bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cefiderocol heteroresistance associated with mutations in TonB-dependent receptor genes inPseudomonas aeruginosaof clinical origin
Authors: Egge Stephanie L. , Rizvi Samie A. , Simar Shelby R. , Alcalde Manuel , Martinez Jose R.W. , Hanson Blake M. , Dinh An Q. , Baptista Rodrigo P. , Tran Truc T. , Shelburne Samuel A. , Munita Jose M. , Arias Cesar A. , Hakki Morgan , Miller William R. 
Published: February 2024

AbstractThe siderophore-cephalosporin cefiderocol(FDC) presents a promising treatment option for carbapenem-resistant (CR)P. aeruginosa(PA). FDC circumvents traditional porin and efflux mediated resistance by utilizing TonB-dependent receptors (TBDRs) to access the periplasmic space. Emerging FDC resistance has been associated with loss of function mutations within TBDR genes or the regulatory genes controlling TBDR expression. Further, difficulties with antimicrobial susceptibility testing (AST) and unexpected negative clinical treatment outcomes have prompted concerns for heteroresistance, where a single lineage isolate contains resistant subpopulations not detectable by standard AST. This study aimed to evaluate the prevalence of TBDR mutations among clinical isolates ofP. aeruginosaand the phenotypic effect on FDC susceptibility and heteroresistance. We evaluated the sequence ofpirR,pirS,pirA,piuAorpiuDfrom 498 unique isolates collected before the introduction of FDC from 4 clinical sites in Portland, OR (1), Houston, TX (2), and Santiago, Chile (1). At some clinical sites, TBDR mutations were seen in up to 25% of isolates, and insertion, deletion, or frameshift mutations were predicted to impair protein function were seen in 3% of all isolates (n=15). Using population analysis profile testing, we found thatP. aeruginosawith major TBDR mutations were enriched for a heteroresistant phenotype and undergo a shift in the susceptibility distribution of the population as compared to susceptible strains with wild type TBDR genes. Our results indicate that mutations in TBDR genes predate the clinical introduction of FDC, and these mutations may predispose to the emergence of FDC resistance.
Stratification of viral shedding patterns in saliva of COVID-19 patients
Authors: Park Hyeongki , Yoshimura Raiki , Iwanami Shoya , Kim Kwang Su , Ejima Keisuke , Nakamura Naotoshi , Aihara Kazuyuki , Miyazaki Yoshitsugu , Umeyama Takashi , Miyazawa Ken , Morita Takeshi , Watashi Koichi , Brooke Christopher B. , Ke Ruian , Iwami Shingo , Miyazaki Taiga 
Published: February 2024

AbstractLiving with COVID-19 requires continued vigilance against the spread and emergence of variants of concern (VOCs). Rapid and accurate saliva diagnostic testing, alongside basic public health responses, is a viable option contributing to effective transmission control. Nevertheless, our knowledge regarding the dynamics of SARS-CoV-2 infection in saliva is not as advanced as our understanding of the respiratory tract. Here we analyzed longitudinal viral load data of SARS-CoV-2 in saliva samples from 144 patients with mild COVID-19 (a combination of our collected data and published data). Using a mathematical model, we successfully stratified infection dynamics into three distinct groups with clear patterns of viral shedding: viral shedding durations in the three groups were 11.5 days (95% CI: 10.6 to 12.4), 17.4 days (16.6 to 18.2), and 30.0 days (28.1 to 31.8), respectively. Surprisingly, this stratified grouping remained unexplained despite our analysis of 47 types of clinical data, including basic demographic information, clinical symptoms, results of blood tests, and vital signs. Additionally, we quantified the expression levels of 92 micro-RNAs in a subset of saliva samples, but these also failed to explain the observed stratification, although the mir-1846 level may have been weakly correlated with peak viral load. Our study provides insights into SARS-CoV-2 infection dynamics in saliva, highlighting the challenges in predicting the duration of viral shedding without indicators that directly reflect an individual’s immune response, such as antibody induction. Given the significant individual heterogeneity in the kinetics of saliva viral shedding, identifying biomarker(s) for viral shedding patterns will be crucial for improving public health interventions in the era of living with COVID-19.
Distinct platelet interactions with soluble and immobilized von Willebrand factor modulate platelet adhesion and aggregation with differential impact on hemostasis and thrombosis
Authors: Chen Yunfeng , Ruggeri Zaverio M. 
Published: February 2024

