bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and functional analysis ofToxoplasmaGolgi-associated proteins identified by proximity labelling
Authors: Pasquarelli Rebecca R. , Quan Justin J. , Cheng Emily S. , Yang Vivian , Britton Timmie A. , Sha Jihui , Wohlschlegel James A. , Bradley Peter J. 
Published: February 2024

AbstractToxoplasma gondiipossesses a highly polarized secretory pathway that contains both broadly conserved eukaryotic organelles and unique apicomplexan organelles which play essential roles in the parasite’s lytic cycle. As in other eukaryotes, theT. gondiiGolgi apparatus sorts and modifies proteins prior to their distribution to downstream organelles. Many of the typical trafficking factors found involved in these processes are missing from apicomplexan genomes, suggesting that these parasites have evolved unique proteins to fill these roles. Here we identify a novel Golgi-localizing protein (ULP1) which contains structural homology to the eukaryotic trafficking factor p115/Uso1. We demonstrate that depletion of ULP1 leads to a dramatic reduction in parasite fitness and replicative ability. Using ULP1 as bait for TurboID proximity labelling and immunoprecipitation, we identify eleven more novel Golgi-associated proteins and demonstrate that ULP1 interacts with theT. gondiiCOG complex. These proteins include both conserved trafficking factors and parasite-specific proteins. Using a conditional knockdown approach, we assess the effect of each of these eleven proteins on parasite fitness. Together, this work reveals a diverse set of novelT. gondiiGolgi-associated proteins that play distinct roles in the secretory pathway. As several of these proteins are absent outside of the Apicomplexa, they represent potential targets for the development of novel therapeutics against these parasites.ImportanceApicomplexan parasites such asToxoplasma gondiiinfect a large percentage of the world’s population and cause substantial human disease. These widespread pathogens use specialized secretory organelles to infect their host cells, modulate host cell functions, and cause disease. While the functions of the secretory organelles are now better understood, the Golgi apparatus of the parasite remains largely unexplored, particularly regarding parasite-specific innovations that may help direct traffic intracellularly. In this work, we characterize ULP1, a protein that is unique to parasites but shares structural similarity to the eukaryotic trafficking factor p115/Uso1. We show that ULP1 plays an important role in parasite replication and demonstrate that it interacts with the conserved oligomeric Golgi (COG) complex. We then use ULP1 proximity labelling to identify eleven additional Golgi-associated proteins which we functionally analyze via conditional knockdown. This work expands our knowledge of theToxoplasmaGolgi apparatus and identifies potential targets for therapeutic intervention.
Niche exclusion of a lung pathogen in mice with designed probiotic communities
Authors: Hern Kelsey E , Phillips Ashlee M , Mageeney Catherine M. , Williams Kelly P. , Sinha Anupama , Carlson Hans K , Collette Nicole M , Branda Steven S , Arkin Adam P 
Published: February 2024

AbstractFor years, the airway microbiota have been theorized to be gatekeepers of respiratory health, as pathogens entering the airway make contact with resident microbes prior to or coincident with their interaction with host cells. Thus, modification of the native airway community may serve as a means of altering the local environment in favor of health. While probiotic supplementation to prevent pathogen infiltration has been explored extensively in the gut, little has been done to study this phenomenon in the lower respiratory tract. In this work, we hypothesize that synthetic bacterial communities introduced into the airway can serve as prophylactic countermeasures against infection by a model bacterial pathogen (Burkholderia thailandensis) in mice. We demonstrate that understanding of antagonistic interactions between a pathogen and airway microbiotain vitrocan guide identification of probiotics with protective capabilitiesin vivo. While production of secondary metabolites appears to play a role in pathogen antagonism, exploitative competition appears to be the predominant mechanism by which the organisms studied here inhibitB. thailandensis. Specifically we show that niche overlap and resource competition between the probiotic and pathogen are predictive of probiotic performancein vivo. This work serves as a foundation for the rational design of probiotic communities for protection against and treatment of respiratory infections.
Conserved Pseudouridines in Helix 69 of the Ribosome are Important for Ribosome Dynamics in Translation
Authors: Jin Hong , Chen Xin 
Published: February 2024

