Texas, USA. Rapid dissemination to more than 190 farms in 13 states followed. Here, we provide results of two independent clade 2.3.4.4b experimental infection studies evaluating (i) oronasal susceptibility and transmission in calves to a US H5N1 bovine isolate genotype B3.13 (H5N1 B3.13) and (ii) susceptibility of lactating cows following direct mammary gland inoculation of either H5N1 B3.13 or a current EU H5N1 wild bird isolate genotype euDG (H5N1 euDG). Inoculation of the calves resulted in moderate nasal replication and shedding with no severe clinical signs or transmission to sentinel calves. In dairy cows, infection resulted in no nasal shedding, but severe acute mammary gland infection with necrotizing mastitis and high fever was observed for both H5N1 genotypes/strains. Milk production was rapidly and drastically reduced and the physical condition of the cows was severely compromised. Virus titers in milk rapidly peaked at 108TCID50/mL, but systemic infection did not ensue. Notably, adaptive mutation PB2 E627K emerged after intramammary replication of H5N1 euDG. Our data suggest that in addition to H5N1 B3.13, other HPAIV H5N1 strains have the potential to replicate in the udder of cows and that milk and milking procedures, rather than respiratory spread, are likely the primary routes of H5N1 transmission between cattle.
Extraction-free colorimetric RT-LAMP for SARS-CoV-2 RNA detection from saliva
Authors: Yang Yuying , Liu Xing , Tie Songyan , Li Xin , Yang Xin , Cao Jianzhong 
Published: August 2024

AbstractAimTo develop a rapid and easy diagnostic assay for detection of SARS-CoV-2 RNA presented in saliva samples.MethodThe color-based RT-LAMP was used to detect nucleocapsid (N) gene of SARS-CoV-2 without RNA extraction from saliva.ResultsRNA spiked saliva can be used directly for cDNA synthesis after heat inactivation of the saliva and diluted 2-fold with either water or PBS. For both PCR and LAMP, 20% of saliva did not have obvious effect on the reaction. Saliva did not interfere with RT-LAMP when the volume of saliva was less than 20% of the total volume. The sensitivity of the RT-LAMP reached to 1.034×10-5ng/µl (475 copies/μl). The RT-LAMP assay was validated by testing 20 RNA spiked saliva samples. The assay specificity was similar to that of data without saliva.ConclusionsThe RT-LAMP colorimetric assay can be used as a screening method with the advantages of being rapid, easy to use than the qRT-PCR.
A Refined Analysis of Neanderthal-Introgressed Sequences in Modern Humans with a Complete Reference Genome
Authors: Liang Shen-Ao , Ren Tianxin , Zhang Jiayu , He Jiahui , Wang Xuankai , Jiang Xinrui , He Yuan , McCoy Rajiv , Fu Qiaomei , Akey Joshua M. , Mao Yafei , Chen Lu 
Published: August 2024

AbstractBackgroundLeveraging long-read sequencing technologies, the first complete human reference genome, T2T-CHM13, corrects the assembly errors in prior references and addresses the remaining 8% of the genome. While the studies on archaic admixture in modern humans so far have been relying on the GRCh37 reference due to the archaic genome data, the impact of T2T-CHM13 in this field remains unknown.ResultsWe remapped the sequencing reads of the high-quality Altai Neanderthal and Denisovan genomes onto GRCh38 and T2T-CHM13 respectively. Compared with GRCh37, we found T2T-CHM13 has a significant improvement of read mapping quality in archaic samples. We then applied IBDmix to identify Neanderthal introgressed sequences in 2,504 individuals from 26 geographically diverse populations in different references. We observed different pre-phasing filtering strategies prevalently used in public data can largely impact determination of archaic ancestry, calling for consideration on the choice of filters. We discovered ~51Mb T2T-CHM13 unique Neanderthal sequences, which are predominantly located in regions where the variants distinct between the GRCh38 and T2T-CHM13 assemblies emerge. Besides, we unfolded new instances of population-specific archaic introgression in diverse populations, covering genes involved in metabolism, olfactory-related, and icon-channel. Finally, we integrated the introgressed sequences and adaptive signals with all references into a visualization database website, called ASH (www.arcseqhub.com), to facilitate the utilization of archaic alleles and adaptive signals in human genomics and evolutionary research.ConclusionsOur study refines the detection of archaic variations in modern humans, highlights the importance of T2T-CHM13 reference utility, and provides novel insights into functional consequences of archaic hominin admixture.
Sputnik virophage disrupts the transcriptional regulation of its host giant virus
Authors: Chen Jingjie , Ogata Hiroyuki , Hikida Hiroyuki 
Published: August 2024

AbstractSputnik virophages are small double-stranded DNA (dsDNA) viruses that replicate only inside host amoebae infected with giant dsDNA viruses, mimiviruses. Sputnik infection affects mimivirus replication, but their molecular interaction remains poorly understood. Here, we performed a time-course transcriptome analysis ofAcanthamoeba castellaniicells infected with Acanthamoeba polyphaga mimivirus (APMV) (hereafter referred to as Sputnik−cells) and those infected with both APMV and Sputnik 3 virophage (Sputnik+cells). The gene expression patterns of the amoebae were similar between these two conditions, whereas the expression of APMV genes was drastically affected by Sputnik, depending on the timing of their expression. Early expressed APMV genes showed similar expression patterns in both conditions at the early stage of infection. However, at late stages, their expression levels remained higher in Sputnik+cells than in Sputnik−cells, suggesting a prolongation of early gene expression by Sputnik. Late expressed APMV genes showed lower expression at earlier stages in Sputnik+cells, but their expression levels reached or exceeded those in Sputnik−cells at later stages, indicating a delay of gene expression. Overall, our results demonstrated that Sputnik infection drastically alters the transcriptome of APMV rather than amoeba, likely by disturbing the transition from early to late stages of APMV infection.
SARS-COV-2 nucleocapsid protein hijacks multiple components of the host nuclear transport machinery for distinct functions
Authors: Harrison Angela R. , Wang Sui Z. , Wagstaff Kylie M. 
Published: August 2024

AbstractMany viruses target the host nuclear transport machinery to traffic their own proteins or restrict trafficking of host cargo, including mediators of antiviral immune signalling. Nucleocapsid (N) proteins from several coronaviruses traffic to the nucleus/nucleolus, with roles in cell cycle regulation. While N-protein from severe acute respiratory syndrome virus 2 (SARS-COV-2), the causative agent of the global COVID-19 pandemic, is widely reported to localise to the cytoplasm, we identify multiple, functionally distinct interactions of N-protein with the host’s nuclear transport machinery. Using quantitative cell imaging, including fluorescence recovery after photobleaching, and protein-protein interaction analysis, we describe a sub-population of SARS-COV-2 N-protein that localises more diffusely between the nucleus and cytoplasm, undergoes active nuclear import, and re-localises nuclear import receptors (karyopherins) KPNB1 and KPNA2 to the nucleus and cytoplasm, respectively. Truncation analyses identify at least two distinct KPNA2/KPNB1 binding sites located in the N-terminal and C-terminal regions of N-protein. Interestingly, while mutation of K/R-rich sites within these domains reduces KPNA2/KPNB1 binding and disables re-localisation of KPNA2, re-localisation of KPNB1 and nuclear import of N-protein remain intact, indicating that these are molecularly and functionally distinct mechanisms. siRNA knockdown confirms a role for KPNB1 in N-protein nuclear trafficking, while KPNA2 binding and mislocalisation may be antagonistic. Thus, SARS-COV-2 N-protein binds to karyopherinsviamultiple distinct sites to facilitate import and other functions.