AbstractArterial thrombosis is a prevailing and lethal pathological condition that remains difficult to treat or prevent without potentially serious side effects, mostly hemorrhagic in nature. Platelets and von Willebrand factor (VWF) have a recognized major role in the pathogenesis of arterial thrombosis. Platelets bind to surface immobilized VWF for initial adhesion to injured vascular sites, but also interact with soluble VWF to aggregate into thrombi, particularly under flow conditions creating elevated shear stress. Whether the binding of immobilized and soluble VWF to platelets is regulated by separate mechanisms and how they respectively regulate hemostasis and thrombosis remains unclear. Using targeted mutagenesis we engineered VWF to achieve modified binding kinetics with the platelet receptor glycoprotein (GP) Ibα and discovered that the interactions of immobilized and soluble VWF with platelets can be differentially regulated with distinct consequences on platelet adhesion and aggregation. Based on these results, we studied a monoclonal antibody, NMC4, known to bind to an epitope in the VWFA1 domain and to inhibit preferentially platelet aggregation under elevated shear stress conditions. We found that NMC4 was less efficient in reducing platelet adhesion to immobilized VWF than platelet aggregation mediated by soluble VWF and, surprisingly, also inhibited arterial thrombosis in a mouse model of ferric chloride-induced carotid artery occlusion at a dose that failed to prolong post-injury bleeding. Thus, our current findings help delineate interrelated biochemical and biophysical mechanisms underlying VWF function in vascular health; and suggest selective inhibition of VWF-mediated platelet aggregation as opposed to adhesion as a strategy to prevent arterial thrombosis while minimizing bleeding complications.
nanoBERT: A deep learning model for gene agnostic navigation of the nanobody mutational space
Authors: Hadsund Johannes Thorling , Satława Tadeusz , Janusz Bartosz , Shan Lu , Zhou Li , Röttger Richard , Krawczyk Konrad 
Published: February 2024

AbstractNanobodies are a subclass of immunoglobulins, whose binding site consists of only one peptide chain, bestowing favorable biophysical properties. Recently, the first nanobody therapy was approved, paving the way for further clinical applications of this antibody format. Further development of nanobody-based therapeutics could be streamlined by computational methods. One of such methods is infilling - positional prediction of biologically feasible mutations in nanobodies. Being able to identify possible positional substitutions based on sequence context, facilitates functional design of such molecules. Here we present nanoBERT, a nanobody-specific transformer to predict amino acids in a given position in a query sequence. We demonstrate the need to develop such machine-learning based protocol as opposed to gene-specific positional statistics since appropriate genetic reference is not available. We benchmark nanoBERT with respect to human-based language models and ESM-2, demonstrating the benefit for domain-specific language models. We also demonstrate the benefit of employing nanobody-specific predictions for fine-tuning on experimentally measured thermostability dataset. We hope that nanoBERT will help engineers in a range of predictive tasks for designing therapeutic nanobodies.Availabilityhttps://huggingface.co/NaturalAntibody/
GlycansToGraphs: visualizing and simplifying complex mass spectra
Authors: Bonner R. , Jacquet C. , Hopfgartner G. 
Published: February 2024

1.AbstractWe describe a software tool, GlycansToGraphs, used to identify and visualize relationships between masses in MS or MS/MS spectra and illustrate its application to data dependent acquisition (DDA) spectra of glycopeptides. The software is written in python 3.11 and uses the ‘streamlit’ package (1.29) to generate a User Interface (UI) in a web browser. It uses simple text input files, does not require databases (glycan or protein) and the user can define any mass difference that the software searches for in an unbiased manner. Located mass differences generate graphs with edges that correspond to the relationships between nodes (masses) and collections of connected nodes, known as components, which can be analyzed to extract sequences of relationships.
EcoLiDAR: An economical LiDAR scanner for ecological research
Authors: Mendes Calebe Pereira , Lim Norman T-Lon 
Published: February 2024