ABSTRACTThe widespread distribution of pseudouridine (Ψ), an isomer of the canonical uridine base, in RNA indicates its functional importance to the cell. In eukaryotes, it is estimated that around 2% of ribosomal RNA nucleotides are pseudouridines, most of which are located in functional regions of the ribosome. Defects in RNA pseudouridylation induce a range of detrimental effects from compromised cellular protein biosynthesis to disease phenotypes in humans. However, genome-wide changes to mRNA translation profiles by ribosomes lacking specific conserved pseudouridines have not been extensively studied. Here, using a new genomic method called 5P-Seq andin vitrobiochemistry, we investigated changes in ribosome dynamics and cellular translation profiles upon loss of Ψ2258 and Ψ2260 in helix 69, the two most conserved pseudouridines in the ribosomes. We found that inhibiting the formation of these two pseudouridines challenges ribosomes to maintain the correct open reading frame and causes generally faster ribosome dynamics in translation. Furthermore, mutant ribosomes are more prone to pause while translating a subset of GC-rich codons, especially rare codons such as Arg (CGA) and Arg (CGG). Our data suggest the presence of Ψ2258 and Ψ2260 contributes to the dynamics of the H69 RNA stem-loop, and helps to maintain functional interactions with the tRNAs as they move within the ribosome. The optimality of this ribosome-tRNA interaction is likely to be more critical for those limited tRNAs that decode rare codons. Consistent with the changes in ribosome dynamics, our data also show that IRES-mediated translation is compromised in the mutant ribosome. These results explain the importance of Ψ2258 and Ψ2260 in H69 to maintain cellular fitness. The strong conservation of Ψ2258 and Ψ2260 in the ribosomes from bacteria to humans indicates their functional significance in modulating ribosome functions. We anticipate that the identified functions of these covalent modifications will be conserved in other species.
Semi-synthetic glycoconjugate vaccine candidate againstCryptococcus neoformans
Authors: Crawford Conor J. , Liporagi-Lopes Livia , Coelho Carolina , Santos Junior Samuel R. , Nicola André Moraes , Wear Maggie P. , Vij Raghav , Oscarson Stefan , Casadevall Arturo 
Published: February 2024

AbstractCryptococcus neoformansis a fungus classified by the World Health Organization as a critically important pathogen, posing a significant threat to immunocompromised individuals. In this study, we present the chemical synthesis and evaluation of two semi-synthetic vaccine candidates targeting the capsular polysaccharide glucuronoxylomannan (GXM) ofC. neoformans.These semi-synthetic glycoconjugate vaccines contain the identical synthetic decasaccharide (M2 motif) antigen. This motif is present in serotype A strains, which constitute 95% of clinical cryptococcosis cases. This synthetic oligosaccharide was conjugated to two proteins (CRM197 and Anthrax 63 kDa PA) and tested for immunogenicity in mice. The conjugates elicited a specific antibody response that bound to the M2 motif but also exhibited additional cross-reactivity towards M1 and M4 GXM motifs. Both glycoconjugates produced antibodies that bound to GXM in ELISA assays and to live fungal cells. Mice immunized with the CRM197 glycoconjugate produced opsonic antibodies and displayed trends toward increased median survival relative to mice given a mock PBS injection (18 vs 15 days,p= 0.06). While these findings indicate promise, achieving a successful vaccine demands further optimization of the glycoconjugate. It could serve as a component in a multi-valent GXM motif vaccine, enhancing both strength and breadth of immune responses.
Quantifying association of early proteinuria and eGFR changes with long-term kidney failure hazard in C3G and IC-MPGN
Authors: Masoud Sherry , Wong Katie , Pitcher David , Downward Lewis , Proudfoot Clare , Webb Nicholas J.A. ,   RaDaR Consortium, Wong Edwin K.S. , Gale Daniel P. 
Published: February 2024