AbstractDespite recent popularization and widespread use in modern electronic devices, LiDAR technology remains expensive for research purposes, in part due to the very high performance offered by commercially available LiDAR scanners. However, such high performance is not always needed, and the expensive price ends up making LiDAR scanners inaccessible for research projects with reduced budget, such as those in developing countries. Here we designed and built a simple ground-based LiDAR scanner, with performance sufficient to fulfil the requirements for a variety of ecological research projects, while being cheap and easy to build. We managed to assemble a LiDAR scanner under 400 USD (as of 2021), and it is simple enough to be built by personnel with minimal engineering background. We also demonstrated the quality of the resulting point clouds by scanning a test site and producing some common LiDAR products. Although not adequate for mapping large area due to its limited range, our LiDAR design is open, customizable, and can produce adequate results while costing ∼1% of “low-cost” scanners available in the market. As such, our LiDAR scanner opens a world of new opportunities, particularly for projects in developing countries.
Impact of extended Elexacaftor/Tezacaftor/Ivacaftor therapy on the gut microbiome in cystic fibrosis
Authors: Marsh Ryan , Dos Santos Claudio , Yule Alexander , Dellschaft Neele S , Hoad Caroline L , Ng Christabella , Major Giles , Smyth Alan R , Rivett Damian , van der Gast Christopher 
Published: February 2024

AbstractBackgroundThere is a paucity of knowledge on the longer-term effects of CF transmembrane conductance regulator (CFTR) modulator therapies upon the gut microbiome and associated outcomes. In a pilot study, we investigated longitudinal Elexacaftor/Tezacaftor/Ivacaftor (ETI) therapy on the gut microbiota, metabolomic functioning, and clinical outcomes in people with CF (pwCF).Study designFaecal samples from 20 pwCF were acquired before and then following 3, 6, and 17+ months of ETI therapy. Samples were subjected to microbiota sequencing and targeted metabolomics to profile and quantify short-chain fatty acid composition. Ten healthy matched controls were included for comparison. Clinical data, including markers of intestinal function were integrated to investigate relationships.ResultsExtended ETI therapy increased core microbiota diversity and composition, which translated to gradual shifts in whole microbiota composition towards that observed in healthy controls. Despite becoming more similar over time, CF microbiota and functional metabolite compositions remained significantly different to healthy controls. Antibiotic treatment for pulmonary infection significantly explained a relatively large degree of variation within the whole microbiota and rarer satellite taxa. Clinical outcomes were not significantly different following ETI.ConclusionsA positive trajectory towards the microbiota observed in healthy controls was found. However, we posit that progression was predominately impeded by pulmonary antibiotics administration. We recommend future studies use integrated omics approaches within a combination of long-term longitudinal patient studies and model experimental systems. This will deepen our understanding of the impacts of CFTR modulator therapy and respiratory antibiotic interventions upon the gut microbiome and gastrointestinal pathophysiology in CF.
Biogenesis of cytochromescandc1in the electron transport chain of malaria parasites
Authors: García-Guerrero Aldo E. , Marvin Rebecca G. , Blackwell Amanda Mixon , Sigala Paul A. 
Published: February 2024

ABSTRACTPlasmodiummalaria parasites retain an essential mitochondrional electron transport chain (ETC) that is critical for growth within humans and mosquitoes and a key antimalarial drug target. ETC function requires cytochromescandc1that are unusual among heme proteins due to their covalent binding to heme via conserved CXXCH sequence motifs. Heme attachment to these proteins in most eukaryotes requires the mitochondrial enzyme holocytochromecsynthase (HCCS) that binds heme and the apo cytochrome to facilitate biogenesis of the mature cytochromecorc1. Although humans encode a single bifunctional HCCS that attaches heme to both proteins,Plasmodiumparasites are like yeast and encode two separate HCCS homologs thought to be specific for heme attachment to cytc(HCCS) or cytc1(HCC1S). To test the function and specificity ofP. falciparumHCCS and HCC1S, we used CRISPR/Cas9 to tag both genes for conditional expression. HCC1S knockdown selectively impaired cytc1biogenesis and caused lethal ETC dysfunction that was not reversed by over-expression of HCCS. Knockdown of HCCS caused a more modest growth defect but strongly sensitized parasites to mitochondrial depolarization by proguanil, revealing key defects in ETC function. These results and prior heterologous studies inE. coliof cytchemylation byP. falciparumHCCS and HCC1S strongly suggest that both homologs are essential for mitochondrial ETC function and have distinct specificities for biogenesis of cytcandc1, respectively, in parasites. This study lays a foundation to develop novel strategies to selectively block ETC function in malaria parasites.
Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes
Authors: Chen Xi Dawn , Chen Zeyu , Wythes George , Zhang Yifan , Orr Benno C. , Sun Gary , Thao Ka , Vallurupalli Mounica , Sun Jing , Borji Mehdi , Tkacik Emre , Chen Haiqi , Bernstein Bradley E. , Chen Fei 
Published: February 2024

AbstractA major challenge in human genomics is to decipher the context specific relationship of sequence to function. However, existing tools for locus specific hypermutation and evolution in the native genome context are limited. Here we present a novel programmable platform for long-range, locus-specific hypermutation called helicase-assisted continuous editing (HACE). HACE leverages CRISPR-Cas9 to target a processive helicase-deaminase fusion that incurs mutations across large (>1000 bp) genomic intervals. We applied HACE to identify mutations in MEK1 that confer kinase inhibitor resistance, to dissect the impact of individual variants in SF3B1-dependent mis-splicing, and to evaluate noncoding variants in a stimulation-dependent immune enhancer of CD69. HACE provides a powerful tool for investigating coding and noncoding variants, uncovering combinatorial sequence-to-function relationships, and evolving new biological functions.One Sentence SummaryWe developed a tool for continuous, long-range, targeted diversification of endogenous mammalian genomes and used it to explore the function of genetic variants in both coding and non-coding regions.
Loss of CLN3 in microglia leads to impaired lipid metabolism and myelin turnover
Authors: Yasa Seda , Butz Elisabeth S. , Colombo Alessio , Chandrachud Uma , Montore Luca , Sheridan Steven D. , Müller Stephan A. , Lichtenthaler Stefan F. , Tahirovic Sabina , Cotman Susan L. 
Published: February 2024

AbstractBackgroundMicroglia are the primary brain cell type regulating neuroinflammation and they are important for healthy aging. Genes regulating microglial function are associated with an increased risk of neurodegenerative disease. Loss-of-function mutations inCLN3, which encodes an endolysosomal membrane protein, lead to the most common childhood-onset form of neurodegeneration, featuring early-stage neuroinflammation that long precedes neuronal cell loss. How loss of CLN3 function leads to this early neuroinflammation is not yet understood.MethodsHere, we have comprehensively studied microglia fromCln3Δex7/8mice, a genetically accurate CLN3 disease model. Microglia were isolated from young and oldCln3Δex7/8mice for downstream molecular and functional studies.ResultsWe show that loss of CLN3 function in microglia leads to classic age-dependent CLN3-disease lysosomal storage as well as an altered morphology of the lysosome, mitochonodria and Golgi compartments. Consistent with these morphological alterations, we also discovered pathological proteomic signatures implicating defects in lysosomal function and lipid metabolism processes at an early disease stage. CLN3-deficient microglia were unable to efficiently turnover myelin and metabolize its associated lipids, showing severe defects in lipid droplet formation and significant accumulation of cholesterol, phenotypes that were corrected by treatment with autophagy inducers and cholesterol lowering drugs. Finally, we observed reduced myelination in aging homozygousCln3Δex7/8mice suggesting altered myelin turnover by microglia impacts myelination in the CLN3-deficient brain.ConclusionOur results implicate a cell autonomous defect in CLN3-deficient microglia that impacts the ability of these cells to support neuronal cell health. These results strongly suggest microglial targeted therapies should be considered for CLN3 disease.
A Retrospective Analysis of Career Outcomes in Neuroscience
Authors: Ullrich Lauren E. , Ogawa John R. , Jones-London Michelle D. 
Published: February 2024