AbstractBackgroundC3 glomerulopathy (C3G) and immune-complex membranoproliferative glomerulonephritis (IC-MPGN) are rare disorders that frequently result in kidney failure over the long-term. At present, there are no disease-specific treatments approved for these disorders, although there is much interest in the therapeutic potential of complement inhibition. However, the limited duration and necessarily small size of controlled trials means there is a need to quantify how well short-term changes in eGFR and proteinuria predict the clinically important outcome of kidney failure. We aimed to address this using longitudinal data from the UK National Registry of Rare Kidney Diseases (RaDaR).MethodsRaDaR involves both retrospective and prospective data collection with linkage to hospital laboratories via automated feeds. 667 patients were included. Analyses of kidney survival were conducted using Kaplan–Meier and Cox regression. eGFR slope was estimated using linear mixed models.ResultsOver a median of 10.1 (IQR 6.9-14.3) years follow-up, 253/667 (38%) reached kidney failure. There was no difference in progression to kidney failure between C3G, IC-MPGN and Primary MPGN Not Otherwise Specified subgroups (p=0.75). Baseline urine protein creatinine ratio (UPCR), although high, was not associated with kidney failure risk. 2-year eGFR slope had a modest effect on kidney failure risk. In contrast, both 20-50% and 0.44g/g (50mg/mmol) reductions in time-averaged UPCR at 12 months were strongly associated with lower kidney failure risk (p≤0.002). Most notably, those with a UPCR <0.88g/g (<100mg/mmol) at 12 months had a substantially lower risk of kidney failure (HR 0.15 (95%CI 0.05-0.41).ConclusionsWe quantified the relationships between early changes in both eGFR and proteinuria with long-term kidney survival. We demonstrate that proteinuria a short time after diagnosis is a strong predictor of long-term outcome and that a UPCR <0.88g/g (<100mg/mmol) at 1 year is associated with a substantially lower kidney failure risk.
Geldof Expert Consensus Classification of Perianal Fistulizing Crohn’s Disease: A Real-World Application in a Serial Fistula MRI Cohort
Authors: Schroeder Matthew , Abushamma Suha , George Alvin T. , Balakrishna Ravella , Hickman John , Elumalai Anusha , Wise Paul , Zulfiqar Maria , Ludwig Daniel R , Shetty Anup , Viswanath Satish E. , Luo Chongliang , Sebastian Shaji , Ballard David H. , Deepak Parakkal 
Published: February 2024

AbstractBackground and AimsPerianal fistulizing Crohn’s disease (CD-PAF) is an aggressive phenotype of Crohn’s disease (CD) defined by frequent relapses and disabling symptoms. A novel consensus classification system was recently outlined by Geldof et al. that seeks to unify disease severity with patient-centered goals but has not yet been validated. We aimed to apply this to a real-world cohort and identify factors that predict transition between classes over time.MethodsWe identified all patients with CD-PAF and at least one baseline and one follow-up pelvic (pMRI). Geldof Classification, disease characteristics, and imaging indices were collected retrospectively at time periods corresponding with respective MRIs.ResultsWe identified 100 patients with CD-PAF of which 96 were assigned Geldof Classes 1 – 2c at baseline. Most patients (78.1%) started in Class 2b, but changes in classification were observed in 52.1% of all patients. Male sex (72.0%, 46.6%, 40.0%, p = 0.03) and prior perianal surgery (52.0% vs 44.6% vs 40.0%, p = 0.02) were more frequently observed in those with improved. Baseline pMRI indices were not associated with changes in classification, however, greater improvements in mVAI, MODIFI-CD, and PEMPAC were seen among those who improved. Linear mixed effect modeling identified only male sex (−0.31, 95% CI −0.60 to −0.02) with improvement in class.ConclusionGeldof classification highlights the dynamic nature of CD-PAF over time, however, our ability to predict transitions between classes remains limited and requires prospective assessment. Improvement in MRI index scores over time was associated with a transition to lower Geldof classification.
Selection of artemisinin partial resistance Kelch13 mutations in Uganda in 2016-22 was at a rate comparable to that seen previously in South-East Asia
Authors: Meier-Scherling Cecile P. G. , Watson Oliver J , Asua Victor , Ghinai Isaac , Katairo Thomas , Garg Shreeya , Conrad Melissa , Rosenthal Philip J. , Okell Lucy C , Bailey Jeffrey A. 
Published: February 2024