ABSTRACTWhat factors are associated with different career outcomes among biomedical PhDs? Much of the research to-date has focused on drivers of interest in (and intention to pursue) various careers, especially during graduate school, but fewer studies have investigated the ultimate career outcomes of participants. Even less is known about what factors matter most for groups historically underrepresented in the US STEM workforce, such as for women, some racial and ethnic groups, and persons with disabilities (National Center for Science and Engineering Statistics (NCSES), 2021a). This study reports a new analysis of data from 781 PhD neuroscientists that were obtained from a retrospective survey (reported in Ullrich et al. (2021)) to investigate the factors that influence the career sector in which neuroscience PhDs are employed, and whether there were group differences according to social identity. We find evidence of academia as a “default path” for incoming PhD students, but interest in different careers changes gradually over time. Those who remained in academia had greater acceptance of the structural aspects of academic careers, such as the promotion and tenure process, and greater faculty support during their postdoctoral training. Conversely, prioritizing monetary compensation and wanting varied work were associated with not being in academia, while a strong interest in research was positively associated with being in non-academic research. Somewhat surprisingly, there were few interactions with gender, and no interactions with underrepresentation status. Our findings also underscore the role of advisors, networking, and personal relationships in securing employment in STEM.
Restricted intake of sulfur-containing amino acids reversed the hepatic injury induced by excessDesulfovibriothrough gut-liver axis
Authors: Zhou Lingxi , Lu Gexue , Nie Yawen , Ren Yilin , Shi Jin-Song , Xue Yuzheng , Xu Zheng-Hong , Geng Yan 
Published: February 2024

AbstractGut-liver axis has been a study focus for liver diseases. Diet is a key player in influencing the gut microbiota. However, the effect of different dietary patterns on gut microbiota and liver functions remains unclear. Here, we used mouse standard chow and purified diet to mimic two common human dietary patterns: healthy grain and planted-based diet and Western style diet, respectively and explored their impacts on the gut microbiota and liver. Gut microbiota experienced a great shift with notable increase inDesulfovibrio, gut bile acid (BA) concentration elevated significantly, and liver inflammation was observed in mice fed with the purified diet. Liver inflammation due to translocation of toxic lipopolysaccharides (LPS) and hydrophobic BAs from the damaged gut barrier was also observed in mice fed with the chow diet after receivingDesulfovibrio desulfuricansATCC 29577 (DSV). Restricted intake of sulfur-containing amino acids reversed the liver injury due to excessDesulfovibriothrough lowering the gut BA concentration and enhancing the hepatic antioxidant and detoxifying ability.Ex vivofermentation of human fecal microbiota with primary BAs also demonstrated that DSV enhanced production of secondary BAs. Germ-free mice had higher concentration of both conjugated and unconjugated primary BAs in their gut after receiving DSV.
Bio-orthogonal Glycan Imaging of Culture Cells and Whole AnimalC. eleganswith Expansion Microscopy
Authors: Kuo Joe Chin-Hun , Colville Marshall J. , Sorkin Michelle R. , Kuo Jacky Lok Ka , Huang Ling Ting , Thornlow Dana N. , Beacham Gwendolyn M. , Hollopeter Gunther , DeLisa Matthew P. , Alabi Christopher A. , Paszek Matthew J. 
Published: February 2024

AbstractComplex carbohydrates called glycans play crucial roles in the regulation of cell and tissue physiology, but how glycans map to nanoscale anatomical features must still be resolved. Here, we present the first nanoscale map of mucin-typeO-glycans throughout the entirety of theCaenorhabditis elegansmodel organism. We construct a library of multifunctional linkers to probe and anchor metabolically labelled glycans in expansion microscopy (ExM), an imaging modality that overcomes the diffraction limit of conventional optical microscopes through the physical expansion of samples embedded in a polyelectrolyte gel matrix. A flexible strategy is demonstrated for the chemical synthesis of linkers with a broad inventory of bio-orthogonal functional groups, fluorophores, anchorage chemistries, and linker arms. EmployingC. elegansas a test bed, we resolve metabolically labelledO-glycans on the gut microvilli and other nanoscale anatomical features using our ExM reagents and optimized protocols. We use transmission electron microscopy images ofC. elegansnano-anatomy as ground truth data to validate the fidelity and isotropy of gel expansion. We construct whole organism maps ofC. elegans O-glycosylation in the first larval stage and identifyO-glycan “hotspots” in unexpected anatomical locations, including the body wall furrows. BeyondC. elegans, we provide validated ExM protocols for nanoscale imaging of metabolically labelled glycans on cultured mammalian cells. Together, our results suggest the broad applicability of the multifunctional reagents for imaging glycans and other metabolically labelled biomolecules at enhanced resolutions with ExM.Graphical abstract