AbstractBackgroundArtemisinin partial resistance, mediated by mutations in thePlasmodium falciparumKelch13 protein (K13), rapidly spread in South-East Asia (SEA), undermining antimalarial efficacies of artemisinin-based combination therapies (ACT). Validated K13 mutations have recently arisen in Africa, but rates of increase are not well characterized.MethodsWe investigated K13 mutation prevalence at 16 sites in Uganda (2016-2022, 6586 samples), and five sites in SEA (2003-2018, 5465 samples) by calculating selection coefficients using Bayesian mixed-effect linear models. We then tested whether SEA K13 mutation prevalence could have been forecast accurately using up to the first five years of available data and forecast future K13 mutation prevalence in Uganda.FindingsThe selection coefficient for the prevalence of relevant K13 mutations (441L, 469F/Y, 561H, 675V) was estimated at s=0·383 (95% CrI: 0·247 - 0·528) per year, a 38% relative prevalence increase. Selection coefficients across Uganda were s=0·968 (0·463 - 1·569) for 441L, s=0·153 (- 0·445 - 0·727) for 469F, s=0·222 (−0·011 - 0·398) for 469Y, and s=0·152 (−0·023 - 0·312) for 675V. In SEA, the selection coefficient was s=−0·005 (−0·852 - 0·814) for 539T, s=0·574 (−0·092 - 1·201) for 580Y, and s=0·308 (0·089 - 0·536) for all validated K13 mutations. Forecast prevalences for Uganda assuming constant selection neared fixation (>95% prevalence) within a decade (2028-2033) for combined K13 mutations.InterpretationThe selection of K13 mutations in Uganda was at a comparable rate to that observed in SEA, suggesting K13 mutations may continue to increase quickly in Uganda.FundingNIH R01AI156267, R01AI075045, and R01AI089674.
Can machine learning or deep learning discover novel signatures of illness in continuous cardiorespiratory monitoring data?
Authors: Sullivan Brynne A. , Mesner Ian G. , Niestroy Justin , Lake Douglas E. , Fairchild Karen D. , Moorman J. Randall 
Published: February 2024

AbstractBackgroundCardiorespiratory deterioration due to sepsis is a leading cause of morbidity and mortality for extremely premature infants with very low birth weight (VLBW, birthweight <1500g). Abnormal heart rate (HR) patterns precede the clinical diagnosis of late-onset sepsis in this population. Decades ago, clinicians recognized a pattern of reduced HR variability and increased HR decelerations in electrocardiogram tracings of septic preterm infants. A predictive logistic regression model was developed from this finding using mathematical algorithms that detect this signature of illness. Display of this model as the fold increase in risk of imminent sepsis reduced mortality in a large randomized trial. Here, we sought to determine if machine learning or deep learning approaches would identify this uncommon but distinctive signature of sepsis in VLBW infants.MethodsWe studied VLBW infants admitted from 2012 to 2021 to a regional Level IV NICU. We collected one-hour HR time series data from bedside monitoring sampled at 0.5 Hz (n=300 HR values per series) throughout the NICU admission. First, we applied the principles of highly comparative time series analysis (HCTSA) to generate many mathematical time series features and combined them in a machine learning model. Next, we used deep learning in the form of a convolutional neural network on the raw data to learn the HR features. The output was a set of HR records determined by HCTSA or deep learning to be at high risk for imminent sepsis.ResultsWe analyzed data from 566 infants with 61 episodes of sepsis. HCTSA and deep learning models predicted sepsis with high out-of-sample validation metrics. The riskiest records determined by both approaches demonstrated the previously identified HR signatures-reduced variability and increased decelerations.ConclusionsWe tested the ability of unguided machine learning approaches to detect the novel HR signature of sepsis in VLBW infants previously identified by human experts. Our main finding is that the computerized approach returned the same result - it identified heart rate characteristics of reduced variability and transient decelerations. We conclude that unguided machine learning can be as effective as human experts in identifying even a very rare phenotype in clinical data.
Personalized allele-specific CRISPR-Cas9 strategies for myofibrillar myopathy 6
Authors: Shin Jun Wan , Kim Kyung-Hee , Lee Yukyeong , Choi Doo Eun , Lee Jong-Min 
Published: February 2024

AbstractMyofibrillar myopathy 6 (MFM6) is a rare childhood-onset myopathy characterized by myofibrillar disintegration, muscle weakness, and cardiomyopathy. The genetic cause of MFM6 is p.Pro209Leu mutation (rs121918312-T) in theBAG3gene, which generates the disease outcomes in a dominant fashion. Since the consequences of theBAG3mutation are strong and rapidly progressing, most MFM6 patients are due tode novomutation. There are no effective treatments for MFM6 despite its well-known genetic cause. Given p.Pro209Leu mutation is dominant, regenerative medicine approaches employing orthologous stem cells in which mutantBAG3is inactivated offer a promising avenue. Here, we developed personalized allele-specific CRISPR-Cas9 strategies capitalizing on PAM-altering SNP and PAM-proximal SNP. In order to identify the disease chromosome carrying thede novomutation in our two affected individuals, haplotype phasing through cloning-sequencing was performed. Based on the sequence differences between mutant and normalBAG3, we developed personalized allele-specific CRISPR-Cas9 strategies to selectively inactivate the mutant allele 1) by preventing the transcription of the mutantBAG3and 2) by inducing nonsense-mediated decay (NMD) of mutantBAG3mRNA. Subsequent experimental validation in patient-derived induced pluripotent stem cell (iPSC) lines showed complete allele specificities of our CRISPR-Cas9 strategies and molecular consequences attributable to inactivated mutantBAG3. In addition, mutant allele-specific CRISPR-Cas9 targeting did not alter the characteristics of iPSC or the capacity to differentiate into cardiomyocytes. Together, our data demonstrate the feasibility and potential of personalized allele-specific CRISPR-Cas9 approaches to selectively inactivate the mutantBAG3to generate cell resources for regenerative medicine approaches for MFM6.
COVID-19 Trends at The University of Tennessee: Predictive Insights from Raw Sewage SARS-CoV-2 Detection and Evaluation and PMMoV as an Indicator for Human Waste
Authors: Li Y. , Ash K. T. , Alamilla I. , Joyner D. C. , Williams D. E. , McKay P. J. , Green B. M. , DeBlander S. E. , North C. M. , Kara-Murdoch F. , Swift C. M. , Hazen T. C. 
Published: February 2024

AbstractWastewater-based epidemiology (WBE) has become a valuable tool for monitoring the prevalence of SARS-CoV-2 on university campuses. However, concerns about effectiveness of raw sewage as a COVID-19 early warning system still exist, and it’s not clear how useful normalization by simultaneous comparison of Pepper Mild Mottle Virus (PMMoV) is in addressing variations resulting from fecal discharge dilution. This study aims to contribute insights into these aspects by conducting an academic-year field trial at the student residences on the University of Tennessee, Knoxville campus, raw sewage. This was done to investigate the correlations between SARS-CoV-2 concentrations, both with and without PMMoV normalization, and various parameters, including active COVID-19 cases, self-isolations, and their combination among all student residents. Significant positive correlations between SARS-CoV-2 concentrations a week prior, during the monitoring week, and the subsequent week with active cases. Despite these correlations, normalization by PMMoV does not enhance these associations. These findings suggest the potential utility of SARS-CoV-2 concentrations as an early warning indicator and provide valuable insights into the application and limitations of WBE for COVID-19 surveillance, specifically within the context of raw sewage on university campuses.
A functional genomic framework to elucidate novel causal non-alcoholic fatty liver disease genes
Authors: Saliba-Gustafsson Peter , Justesen Johanne M. , Ranta Amanda , Sharma Disha , Bielczyk-Maczynska Ewa , Li Jiehan , Najmi Laeya A. , Apodaka Maider , Aspichueta Patricia , Björck Hanna M. , Eriksson Per , Franco-Cereceda Anders , Gloudemans Mike , Mujica Endrina , Hoed Marcel den , Assimes Themistocles L. , Quertermous Thomas , Carcamo-Orive Ivan , Park Chong Y. , Knowles Joshua W. 
Published: February 2024

AbstractBackground & AimsNon-alcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver pathology in western countries, with serious public health consequences. Efforts to identify causal genes for NAFLD have been hampered by the relative paucity of human data from gold-standard magnetic resonance quantification of hepatic fat. To overcome insufficient sample size, genome-wide association studies using NAFLD surrogate phenotypes have been used, but only a small number of loci have been identified to date. In this study, we combined GWAS of NAFLD composite surrogate phenotypes with genetic colocalization studies followed by functional in vitro screens to identify bona fide causal genes for NAFLD.Approach & ResultsWe used the UK Biobank to explore the associations of our novel NAFLD score, and genetic colocalization to prioritize putative causal genes forin vitrovalidation. We created a functional genomic framework to study NAFLD genesin vitrousing CRISPRi. Our data identifyVKORC1, TNKS, LYPLAL1andGPAMas regulators of lipid accumulation in hepatocytes and suggest the involvement ofVKORC1in the lipid storage related to the development of NAFLD.ConclusionsComplementary genetic and genomic approaches are useful for the identification of NAFLD genes. Our data supportsVKORC1as abona fideNAFLD gene. We have established a functional genomic framework to study at scale putative novel NAFLD genes from human genetic association studies.